<?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</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> ::
Package Ais
</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-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Ais-module.html">Package Bio.Ais</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># This module was deprecated, as it does not seem to have any users,</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># no documentation, and the example script is broken.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">Immune system simulation based on ideas from Immunocomputing: a survey.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">I.Antoniou, S.Gutnikov, V.Ivanov, Yu.Melnikov, A.Tarakanov</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">12. Forrest S., Perelson A. Aleen L. and Cherukuri R. </tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Self-nonself disctimination in a computer. Proc. of IEEE symposium on reseqrch</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">in security and privacy. Oakland, USA, 1994, 202-212.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">Immune system simulation.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">Accepts an initial set of sequences to be protected.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">Creates a set of randomly scrambled sequences and uses a lazy check to remove</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">those that trigger on members of the protected set.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">The detector for a suspicious sequence checks for a close match to a scrambled sequence.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">The detectors start out with equal weights. When a detector finds a suspicious antigen,</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">its weight is incremented so its chances of being selected in the future increases.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">Intended only for experimentation.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.AIS was deprecated, as it does not seem to have any users. If you do use this module, please contact the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module"</tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">urllib</tt> <tt class="py-keyword">import</tt> <tt class="py-name">FancyURLopener</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">urllib</tt> <tt class="py-keyword">import</tt> <tt class="py-name">urlencode</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.SGMLExtractor=Bio.SGMLExtractor-module.html,Class Bio.SGMLExtractor.SGMLExtractor=Bio.SGMLExtractor.SGMLExtractor-class.html"><a title="Bio.SGMLExtractor
Bio.SGMLExtractor.SGMLExtractor" class="py-name" href="#" onclick="return doclink('link-1', 'SGMLExtractor', 'link-1');">SGMLExtractor</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Class Bio.SGMLExtractor.SGMLExtractorHandle=Bio.SGMLExtractor.SGMLExtractorHandle-class.html"><a title="Bio.SGMLExtractor.SGMLExtractorHandle" class="py-name" href="#" onclick="return doclink('link-2', 'SGMLExtractorHandle', 'link-2');">SGMLExtractorHandle</a></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.NetCatch=Bio.NetCatch-module.html,Class Bio.NetCatch.NetCatch=Bio.NetCatch.NetCatch-class.html"><a title="Bio.NetCatch
Bio.NetCatch.NetCatch" class="py-name" href="#" onclick="return doclink('link-4', 'NetCatch', 'link-4');">NetCatch</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.NetCatch
Bio.NetCatch.NetCatch" class="py-name" href="#" onclick="return doclink('link-5', 'NetCatch', 'link-4');">NetCatch</a></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.NetCatch
Bio.NetCatch.NetCatch" class="py-name" href="#" onclick="return doclink('link-7', 'NetCatch', 'link-4');">NetCatch</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Class Bio.NetCatch.ExtractUrls=Bio.NetCatch.ExtractUrls-class.html"><a title="Bio.NetCatch.ExtractUrls" class="py-name" href="#" onclick="return doclink('link-8', 'ExtractUrls', 'link-8');">ExtractUrls</a></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-10', 'Seq', 'link-10');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-11', 'Seq', 'link-10');">Seq</a></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-12" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-12', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Package Bio.Align=Bio.Align-module.html"><a title="Bio.Align" class="py-name" href="#" onclick="return doclink('link-13', 'Align', 'link-13');">Align</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Module Bio.Align.Generic=Bio.Align.Generic-module.html"><a title="Bio.Align.Generic" class="py-name" href="#" onclick="return doclink('link-14', 'Generic', 'link-14');">Generic</a></tt> <tt class="py-keyword">import</tt> <tt id="link-15" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-15', 'Alignment', 'link-15');">Alignment</a></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-16" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-16', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Align" class="py-name" href="#" onclick="return doclink('link-17', 'Align', 'link-13');">Align</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Module Bio.Align.AlignInfo=Bio.Align.AlignInfo-module.html"><a title="Bio.Align.AlignInfo" class="py-name" href="#" onclick="return doclink('link-18', 'AlignInfo', 'link-18');">AlignInfo</a></tt> <tt class="py-keyword">import</tt> <tt id="link-19" class="py-name" targets="Class Bio.Align.AlignInfo.SummaryInfo=Bio.Align.AlignInfo.SummaryInfo-class.html"><a title="Bio.Align.AlignInfo.SummaryInfo" class="py-name" href="#" onclick="return doclink('link-19', 'SummaryInfo', 'link-19');">SummaryInfo</a></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-20" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-20', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-21', 'Alphabet', 