AbstractCellCycleModel.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#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 & 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();

    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();

    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_*/