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<h1>itkBioGenome.h</h1><a href="itkBioGenome_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*=========================================================================</span>
<a name="l00002"></a>00002 <span class="comment"></span>
<a name="l00003"></a>00003 <span class="comment"> Program: Insight Segmentation & Registration Toolkit</span>
<a name="l00004"></a>00004 <span class="comment"> Module: $RCSfile: itkBioGenome.h,v $</span>
<a name="l00005"></a>00005 <span class="comment"> Language: C++</span>
<a name="l00006"></a>00006 <span class="comment"> Date: $Date: 2008-10-20 21:28:21 $</span>
<a name="l00007"></a>00007 <span class="comment"> Version: $Revision: 1.4 $</span>
<a name="l00008"></a>00008 <span class="comment"></span>
<a name="l00009"></a>00009 <span class="comment"> Copyright (c) Insight Software Consortium. All rights reserved.</span>
<a name="l00010"></a>00010 <span class="comment"> See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.</span>
<a name="l00011"></a>00011 <span class="comment"></span>
<a name="l00012"></a>00012 <span class="comment"> This software is distributed WITHOUT ANY WARRANTY; without even</span>
<a name="l00013"></a>00013 <span class="comment"> the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR</span>
<a name="l00014"></a>00014 <span class="comment"> PURPOSE. See the above copyright notices for more information.</span>
<a name="l00015"></a>00015 <span class="comment"></span>
<a name="l00016"></a>00016 <span class="comment">=========================================================================*/</span>
<a name="l00017"></a>00017 <span class="preprocessor">#ifndef __itkBioGenome_h</span>
<a name="l00018"></a>00018 <span class="preprocessor"></span><span class="preprocessor">#define __itkBioGenome_h</span>
<a name="l00019"></a>00019 <span class="preprocessor"></span>
<a name="l00020"></a>00020 <span class="preprocessor">#if defined(_MSC_VER)</span>
<a name="l00021"></a>00021 <span class="preprocessor"></span><span class="preprocessor">#pragma warning ( disable : 4786 )</span>
<a name="l00022"></a>00022 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00023"></a>00023 <span class="preprocessor"></span>
<a name="l00024"></a>00024 <span class="preprocessor">#if defined(_WIN32)</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span><span class="preprocessor">#include "<a class="code" href="itkWindows_8h.html">itkWindows.h</a>"</span>
<a name="l00026"></a>00026 <span class="preprocessor">#endif</span>
<a name="l00027"></a>00027 <span class="preprocessor"></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <map></span>
<a name="l00029"></a>00029 <span class="preprocessor">#include <string></span>
<a name="l00030"></a>00030 <span class="preprocessor">#include "vcl_cmath.h"</span>
<a name="l00031"></a>00031
<a name="l00032"></a>00032 <span class="keyword">namespace </span>itk {
<a name="l00033"></a>00033
<a name="l00034"></a>00034 <span class="keyword">namespace </span>bio {
<a name="l00035"></a>00035
<a name="l00043"></a><a class="code" href="classitk_1_1bio_1_1Genome.html">00043</a> <span class="keyword">class </span><a class="code" href="classitk_1_1bio_1_1Genome.html" title="This class implement the abstraction of a biological genome.">Genome</a>
<a name="l00044"></a>00044 {
<a name="l00045"></a>00045 <span class="keyword">public</span>:
<a name="l00046"></a><a class="code" href="classitk_1_1bio_1_1Genome.html#1e49fc43aeb7fbbacca8c4c17642d10d">00046</a> <span class="keyword">typedef</span> std::string <a class="code" href="classitk_1_1bio_1_1Genome.html#1e49fc43aeb7fbbacca8c4c17642d10d">GeneIdType</a>;