'link-21');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-22" class="py-name" targets="Class Bio.Alphabet.DNAAlphabet=Bio.Alphabet.DNAAlphabet-class.html"><a title="Bio.Alphabet.DNAAlphabet" class="py-name" href="#" onclick="return doclink('link-22', 'DNAAlphabet', 'link-22');">DNAAlphabet</a></tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-23" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-23', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-24', 'Alphabet', 'link-21');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-25" class="py-name" targets="Class Bio.Alphabet.Gapped=Bio.Alphabet.Gapped-class.html"><a title="Bio.Alphabet.Gapped" class="py-name" href="#" onclick="return doclink('link-25', 'Gapped', 'link-25');">Gapped</a></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-26" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-26', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.SGMLExtractor
Bio.SGMLExtractor.SGMLExtractor" class="py-name" href="#" onclick="return doclink('link-27', 'SGMLExtractor', 'link-1');">SGMLExtractor</a></tt> <tt class="py-keyword">import</tt> <tt id="link-28" class="py-name"><a title="Bio.SGMLExtractor.SGMLExtractorHandle" class="py-name" href="#" onclick="return doclink('link-28', 'SGMLExtractorHandle', 'link-2');">SGMLExtractorHandle</a></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-29" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-29', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Module Bio.HotRand=Bio.HotRand-module.html"><a title="Bio.HotRand" class="py-name" href="#" onclick="return doclink('link-30', 'HotRand', 'link-30');">HotRand</a></tt> <tt class="py-keyword">import</tt> <tt id="link-31" class="py-name" targets="Class Bio.HotRand.HotRandom=Bio.HotRand.HotRandom-class.html"><a title="Bio.HotRand.HotRandom" class="py-name" href="#" onclick="return doclink('link-31', 'HotRandom', 'link-31');">HotRandom</a></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
<a name="match_sequence"></a><div id="match_sequence-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="match_sequence-toggle" onclick="return toggle('match_sequence');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais-module.html#match_sequence">match_sequence</a><tt class="py-op">(</tt> <tt class="py-param">first</tt><tt class="py-op">,</tt> <tt class="py-param">second</tt><tt class="py-op">,</tt> <tt class="py-param">threshold</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="match_sequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="match_sequence-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">len_first</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">first</tt> <tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">len_second</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">second</tt> <tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">len_first</tt> <tt class="py-op">></tt> <tt class="py-name">len_second</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">len_min</tt> <tt class="py-op">=</tt> <tt class="py-name">len_second</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">len_min</tt> <tt class="py-op">=</tt> <tt class="py-name">len_first</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-32" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.threshold()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#threshold,Method Bio.Compass._Consumer.threshold()=Bio.Compass._Consumer-class.html#threshold"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-32', 'threshold', 'link-32');">threshold</a></tt> <tt class="py-op">></tt> <tt class="py-name">len_min</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-33', 'threshold', 'link-32');">threshold</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len_min</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">max_match</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">match_count</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len_min</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">first</tt><tt class="py-op">[</tt> <tt class="py-name">j</tt> <tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">second</tt><tt class="py-op">[</tt> <tt class="py-name">j</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">match_count</tt> <tt class="py-op">=</tt> <tt class="py-name">match_count</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">match_count</tt> <tt class="py-op">></tt> <tt class="py-name">max_match</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">max_match</tt> <tt class="py-op">=</tt> <tt class="py-name">match_count</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">match_count</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">max_match</tt> <tt class="py-op">>=</tt> <tt id="link-34" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-34', 'threshold', 'link-32');">threshold</a></tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
<a name="Lymphocyte"></a><div id="Lymphocyte-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="Lymphocyte-toggle" onclick="return toggle('Lymphocyte');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Ais.Lymphocyte-class.html">Lymphocyte</a><tt class="py-op">:</tt> </tt>
</div><div id="Lymphocyte-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Lymphocyte-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="Lymphocyte.__init__"></a><div id="Lymphocyte.__init__-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="Lymphocyte.__init__-toggle" onclick="return toggle('Lymphocyte.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Lymphocyte-class.html#__init__">__init__</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">residues</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Lymphocyte.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Lymphocyte.__init__-expanded"><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt class="py-name">residues</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">may_be_autoimmune</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div></div><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="Immune"></a><div id="Immune-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="Immune-toggle" onclick="return toggle('Immune');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html">Immune</a><tt class="py-op">:</tt> </tt>
