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itkBioGenome.h
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itkBioGenome.h
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkBioGenome.h
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkBioGenome_h
#define __itkBioGenome_h
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif
#if defined(_WIN32)
#include "itkWindows.h"
#endif
#include <map>
#include <string>
#include "vcl_cmath.h"
namespace itk {
namespace bio {
/** \class Genome
* \brief This class implement the abstraction of a biological genome.
*
* The genome is considered to be a sequence of genes each one having
* a name and a level of expression. This class is intended to be used
* by artificial cells implementing cellular algorithms for image processing.
*/
class Genome
{
public:
typedef std::string GeneIdType;
typedef std::map< GeneIdType, double > MapType;
public:
Genome();
virtual ~Genome();
void Copy( const Genome & genome );
void InsertGene( const GeneIdType & geneId );
void KnockOutGene( const GeneIdType & geneId );
double GetExpressionLevel( const GeneIdType & geneId );
void SetExpressionLevel( const GeneIdType & geneId, double level );
/** This method computes a normalized Sigmoide function that can
* be used for gene network computations. */
static double Sigmoide( double threshold, double slant, double value )
{
return vcl_atan(( value - threshold ) / slant ) / 3.1416 + 0.5001;
}
private:
MapType m_Map;
};
} // end namespace bio
} // end namespace itk
#endif