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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 itkBioGeneNetwork_h
#define itkBioGeneNetwork_h
#include "itkMacro.h"
#include "ITKBioCellExport.h"
#include <vector>
namespace itk
{
namespace bio
{
/** \class GeneNetwork
* \brief This class implements the abstraction of a biological gene network.
*
* This class is implemented to iteratively compute the state of the gene network
* following update rules (typical Partial Differential Equations).
*
* \ingroup ITKBioCell
*/
class ITKBioCell_EXPORT GeneNetwork
{
public:
typedef std::vector< float > ProteomeType;
typedef std::vector< float > DomainsType;
public:
GeneNetwork();
virtual ~GeneNetwork();
void Copy(const GeneNetwork & genome);
private:
// This array contains the concentrations of each protein
// in the cell at a certain time.
ProteomeType m_ProteinConcentration;
// This array contains the concentrations of domain affinities
// in the cell at a certain time. Since each protein may
// have multiple domains and each domain has affinities
// for standard domains in the regulatory section of genes,
// this array is indexed by the domains in the regulatory
// section. The final value on each entry indicates the
// probability of a domain to be bound during a certain time
// interval.
DomainsType m_DomainConcentration;
};
} // end namespace bio
} // end namespace itk
#endif
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