</div><div id="Immune-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Immune-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> friendly should be an instance of Align. It should contain the set of</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> protected sequences.</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="Immune.__init__"></a><div id="Immune.__init__-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="Immune.__init__-toggle" onclick="return toggle('Immune.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#__init__">__init__</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">friendly_seq</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-string">'acgt'</tt><tt class="py-op">,</tt> <tt class="py-param">tuner_dict</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-param">hot_mode</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.__init__-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hot_mode</tt> <tt class="py-op">=</tt> <tt class="py-name">hot_mode</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hot_mode</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Variable Bio.HotRand.hot_random=Bio.HotRand-module.html#hot_random"><a title="Bio.HotRand.hot_random" class="py-name" href="#" onclick="return doclink('link-35', 'hot_random', 'link-35');">hot_random</a></tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Bio.HotRand.HotRandom" class="py-name" href="#" onclick="return doclink('link-36', 'HotRandom', 'link-31');">HotRandom</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.Ais.Immune.set_defaults()=Bio.Ais.Immune-class.html#set_defaults"><a title="Bio.Ais.Immune.set_defaults" class="py-name" href="#" onclick="return doclink('link-37', 'set_defaults', 'link-37');">set_defaults</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tuner_dict</tt> <tt class="py-op">=</tt> <tt class="py-name">tuner_dict</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tuner_dict</tt><tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">default_tuner_dict</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.Ais.Immune.tune()=Bio.Ais.Immune-class.html#tune"><a title="Bio.Ais.Immune.tune" class="py-name" href="#" onclick="return doclink('link-38', 'tune', 'link-38');">tune</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Ais.Immune.build_align()=Bio.Ais.Immune-class.html#build_align"><a title="Bio.Ais.Immune.build_align" class="py-name" href="#" onclick="return doclink('link-39', 'build_align', 'link-39');">build_align</a></tt><tt class="py-op">(</tt> <tt class="py-name">friendly_seq</tt> <tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">friendly</tt> <tt class="py-op">=</tt> <tt class="py-name">friendly</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-40', 'alphabet', 'link-40');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-41', 'alphabet', 'link-40');">alphabet</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Ais.Immune.lymphocyte_factory()=Bio.Ais.Immune-class.html#lymphocyte_factory"><a title="Bio.Ais.Immune.lymphocyte_factory" class="py-name" href="#" onclick="return doclink('link-42', 'lymphocyte_factory', 'link-42');">lymphocyte_factory</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="Immune.set_defaults"></a><div id="Immune.set_defaults-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="Immune.set_defaults-toggle" onclick="return toggle('Immune.set_defaults');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#set_defaults">set_defaults</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.set_defaults-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.set_defaults-expanded"><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">default_tuner_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> \ </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-string">'num_lymphocytes'</tt> <tt class="py-op">:</tt> <tt class="py-number">20</tt><tt class="py-op">,</tt> \ </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-string">'num_tosses'</tt> <tt class="py-op">:</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> \ </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-string">'threshold'</tt> <tt class="py-op">:</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> \ </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-string">'segment_size'</tt> <tt class="py-op">:</tt> <tt class="py-number">60</tt><tt class="py-op">,</tt> \ </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-string">'replicant_num'</tt> <tt class="py-op">:</tt> <tt class="py-number">1</tt> \ </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
</div><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="Immune.tune"></a><div id="Immune.tune-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="Immune.tune-toggle" onclick="return toggle('Immune.tune');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#tune">tune</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.tune-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.tune-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt> <tt id="link-43" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-43', 'key', 'link-43');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tuner_dict</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-44', 'key', 'link-43');">key</a></tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-45', 'key', 'link-43');">key</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-46', 'strip', 'link-46');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt class="py-name">val</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-47', 'strip', 'link-46');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">[</tt> <tt id="link-48" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-48', 'key', 'link-43');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt>
