AbstractCellCycleModel.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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 "CellProliferativeTypes.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 & mCellProliferativeType;
        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;

    CellProliferativeType mCellProliferativeType;

    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();

    void SetStemCellG1Duration(double stemCellG1Duration);

    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();

    CellProliferativeType GetCellProliferativeType() const;

    void SetCellProliferativeType(CellProliferativeType cellType);

    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_*/