AbstractOdeSrnModel.hpp

/*

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*/

#ifndef ABSTRACTODESRN_HPP_
#define ABSTRACTODESRN_HPP_

#include <vector>
#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
#include <boost/serialization/base_object.hpp>
#include "AbstractSrnModel.hpp"
#include "CellCycleModelOdeHandler.hpp"
#include "SimulationTime.hpp"

//class AbstractSrnModel; ///\todo #2752 remove this commented code

class AbstractOdeSrnModel : public AbstractSrnModel, public CellCycleModelOdeHandler
{
private:

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

protected:

    bool mFinishedRunningOdes;

    std::vector<double> mInitialConditions;

    unsigned mStateSize;

    using AbstractSrnModel::Initialise;
    void Initialise(AbstractOdeSystem* pOdeSystem);

    using AbstractSrnModel::CreateSrnModel;
    AbstractSrnModel* CreateSrnModel(AbstractOdeSrnModel* pModel);

public:
    AbstractOdeSrnModel(unsigned stateSize,
                        boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>());

    virtual ~AbstractOdeSrnModel();

    virtual void SimulateToCurrentTime();

    virtual void ResetForDivision();

    void SetFinishedRunningOdes(bool finishedRunningOdes);

    void SetInitialConditions(std::vector<double> initialConditions);

    const std::vector<double>& GetStateVariables();

    virtual void OutputSrnModelParameters(out_stream& rParamsFile);
};

CLASS_IS_ABSTRACT(AbstractOdeSrnModel)

#endif /* ABSTRACTODESRN_HPP_ */