</div><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="Immune.build_align"></a><div id="Immune.build_align-def"><a name="L125"></a><tt class="py-lineno">125</tt> <a class="py-toggle" href="#" id="Immune.build_align-toggle" onclick="return toggle('Immune.build_align');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#build_align">build_align</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.build_align-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.build_align-expanded"><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt id="link-49" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.align()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#align,Class Bio.FSSP.fssp_rec.align=Bio.FSSP.fssp_rec.align-class.html,Function Bio.Wise.align()=Bio.Wise-module.html#align,Function Bio.Wise.dnal.align()=Bio.Wise.dnal-module.html#align,Function Bio.Wise.psw.align()=Bio.Wise.psw-module.html#align,Variable Bio.pairwise2.align=Bio.pairwise2-module.html#align"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-49', 'align', 'link-49');">align</a></tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-50', 'Alignment', 'link-15');">Alignment</a></tt><tt class="py-op">(</tt> <tt id="link-51" class="py-name"><a title="Bio.Alphabet.Gapped" class="py-name" href="#" onclick="return doclink('link-51', 'Gapped', 'link-25');">Gapped</a></tt><tt class="py-op">(</tt> <tt id="link-52" class="py-name"><a title="Bio.Alphabet.DNAAlphabet" class="py-name" href="#" onclick="return doclink('link-52', 'DNAAlphabet', 'link-22');">DNAAlphabet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-53', 'alphabet', 'link-40');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-54', 'alphabet', 'link-40');">alphabet</a></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">len_seq</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt id="link-55" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-55', 'seq', 'link-55');">seq</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">step</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">segment_size</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len_seq</tt><tt class="py-op">,</tt> <tt class="py-name">step</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt id="link-56" class="py-name" targets="Method Bio.GFF.Connection.segment()=Bio.GFF.Connection-class.html#segment,Method Bio.GenBank._FeatureConsumer.segment()=Bio.GenBank._FeatureConsumer-class.html#segment,Method Bio.GenBank._RecordConsumer.segment()=Bio.GenBank._RecordConsumer-class.html#segment,Variable Bio.expressions.blocks.segment=Bio.expressions.blocks-module.html#segment,Variable Bio.expressions.genbank.segment=Bio.expressions.genbank-module.html#segment"><a title="Bio.GFF.Connection.segment
Bio.GenBank._FeatureConsumer.segment
Bio.GenBank._RecordConsumer.segment
Bio.expressions.blocks.segment
Bio.expressions.genbank.segment" class="py-name" href="#" onclick="return doclink('link-56', 'segment', 'link-56');">segment</a></tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-57', 'seq', 'link-55');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">j</tt> <tt class="py-op">:</tt> <tt class="py-name">j</tt> <tt class="py-op">+</tt> <tt class="py-name">step</tt><tt class="py-op">]</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt id="link-58" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-58', 'align', 'link-49');">align</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method Bio.Align.Generic.Alignment.add_sequence()=Bio.Align.Generic.Alignment-class.html#add_sequence,Method Bio.Nexus.Nexus.Nexus.add_sequence()=Bio.Nexus.Nexus.Nexus-class.html#add_sequence,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_sequence"><a title="Bio.Align.Generic.Alignment.add_sequence
Bio.Nexus.Nexus.Nexus.add_sequence
Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence" class="py-name" href="#" onclick="return doclink('link-59', 'add_sequence', 'link-59');">add_sequence</a></tt><tt class="py-op">(</tt> <tt id="link-60" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-60', 'name', 'link-60');">name</a></tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name"><a title="Bio.GFF.Connection.segment
Bio.GenBank._FeatureConsumer.segment
Bio.GenBank._RecordConsumer.segment
Bio.expressions.blocks.segment
Bio.expressions.genbank.segment" class="py-name" href="#" onclick="return doclink('link-61', 'segment', 'link-56');">segment</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">friendly</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-62', 'align', 'link-49');">align</a></tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="Immune.select_at_random"></a><div id="Immune.select_at_random-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="Immune.select_at_random-toggle" onclick="return toggle('Immune.select_at_random');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#select_at_random">select_at_random</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">items</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.select_at_random-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.select_at_random-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">max_select</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt id="link-63" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-63', 'items', 'link-63');">items</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hot_mode</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">selector</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.HotRand.hot_random" class="py-name" href="#" onclick="return doclink('link-64', 'hot_random', 'link-35');">hot_random</a></tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Method Bio.HotRand.HotRandom.hot_rand()=Bio.HotRand.HotRandom-class.html#hot_rand"><a title="Bio.HotRand.HotRandom.hot_rand" class="py-name" href="#" onclick="return doclink('link-65', 'hot_rand', 'link-65');">hot_rand</a></tt><tt class="py-op">(</tt> <tt class="py-name">max_select</tt> <tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">selector</tt> <tt class="py-op">=</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">max_select</tt> <tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selector</tt> </tt>
