VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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*/

#ifndef VANLEEUWEN2009WNTSWATCELLCYCLEODESYSTEM_HPP_
#define VANLEEUWEN2009WNTSWATCELLCYCLEODESYSTEM_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/shared_ptr.hpp>

#include <cmath>
#include <iostream>

#include "AbstractOdeSystem.hpp"
#include "AbstractCellMutationState.hpp"
#include "MathsCustomFunctions.hpp"

// Needed here to avoid serialization errors
#include "ApcOneHitCellMutationState.hpp"
#include "ApcTwoHitCellMutationState.hpp"
#include "BetaCateninOneHitCellMutationState.hpp"

class VanLeeuwen2009WntSwatCellCycleOdeSystem : public AbstractOdeSystem
{
private:

    double mk2d;
    double mk3d;
    double mk34d;
    double mk43d;
    double mk23d;
    double mad;
    double mJ11d;
    double mJ12d;
    double mJ13d;
    double mJ61d;
    double mJ62d;
    double mJ63d;
    double mKm1d;
    double mkpd;
    double mphi_r;
    double mphi_i;
    double mphi_j;
    double mphi_p;
    double mk16d;
    double mk61d;
    double mPhiE2F1;

    double mSa;
    double mSca;
    double mSc;
    double mSct;
    double mSd;
    double mSt;
    double mSx;
    double mSy;
    double mDa;
    double mDca;
    double mDc;
    double mDct;
    double mDd;
    double mDdx;
    double mDt;
    double mDu;
    double mDx;
    double mDy;
    double mKc;
    double mKd;
    double mKt;
    double mPc;
    double mPu;
    double mXiD;
    double mXiDx;
    double mXiX;
    double mXiC;

    boost::shared_ptr<AbstractCellMutationState> mpMutationState;

    unsigned mHypothesis;

    double mWntLevel;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOdeSystem>(*this);
    }

public:

    VanLeeuwen2009WntSwatCellCycleOdeSystem(unsigned hypothesis,
                                            double wntLevel = 0.0,
                                            boost::shared_ptr<AbstractCellMutationState> pMutationState=boost::shared_ptr<AbstractCellMutationState>(),
                                            std::vector<double> stateVariables=std::vector<double>());

    ~VanLeeuwen2009WntSwatCellCycleOdeSystem();

    void Init();

    void SetMutationState(boost::shared_ptr<AbstractCellMutationState> pMutationState);

    const boost::shared_ptr<AbstractCellMutationState> GetMutationState() const;

    void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY);

    bool CalculateStoppingEvent(double time, const std::vector<double>& rY);

    double CalculateRootFunction(double time, const std::vector<double>& rY);

    double GetWntLevel() const;

    unsigned GetHypothesis() const;
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(VanLeeuwen2009WntSwatCellCycleOdeSystem)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const VanLeeuwen2009WntSwatCellCycleOdeSystem * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const unsigned hypothesis = t->GetHypothesis();
    ar & hypothesis;

    const double wnt_level = t->GetWntLevel();
    ar & wnt_level;

    const boost::shared_ptr<AbstractCellMutationState> p_mutation_state = t->GetMutationState();
    ar & p_mutation_state;

    const std::vector<double> state_variables = t->rGetConstStateVariables();
    ar & state_variables;
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, VanLeeuwen2009WntSwatCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    unsigned hypothesis;
    ar & hypothesis;

    double wnt_level;
    ar & wnt_level;

    boost::shared_ptr<AbstractCellMutationState> p_mutation_state;
    ar & p_mutation_state;

    std::vector<double> state_variables;
    ar & state_variables;

    // Invoke inplace constructor to initialise instance
    ::new(t)VanLeeuwen2009WntSwatCellCycleOdeSystem(hypothesis, wnt_level, p_mutation_state, state_variables);
}
}
} // namespace ...

#endif /*VANLEEUWEN2009WNTSWATCELLCYCLEODESYSTEM_HPP_*/