<a name="l00047"></a><a class="code" href="classitk_1_1bio_1_1Genome.html#49e053df2ec16bfce47eceda01dadec4">00047</a> <span class="keyword">typedef</span> std::map< GeneIdType, double > <a class="code" href="classitk_1_1bio_1_1Genome.html#49e053df2ec16bfce47eceda01dadec4">MapType</a>;
<a name="l00048"></a>00048
<a name="l00049"></a>00049 <span class="keyword">public</span>:
<a name="l00050"></a>00050 <a class="code" href="classitk_1_1bio_1_1Genome.html#d60e3bbe35c61fb8bbc17b98389728ed">Genome</a>();
<a name="l00051"></a>00051 <span class="keyword">virtual</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#26abb1836847c1076d89c54e0a43853d">~Genome</a>();
<a name="l00052"></a>00052
<a name="l00053"></a>00053 <span class="keywordtype">void</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#3554d014ca8e606ac3994176087a71b6">Copy</a>( <span class="keyword">const</span> <a class="code" href="classitk_1_1bio_1_1Genome.html" title="This class implement the abstraction of a biological genome.">Genome</a> & genome );
<a name="l00054"></a>00054
<a name="l00055"></a>00055 <span class="keywordtype">void</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#3e595259e8cfaf2b3a15257332f41af0">InsertGene</a>( <span class="keyword">const</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#1e49fc43aeb7fbbacca8c4c17642d10d">GeneIdType</a> & geneId );
<a name="l00056"></a>00056 <span class="keywordtype">void</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#34b7277dc55bf6602cb3728bdbfe2200">KnockOutGene</a>( <span class="keyword">const</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#1e49fc43aeb7fbbacca8c4c17642d10d">GeneIdType</a> & geneId );
<a name="l00057"></a>00057
<a name="l00058"></a>00058 <span class="keywordtype">double</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#8451dce8fc8c1b2b5f48d1c5380871d5">GetExpressionLevel</a>( <span class="keyword">const</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#1e49fc43aeb7fbbacca8c4c17642d10d">GeneIdType</a> & geneId );
<a name="l00059"></a>00059 <span class="keywordtype">void</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#103eba965025556f30c5c99c53fde1ca">SetExpressionLevel</a>( <span class="keyword">const</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#1e49fc43aeb7fbbacca8c4c17642d10d">GeneIdType</a> & geneId, <span class="keywordtype">double</span> level );
<a name="l00060"></a>00060
<a name="l00063"></a><a class="code" href="classitk_1_1bio_1_1Genome.html#f99e973efab1e74a5a65105877bcdeb6">00063</a> <span class="keyword">static</span> <span class="keywordtype">double</span> <a class="code" href="classitk_1_1bio_1_1Genome.html#f99e973efab1e74a5a65105877bcdeb6">Sigmoide</a>( <span class="keywordtype">double</span> threshold, <span class="keywordtype">double</span> slant, <span class="keywordtype">double</span> value )
<a name="l00064"></a>00064 {
<a name="l00065"></a>00065 <span class="keywordflow">return</span> vcl_atan(( value - threshold ) / slant ) / 3.1416 + 0.5001;
<a name="l00066"></a>00066 }
<a name="l00067"></a>00067
<a name="l00068"></a>00068 <span class="keyword">private</span>:
<a name="l00069"></a>00069 <a class="code" href="classitk_1_1bio_1_1Genome.html#49e053df2ec16bfce47eceda01dadec4">MapType</a> m_Map;
<a name="l00070"></a>00070
<a name="l00071"></a>00071 };
<a name="l00072"></a>00072
<a name="l00073"></a>00073
<a name="l00074"></a>00074 } <span class="comment">// end namespace bio</span>
<a name="l00075"></a>00075
<a name="l00076"></a>00076 } <span class="comment">// end namespace itk</span>
<a name="l00077"></a>00077
<a name="l00078"></a>00078 <span class="preprocessor">#endif</span>
<a name="l00079"></a>00079 <span class="preprocessor"></span>
</pre></div></div>
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