</div><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="Immune.guess_gaps"></a><div id="Immune.guess_gaps-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="Immune.guess_gaps-toggle" onclick="return toggle('Immune.guess_gaps');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#guess_gaps">guess_gaps</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.guess_gaps-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.guess_gaps-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> Fill gaps with random selction from alphabet</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-66', 'seq', 'link-55');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-67', 'seq', 'link-55');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">dest_index</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt id="link-68" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-68', 'seq', 'link-55');">seq</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-69" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-69', 'seq', 'link-55');">seq</a></tt><tt class="py-op">[</tt> <tt class="py-name">dest_index</tt> <tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-70', 'alphabet', 'link-40');">alphabet</a></tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">source_index</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Method Bio.Ais.Immune.select_at_random()=Bio.Ais.Immune-class.html#select_at_random"><a title="Bio.Ais.Immune.select_at_random" class="py-name" href="#" onclick="return doclink('link-71', 'select_at_random', 'link-71');">select_at_random</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-72', 'alphabet', 'link-40');">alphabet</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-73', 'seq', 'link-55');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-74', 'seq', 'link-55');">seq</a></tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-name">dest_index</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-75', 'alphabet', 'link-40');">alphabet</a></tt><tt class="py-op">[</tt> <tt class="py-name">source_index</tt> <tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt id="link-76" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-76', 'seq', 'link-55');">seq</a></tt><tt class="py-op">[</tt> <tt class="py-name">dest_index</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-77" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-77', 'seq', 'link-55');">seq</a></tt> </tt>
</div><a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="Immune.scramble"></a><div id="Immune.scramble-def"><a name="L154"></a><tt class="py-lineno">154</tt> <a class="py-toggle" href="#" id="Immune.scramble-toggle" onclick="return toggle('Immune.scramble');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#scramble">scramble</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.scramble-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.scramble-expanded"><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> Substitute residues in sequence at random.</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">num_tosses</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">num_tosses</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt id="link-78" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-78', 'seq', 'link-55');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-79" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-79', 'seq', 'link-55');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">toss</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">num_tosses</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">dest_index</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="Bio.Ais.Immune.select_at_random" class="py-name" href="#" onclick="return doclink('link-80', 'select_at_random', 'link-71');">select_at_random</a></tt><tt class="py-op">(</tt> <tt id="link-81" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-81', 'seq', 'link-55');">seq</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">source_index</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Ais.Immune.select_at_random" class="py-name" href="#" onclick="return doclink('link-82', 'select_at_random', 'link-71');">select_at_random</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-83', 'alphabet', 'link-40');">alphabet</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-84" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-84', 'seq', 'link-55');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-85" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-85', 'seq', 'link-55');">seq</a></tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-name">dest_index</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-86', 'alphabet', 'link-40');">alphabet</a></tt><tt class="py-op">[</tt> <tt class="py-name">source_index</tt> <tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt id="link-87" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-87', 'seq', 'link-55');">seq</a></tt><tt class="py-op">[</tt> <tt class="py-name">dest_index</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-88" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-88', 'seq', 'link-55');">seq</a></tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
