AbstractCellCycleModel.hpp

/*

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*/

#ifndef ABSTRACTCELLCYCLEMODEL_HPP_
#define ABSTRACTCELLCYCLEMODEL_HPP_

#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
#include "Identifiable.hpp"

#include <boost/serialization/base_object.hpp>

#include <vector>

#include "OutputFileHandler.hpp"
#include "CellCyclePhases.hpp"
#include "SimulationTime.hpp"
#include "Cell.hpp"

class Cell; // Circular definition (cells need to know about cycle models and vice-versa)
typedef boost::shared_ptr<Cell> CellPtr;

class AbstractCellCycleModel : public Identifiable, boost::noncopyable
{
private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // Make sure the SimulationTime singleton gets saved too
        SerializableSingleton<SimulationTime>* p_time_wrapper = SimulationTime::Instance()->GetSerializationWrapper();
        archive & p_time_wrapper;

        // DO NOT archive & mpCell; -- The CellCycleModel is only ever archived from the Cell
        // which knows this and it is handled in the load_construct of Cell.
        archive & mBirthTime;
        archive & mCurrentCellCyclePhase;
        archive & mG1Duration;
        archive & mReadyToDivide;
        archive & mDimension;
        archive & mMinimumGapDuration;
        archive & mStemCellG1Duration;
        archive & mTransitCellG1Duration;
        archive & mSDuration;
        archive & mG2Duration;
        archive & mMDuration;
    }

protected:

    CellPtr mpCell;

    double mBirthTime;

    CellCyclePhase mCurrentCellCyclePhase;

    double mG1Duration;

    bool mReadyToDivide;

    unsigned mDimension;

    double mMinimumGapDuration;

    double mStemCellG1Duration;

    double mTransitCellG1Duration;

    double mSDuration;

    double mG2Duration;

    double mMDuration;

public:

    AbstractCellCycleModel();

    virtual ~AbstractCellCycleModel();

    void SetCell(CellPtr pCell);

    virtual void Initialise();

    virtual void InitialiseDaughterCell();

    CellPtr GetCell();

    virtual void SetBirthTime(double birthTime);

    void SetDimension(unsigned dimension);

    unsigned GetDimension();

    double GetBirthTime() const;

    double GetAge();

    virtual bool ReadyToDivide();

    virtual void UpdateCellCyclePhase()=0;

    virtual void ResetForDivision();

    virtual AbstractCellCycleModel* CreateCellCycleModel()=0;

    CellCyclePhase GetCurrentCellCyclePhase();

    virtual double GetG1Duration();

    double GetStemCellG1Duration();

    double GetTransitCellG1Duration();

    double GetSG2MDuration();

    virtual double GetSDuration();

    virtual double GetG2Duration();

    virtual double GetMDuration();

    virtual void SetStemCellG1Duration(double stemCellG1Duration);

    virtual void SetTransitCellG1Duration(double transitCellG1Duration);

    void SetSDuration(double sDuration);

    void SetG2Duration(double g2Duration);

    void SetMDuration(double mDuration);

    virtual double GetAverageTransitCellCycleTime();

    virtual double GetAverageStemCellCycleTime();

    virtual bool CanCellTerminallyDifferentiate();

    double GetMinimumGapDuration();

    void SetMinimumGapDuration(double minimumGapDuration);

    void OutputCellCycleModelInfo(out_stream& rParamsFile);

    virtual void OutputCellCycleModelParameters(out_stream& rParamsFile)=0;
};

CLASS_IS_ABSTRACT(AbstractCellCycleModel)

#endif /*ABSTRACTCELLCYCLEMODEL_HPP_*/