AbstractOdeBasedCellCycleModel.hpp

/*

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*/

#ifndef ABSTRACTODEBASEDCELLCYCLEMODEL_HPP_
#define ABSTRACTODEBASEDCELLCYCLEMODEL_HPP_

#include <vector>

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

#include "AbstractCellCycleModel.hpp"
#include "CellCycleModelOdeHandler.hpp"
#include "SimulationTime.hpp"

class AbstractOdeBasedCellCycleModel : public AbstractCellCycleModel, public CellCycleModelOdeHandler
{
private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellCycleModel>(*this);
        archive & boost::serialization::base_object<CellCycleModelOdeHandler>(*this);
        archive & mDivideTime;
        archive & mFinishedRunningOdes;
        archive & mG2PhaseStartTime;
    }

protected:

    double mDivideTime;

    bool mFinishedRunningOdes;

    double mG2PhaseStartTime;

public:

    AbstractOdeBasedCellCycleModel(double lastTime = SimulationTime::Instance()->GetTime(),
                                   boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>());

    virtual ~AbstractOdeBasedCellCycleModel();

    virtual void UpdateCellCyclePhase();

    double GetOdeStopTime();

    void SetBirthTime(double birthTime);

    std::vector<double> GetProteinConcentrations() const;

    void SetProteinConcentrationsForTestsOnly(double lastTime, std::vector<double> proteinConcentrations);

    virtual void ResetForDivision();

    void SetFinishedRunningOdes(bool finishedRunningOdes);

    void SetDivideTime(double divideTime);

    void SetG2PhaseStartTime(double g2PhaseStartTime);

    virtual void OutputCellCycleModelParameters(out_stream& rParamsFile);
};

CLASS_IS_ABSTRACT(AbstractOdeBasedCellCycleModel)

#endif /*ABSTRACTODEBASEDCELLCYCLEMODEL_HPP_*/