<a name="Immune.found_antigen"></a><div id="Immune.found_antigen-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="Immune.found_antigen-toggle" onclick="return toggle('Immune.found_antigen');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#found_antigen">found_antigen</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">detector</tt><tt class="py-op">,</tt> <tt class="py-param">mystery_sequence</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.found_antigen-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.found_antigen-expanded"><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">detector</tt> <tt class="py-op">=</tt> <tt class="py-name">detector</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">mystery_sequence</tt> <tt class="py-op">=</tt> <tt class="py-name">mystery_sequence</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt> <tt id="link-89" class="py-name" targets="Function Bio.Ais.match_sequence()=Bio.Ais-module.html#match_sequence"><a title="Bio.Ais.match_sequence" class="py-name" href="#" onclick="return doclink('link-89', 'match_sequence', 'link-89');">match_sequence</a></tt><tt class="py-op">(</tt> <tt class="py-name">detector</tt><tt class="py-op">,</tt> <tt class="py-name">mystery_sequence</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-90', 'threshold', 'link-32');">threshold</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="Immune.lazy_auto_immune_check"></a><div id="Immune.lazy_auto_immune_check-def"><a name="L173"></a><tt class="py-lineno">173</tt> <a class="py-toggle" href="#" id="Immune.lazy_auto_immune_check-toggle" onclick="return toggle('Immune.lazy_auto_immune_check');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#lazy_auto_immune_check">lazy_auto_immune_check</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.lazy_auto_immune_check-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.lazy_auto_immune_check-expanded"><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">auto_immune</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">candidate</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">friendly</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_all_seqs()=Bio.Align.Generic.Alignment-class.html#get_all_seqs"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-91', 'get_all_seqs', 'link-91');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name" targets="Method Bio.Ais.Immune.found_antigen()=Bio.Ais.Immune-class.html#found_antigen"><a title="Bio.Ais.Immune.found_antigen" class="py-name" href="#" onclick="return doclink('link-92', 'found_antigen', 'link-92');">found_antigen</a></tt><tt class="py-op">(</tt> <tt id="link-93" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-93', 'seq', 'link-55');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">candidate</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-94', 'seq', 'link-55');">seq</a></tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-95', 'data', 'link-95');">data</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">auto_immune</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">auto_immune</tt> </tt>
</div><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="Immune.compute_accum_weight"></a><div id="Immune.compute_accum_weight-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="Immune.compute_accum_weight-toggle" onclick="return toggle('Immune.compute_accum_weight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#compute_accum_weight">compute_accum_weight</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.compute_accum_weight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.compute_accum_weight-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">accum_weight</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-96" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-96', 'index', 'link-96');">index</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">[</tt> <tt id="link-97" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-97', 'index', 'link-96');">index</a></tt> <tt class="py-op">]</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">accum_weight</tt> <tt class="py-op">=</tt> <tt class="py-name">accum_weight</tt> <tt class="py-op">+</tt> <tt class="py-name">lymphocyte</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt><tt class="py-op">.</tt><tt class="py-name">accum_weight</tt> <tt class="py-op">=</tt> <tt class="py-name">accum_weight</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">[</tt> <tt id="link-98" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-98', 'index', 'link-96');">index</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lymphocyte</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accum_weight</tt> <tt class="py-op">=</tt> <tt class="py-name">accum_weight</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accum_weight</tt> </tt>
</div><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="Immune.search_accum_weight"></a><div id="Immune.search_accum_weight-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="Immune.search_accum_weight-toggle" onclick="return toggle('Immune.search_accum_weight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#search_accum_weight">search_accum_weight</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">t</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.search_accum_weight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.search_accum_weight-expanded"><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">last</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt> <tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">min</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-name">last</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">max</tt> <tt class="py-op"><</tt> <tt class="py-name">min</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">min</tt> <tt class="py-op"><=</tt> <tt class="py-name">last</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">min</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">last</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">min</tt> <tt class="py-op">+</tt> <tt class="py-name">max</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">[</tt> <tt class="py-name">m</tt> <tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">accum_weight</tt> <tt class="py-op"><</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">min</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">[</tt> <tt class="py-name">m</tt> <tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">accum_weight</tt> <tt class="py-op">></tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">m</tt> </tt>
