Owen2011OxygenBasedCellCycleModel.hpp

/*

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 */

#ifndef OWEN2011OXYGENBASEDCELLCYCLEMODEL_HPP_
#define OWEN2011OXYGENBASEDCELLCYCLEMODEL_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <vector>
#include "AbstractOdeBasedPhaseBasedCellCycleModel.hpp"
#include "AbstractCellMutationState.hpp"
#include "CancerCellMutationState.hpp"
#include "Owen2011OxygenBasedCellCycleOdeSystem.hpp"
#include "UnitCollection.hpp"

class Owen2011OxygenBasedCellCycleModel : public AbstractOdeBasedPhaseBasedCellCycleModel
{

private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOdeBasedPhaseBasedCellCycleModel>(*this);
        archive & mCurrentQuiescentDuration;
        archive & mCurrentQuiescenceOnsetTime;
        archive & mEnterQuiescenceOxygenConcentration;
        archive & mLeaveQuiescenceOxygenConcentration;
        archive & mCriticalQuiescentDuration;
    }

    void AdjustOdeParameters(double currentTime);

protected:

    units::quantity<unit::time> mOdeIntegrationTimeStep;

    units::quantity<unit::dimensionless> sOnset;

    units::quantity<unit::dimensionless> g2Onset;

    units::quantity<unit::dimensionless> mOnset;

    units::quantity<unit::time> mReferenceTimeScale;

    units::quantity<unit::concentration> mReferenceConcentrationScale;

    units::quantity<unit::solubility> mReferenceSolubility;

    units::quantity<unit::dimensionless> mMaxRandInitialPhase;

    units::quantity<unit::time> mCurrentQuiescentDuration;

    units::quantity<unit::time> mCurrentQuiescenceOnsetTime;

    units::quantity<unit::pressure> mEnterQuiescenceOxygenConcentration;

    units::quantity<unit::pressure> mLeaveQuiescenceOxygenConcentration;

    units::quantity<unit::time> mCriticalQuiescentDuration;

    units::quantity<unit::dimensionless> mp53ThresholdForApoptosisOfNormalCellsInHealthyMicroenvironment;

    units::quantity<unit::dimensionless> mp53ThresholdForApoptosisOfNormalCellsInTumourMicroenvironment;

    units::quantity<unit::dimensionless> mthresholdFractionOfNormalCellNeighbours;

public:

    Owen2011OxygenBasedCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>());

    AbstractCellCycleModel* CreateCellCycleModel();

    void CheckAndLabelCell();

    units::quantity<unit::time> GetCurrentQuiescentDuration();

    units::quantity<unit::time> GetCurrentQuiescenceOnsetTime();

    units::quantity<unit::pressure> GetEnterQuiescenceOxygenConcentration();

    units::quantity<unit::time> GetCriticalQuiescentDuration();

    double GetSDuration() const;

    double GetG2Duration() const;

    double GetMDuration() const;

    double GetPhi();

    double GetVEGF();

    double GetP53();

    units::quantity<unit::pressure> GetLeaveQuiescenceOxygenConcentration();

    void Initialise();

    void InitialiseDaughterCell();

    virtual void OutputCellCycleModelParameters(out_stream& rParamsFile);

    bool ReadyToDivide();

    virtual void ResetForDivision();

    void SetMaxRandInitialPhase(units::quantity<unit::dimensionless> rand_max_phase);

    void SetEnterQuiescenceOxygenConcentration(units::quantity<unit::pressure> enterQuiescenceOxygenConcentration);

    void SetLeaveQuiescenceOxygenConcentration(units::quantity<unit::pressure> leaveQuiescenceOxygenConcentration);

    void SetCriticalQuiescentDuration(units::quantity<unit::time> criticalQuiescentDuration);

    void SetCurrentQuiescenceOnsetTime(units::quantity<unit::time> currentQuiescenceOnsetTime);

    void SetG2Onset(units::quantity<unit::dimensionless> value);

    void SetSOnset(units::quantity<unit::dimensionless> value);

    void SetMOnset(units::quantity<unit::dimensionless> value);

    void SetOdeSolverTimeStep(units::quantity<unit::time> timeStep);

    void SetReferenceTimeScale(units::quantity<unit::time> referenceTimeScale);

    void SetReferenceConcentrationScale(units::quantity<unit::concentration> referenceConcentrationScale);

    void SetThresholdFractionOfNormalCellNeighbours(double value);

    void UpdateQuiescentDuration();

    void UpdateCellCyclePhase();
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(Owen2011OxygenBasedCellCycleModel)
#include "CellCycleModelOdeSolverExportWrapper.hpp"
EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(Owen2011OxygenBasedCellCycleModel)

#endif /*OWEN2011OXYGENBASEDCELLCYCLEMODEL_HPP_*/