Alarcon2004OxygenBasedCellCycleOdeSystem.hpp

/*

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*/

#ifndef _ALARCON2004OXYGENBASEDCELLCYCLEODESYSTEM_HPP_
#define _ALARCON2004OXYGENBASEDCELLCYCLEODESYSTEM_HPP_

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

#include <cmath>

#include "AbstractOdeSystem.hpp"

class Alarcon2004OxygenBasedCellCycleOdeSystem : public AbstractOdeSystem
{
private:

    double ma1;
    double ma2;
    double ma3;
    double ma4;
    double mb3;
    double mb4;
    double mc1;
    double mc2;
    double md1;
    double md2;
    double mJ3;
    double mJ4;
    double mEta;
    double mMstar;
    double mB;
    double mxThreshold;
    double myThreshold;

    double mOxygenConcentration;

    bool mIsLabelled;

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

public:

    Alarcon2004OxygenBasedCellCycleOdeSystem(double oxygenConcentration,
                                             bool isLabelled,
                                             std::vector<double> stateVariables=std::vector<double>());

    ~Alarcon2004OxygenBasedCellCycleOdeSystem();

    void Init();

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

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

    void SetIsLabelled(bool isLabelled);

    bool IsLabelled() const;

    double GetOxygenConcentration() const;
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(Alarcon2004OxygenBasedCellCycleOdeSystem)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const Alarcon2004OxygenBasedCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const double oxygen_concentration = t->GetOxygenConcentration();
    ar & oxygen_concentration;

    const bool is_labelled = t->IsLabelled();
    ar & is_labelled;

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

template<class Archive>
inline void load_construct_data(
    Archive & ar, Alarcon2004OxygenBasedCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    double oxygen_concentration;
    ar & oxygen_concentration;

    bool is_labelled;
    ar & is_labelled;

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

    // Invoke inplace constructor to initialise instance
    ::new(t)Alarcon2004OxygenBasedCellCycleOdeSystem(oxygen_concentration, is_labelled, state_variables);
}
}
} // namespace ...

#endif /*_ALARCON2004OXYGENBASEDCELLCYCLEODESYSTEM_HPP_*/