</div><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="Immune.pick_a_lymphocyte"></a><div id="Immune.pick_a_lymphocyte-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="Immune.pick_a_lymphocyte-toggle" onclick="return toggle('Immune.pick_a_lymphocyte');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#pick_a_lymphocyte">pick_a_lymphocyte</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.pick_a_lymphocyte-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.pick_a_lymphocyte-expanded"><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> Random selection biased by weight</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hot_mode</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.HotRand.hot_random" class="py-name" href="#" onclick="return doclink('link-99', 'hot_random', 'link-35');">hot_random</a></tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.HotRand.HotRandom.hot_rand" class="py-name" href="#" onclick="return doclink('link-100', 'hot_rand', 'link-65');">hot_rand</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accum_weight</tt> <tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accum_weight</tt> <tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt id="link-101" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-101', 'index', 'link-96');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method Bio.Ais.Immune.search_accum_weight()=Bio.Ais.Immune-class.html#search_accum_weight"><a title="Bio.Ais.Immune.search_accum_weight" class="py-name" href="#" onclick="return doclink('link-102', 'search_accum_weight', 'link-102');">search_accum_weight</a></tt><tt class="py-op">(</tt> <tt class="py-name">weight</tt> <tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-103" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-103', 'index', 'link-96');">index</a></tt> </tt>
</div><a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="Immune.random_test"></a><div id="Immune.random_test-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="Immune.random_test-toggle" onclick="return toggle('Immune.random_test');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#random_test">random_test</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">mystery_sequence</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.random_test-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.random_test-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> A single test probably won't catch a corrupted sequence.</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> Lots of tests are required</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-104', 'index', 'link-96');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method Bio.Ais.Immune.pick_a_lymphocyte()=Bio.Ais.Immune-class.html#pick_a_lymphocyte"><a title="Bio.Ais.Immune.pick_a_lymphocyte" class="py-name" href="#" onclick="return doclink('link-105', 'pick_a_lymphocyte', 'link-105');">pick_a_lymphocyte</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">mystery_sequence</tt> <tt class="py-op">=</tt> <tt class="py-name">mystery_sequence</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">[</tt> <tt id="link-106" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-106', 'index', 'link-96');">index</a></tt> <tt class="py-op">]</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">detector</tt> <tt class="py-op">=</tt> <tt class="py-name">lymphocyte</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">suspicious</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Ais.Immune.found_antigen" class="py-name" href="#" onclick="return doclink('link-107', 'found_antigen', 'link-92');">found_antigen</a></tt><tt class="py-op">(</tt> <tt class="py-name">detector</tt><tt class="py-op">,</tt> <tt class="py-name">mystery_sequence</tt> <tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">suspicious</tt><tt class="py-op">:</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">auto_immune</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">lymphocyte</tt><tt class="py-op">.</tt><tt class="py-name">may_be_autoimmune</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">auto_immune</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Method Bio.Ais.Immune.lazy_auto_immune_check()=Bio.Ais.Immune-class.html#lazy_auto_immune_check"><a title="Bio.Ais.Immune.lazy_auto_immune_check" class="py-name" href="#" onclick="return doclink('link-108', 'lazy_auto_immune_check', 'link-108');">lazy_auto_immune_check</a></tt><tt class="py-op">(</tt> <tt class="py-name">detector</tt> <tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">auto_immune</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">[</tt> <tt id="link-109" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-109', 'index', 'link-96');">index</a></tt> <tt class="py-op">]</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name" targets="Method Bio.Ais.Immune.create_lymphocyte()=Bio.Ais.Immune-class.html#create_lymphocyte"><a title="Bio.Ais.Immune.create_lymphocyte" class="py-name" href="#" onclick="return doclink('link-110', 'create_lymphocyte', 'link-110');">create_lymphocyte</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">suspicious</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt><tt class="py-op">.</tt><tt class="py-name">may_be_autoimmune</tt> <tt class="py-op">=</tt> <tt class="py-name">auto_immune</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-name">lymphocyte</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">[</tt> <tt id="link-111" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-111', 'index', 'link-96');">index</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lymphocyte</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.Ais.Immune.compute_accum_weight()=Bio.Ais.Immune-class.html#compute_accum_weight"><a title="Bio.Ais.Immune.compute_accum_weight" class="py-name" href="#" onclick="return doclink('link-112', 'compute_accum_weight', 'link-112');">compute_accum_weight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">suspicious</tt> </tt>
