/usr/include/ITK-4.5/itkBioGenome.h is in libinsighttoolkit4-dev 4.5.0-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#ifndef __itkBioGenome_h
#define __itkBioGenome_h
#if defined( _WIN32 )
#include "itkWindows.h"
#endif
#include "itkMacro.h"
#include <map>
#include <string>
#include "vcl_cmath.h"
namespace itk
{
namespace bio
{
/** \class Genome
* \brief This class implements 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.
*
* \ingroup ITKBioCell
*/
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
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