TissueConfig.hpp

/*

Copyright (C) University of Oxford, 2005-2009

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#ifndef TISSUECONFIG_HPP_
#define TISSUECONFIG_HPP_

#include <boost/serialization/access.hpp>
#include <cassert>
#include "Exception.hpp"

class TissueConfig
{
public:

    static TissueConfig* Instance();

    double GetStemCellG1Duration();
    double GetTransitCellG1Duration();
    double GetHepaOneCellG1Duration();
    double GetMinimumGapDuration();
    double GetSG2MDuration();
    double GetSDuration();
    double GetG2Duration();
    double GetMDuration();
    unsigned GetMaxTransitGenerations();
    double GetCryptLength();
    double GetCryptWidth();
    double GetSpringStiffness();
    double GetMechanicsCutOffLength();
    double GetDampingConstantNormal();
    double GetDampingConstantMutant();
    double GetBetaCatSpringScaler();
    double GetApoptosisTime();
    double GetDivisionRestingSpringLength();
    double GetDivisionSeparation();
    double GetHepaOneCellHypoxicConcentration();
    double GetHepaOneCellQuiescentConcentration();
    double GetWntTransitThreshold();
    double GetWntStemThreshold();
    double GetTopOfLinearWntConcentration();
    double GetCriticalHypoxicDuration();
    double GetCryptProjectionParameterA();
    double GetCryptProjectionParameterB();
    double GetApoptoticSpringTensionStiffness();
    double GetApoptoticSpringCompressionStiffness();
    double GetWntChemotaxisStrength();
    double GetSymmetricDivisionProbability();
    double GetAreaBasedDampingConstantParameter();
    double GetMatureCellTargetArea();
    double GetDeformationEnergyParameter();
    double GetMembraneSurfaceEnergyParameter();
    double GetCellCellAdhesionEnergyParameter();
    double GetCellBoundaryAdhesionEnergyParameter();
    bool GetOutputCellIdData();
    bool GetOutputCellMutationStates();
    bool GetOutputCellAncestors();
    bool GetOutputCellTypes();
    bool GetOutputCellVariables();
    bool GetOutputCellCyclePhases();
    bool GetOutputCellAges();
    bool GetOutputCellAreas();
    bool GetOutputVoronoiData();
    bool GetOutputTissueAreas();

    void SetStemCellG1Duration(double);
    void SetTransitCellG1Duration(double);
    void SetHepaOneCellG1Duration(double);
    void SetMinimumGapDuration(double);
    void SetSDuration(double);
    void SetG2Duration(double);
    void SetMDuration(double);
    void SetMaxTransitGenerations(unsigned);
    void SetCryptLength(double);
    void SetCryptWidth(double);
    void SetSpringStiffness(double);
    void SetMechanicsCutOffLength(double);
    void SetDampingConstantNormal(double);
    void SetDampingConstantMutant(double);
    void SetBetaCatSpringScaler(double);
    void SetApoptosisTime(double);
    void SetDivisionRestingSpringLength(double);
    void SetDivisionSeparation(double);
    void SetHepaOneCellHypoxicConcentration(double);
    void SetHepaOneCellQuiescentConcentration(double);
    void SetWntTransitThreshold(double);
    void SetWntStemThreshold(double);
    void SetTopOfLinearWntConcentration(double);
    void SetCriticalHypoxicDuration(double);
    void SetHepaOneParameters();
    void SetCryptProjectionParameterA(double);
    void SetCryptProjectionParameterB(double);
    void SetApoptoticSpringTensionStiffness(double);
    void SetApoptoticSpringCompressionStiffness(double);
    void SetWntChemotaxisStrength(double);
    void SetSymmetricDivisionProbability(double);
    void SetAreaBasedDampingConstantParameter(double);
    void SetMatureCellTargetArea(double);
    void SetDeformationEnergyParameter(double);
    void SetMembraneSurfaceEnergyParameter(double);
    void SetCellCellAdhesionEnergyParameter(double);
    void SetCellBoundaryAdhesionEnergyParameter(double);
    void SetOutputCellIdData(bool);
    void SetOutputCellMutationStates(bool);
    void SetOutputCellAncestors(bool);
    void SetOutputCellTypes(bool);
    void SetOutputCellVariables(bool);
    void SetOutputCellCyclePhases(bool);
    void SetOutputCellAges(bool);
    void SetOutputCellAreas(bool);
    void SetOutputVoronoiData(bool);
    void SetOutputTissueAreas(bool);

    void Reset();

protected:

    TissueConfig();

    TissueConfig(const TissueConfig&);

    TissueConfig& operator= (const TissueConfig&);

private:

    static TissueConfig *mpInstance;

    double mStemCellG1Duration;

    double mTransitCellG1Duration;

    double mHepaOneCellG1Duration;

    double mMinimumGapDuration;

    double mSDuration;

    double mG2Duration;

    double mMDuration;

    unsigned mMaxTransitGenerations;

    double mCryptLength;

    double mCryptWidth;

    double mSpringStiffness;

    double mMechanicsCutOffLength;

    double mDampingConstantNormal;

    double mDampingConstantMutant;

    double mBetaCatSpringScaler;

    double mApoptosisTime;

    double mDivisionSeparation;

    double mDivisionRestingSpringLength;

    double mHepaOneCellHypoxicConcentration;

    double mHepaOneCellQuiescentConcentration;

    double mWntTransitThreshold;

    double mWntStemThreshold;

    double mTopOfLinearWntConcentration;

    double mCriticalHypoxicDuration;

    double mCryptProjectionParameterA;

    double mCryptProjectionParameterB;

    double mApoptoticSpringTensionStiffness;

    double mApoptoticSpringCompressionStiffness;

    double mWntChemotaxisStrength;

    double mSymmetricDivisionProbability;

    double mAreaBasedDampingConstantParameter;

    double mMatureCellTargetArea;

    double mDeformationEnergyParameter;

    double mMembraneSurfaceEnergyParameter;

    double mCellCellAdhesionEnergyParameter;

    double mCellBoundaryAdhesionEnergyParameter;

    bool mOutputCellIdData;

    bool mOutputCellMutationStates;

    bool mOutputCellAncestors;

    bool mOutputCellTypes;

    bool mOutputCellVariables;

    bool mOutputCellCyclePhases;

    bool mOutputCellAges;

    bool mOutputCellAreas;

    bool mOutputVoronoiData;

    bool mOutputTissueAreas;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & mStemCellG1Duration;
        archive & mTransitCellG1Duration;
        archive & mHepaOneCellG1Duration;
        archive & mMinimumGapDuration;
        archive & mSDuration;
        archive & mG2Duration;
        archive & mMDuration;
        archive & mMaxTransitGenerations;
        archive & mCryptLength;
        archive & mCryptWidth;
        archive & mSpringStiffness;
        archive & mMechanicsCutOffLength;
        archive & mDampingConstantNormal;
        archive & mDampingConstantMutant;
        archive & mBetaCatSpringScaler;
        archive & mApoptosisTime;
        archive & mHepaOneCellHypoxicConcentration;
        archive & mHepaOneCellQuiescentConcentration;
        archive & mWntTransitThreshold;
        archive & mWntStemThreshold;
        archive & mTopOfLinearWntConcentration;
        archive & mCriticalHypoxicDuration;
        archive & mCryptProjectionParameterA;
        archive & mCryptProjectionParameterB;
        archive & mApoptoticSpringTensionStiffness;
        archive & mApoptoticSpringCompressionStiffness;
        archive & mWntChemotaxisStrength;
        archive & mSymmetricDivisionProbability;
        archive & mAreaBasedDampingConstantParameter;
        archive & mMatureCellTargetArea;
        archive & mDeformationEnergyParameter;
        archive & mMembraneSurfaceEnergyParameter;
        archive & mCellCellAdhesionEnergyParameter;
        archive & mCellBoundaryAdhesionEnergyParameter;
        archive & mOutputCellIdData;
        archive & mOutputCellMutationStates;
        archive & mOutputCellAncestors;
        archive & mOutputCellTypes;
        archive & mOutputCellVariables;
        archive & mOutputCellCyclePhases;
        archive & mOutputCellAges;
        archive & mOutputCellAreas;
        archive & mOutputVoronoiData;
        archive & mOutputTissueAreas;
    }
};


#endif /*TISSUECONFIG_HPP_*/

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