</div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="Immune.create_lymphocyte"></a><div id="Immune.create_lymphocyte-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="Immune.create_lymphocyte-toggle" onclick="return toggle('Immune.create_lymphocyte');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#create_lymphocyte">create_lymphocyte</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.create_lymphocyte-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.create_lymphocyte-expanded"><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name" targets="Method Bio.Ais.Immune.guess_gaps()=Bio.Ais.Immune-class.html#guess_gaps"><a title="Bio.Ais.Immune.guess_gaps" class="py-name" href="#" onclick="return doclink('link-113', 'guess_gaps', 'link-113');">guess_gaps</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name" targets="Function Bio.Nexus.Trees.consensus()=Bio.Nexus.Trees-module.html#consensus"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-114', 'consensus', 'link-114');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-115', 'data', 'link-95');">data</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Method Bio.Ais.Immune.scramble()=Bio.Ais.Immune-class.html#scramble"><a title="Bio.Ais.Immune.scramble" class="py-name" href="#" onclick="return doclink('link-116', 'scramble', 'link-116');">scramble</a></tt><tt class="py-op">(</tt> <tt class="py-name">lymphocyte</tt> <tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-117', 'append', 'link-117');">append</a></tt><tt class="py-op">(</tt> <tt id="link-118" class="py-name" targets="Class Bio.Ais.Lymphocyte=Bio.Ais.Lymphocyte-class.html"><a title="Bio.Ais.Lymphocyte" class="py-name" href="#" onclick="return doclink('link-118', 'Lymphocyte', 'link-118');">Lymphocyte</a></tt><tt class="py-op">(</tt> <tt class="py-name">lymphocyte</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Ais.Immune.compute_accum_weight" class="py-name" href="#" onclick="return doclink('link-119', 'compute_accum_weight', 'link-112');">compute_accum_weight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="Immune.lymphocyte_factory"></a><div id="Immune.lymphocyte_factory-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="Immune.lymphocyte_factory-toggle" onclick="return toggle('Immune.lymphocyte_factory');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ais.Immune-class.html#lymphocyte_factory">lymphocyte_factory</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Immune.lymphocyte_factory-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Immune.lymphocyte_factory-expanded"><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">num_lymphocytes</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">num_lymphocytes</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">summary_info</tt> <tt class="py-op">=</tt> <tt id="link-120" class="py-name"><a title="Bio.Align.AlignInfo.SummaryInfo" class="py-name" href="#" onclick="return doclink('link-120', 'SummaryInfo', 'link-19');">SummaryInfo</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">friendly</tt> <tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt id="link-121" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-121', 'consensus', 'link-114');">consensus</a></tt> <tt class="py-op">=</tt> <tt class="py-name">summary_info</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name" targets="Method Bio.Align.AlignInfo.SummaryInfo.dumb_consensus()=Bio.Align.AlignInfo.SummaryInfo-class.html#dumb_consensus"><a title="Bio.Align.AlignInfo.SummaryInfo.dumb_consensus" class="py-name" href="#" onclick="return doclink('link-122', 'dumb_consensus', 'link-122');">dumb_consensus</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-123', 'consensus', 'link-114');">consensus</a></tt> <tt class="py-op">=</tt> <tt id="link-124" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-124', 'consensus', 'link-114');">consensus</a></tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">num_lymphocytes</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.Ais.Immune.guess_gaps" class="py-name" href="#" onclick="return doclink('link-125', 'guess_gaps', 'link-113');">guess_gaps</a></tt><tt class="py-op">(</tt> <tt id="link-126" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-126', 'consensus', 'link-114');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-127', 'data', 'link-95');">data</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">lymphocyte</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Ais.Immune.scramble" class="py-name" href="#" onclick="return doclink('link-128', 'scramble', 'link-116');">scramble</a></tt><tt class="py-op">(</tt> <tt class="py-name">lymphocyte</tt> <tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lymphocytes</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-129', 'append', 'link-117');">append</a></tt><tt class="py-op">(</tt> <tt id="link-130" class="py-name"><a title="Bio.Ais.Lymphocyte" class="py-name" href="#" onclick="return doclink('link-130', 'Lymphocyte', 'link-118');">Lymphocyte</a></tt><tt class="py-op">(</tt> <tt class="py-name">lymphocyte</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.Ais.Immune.compute_accum_weight" class="py-name" href="#" onclick="return doclink('link-131', 'compute_accum_weight', 'link-112');">compute_accum_weight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<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 09:28:05 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>
