AbstractPhaseBasedCellCycleModel.cpp

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*/

#include "AbstractPhaseBasedCellCycleModel.hpp"

AbstractPhaseBasedCellCycleModel::AbstractPhaseBasedCellCycleModel()
    :   AbstractCellCycleModel(),
        mCurrentCellCyclePhase(M_PHASE),
        mG1Duration(DOUBLE_UNSET),
        mMinimumGapDuration(0.01), // an educated guess
        // Default parameter values all have units of hours.
        mStemCellG1Duration(14.0),
        mTransitCellG1Duration(2.0),
        mSDuration(5.0),               // apparently between 5-6 hours normally
        mG2Duration(4.0),              // apparently 3-4 hours normally
        mMDuration(1.0)               // taken from Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)
{
}

AbstractPhaseBasedCellCycleModel::~AbstractPhaseBasedCellCycleModel()
{
}

AbstractPhaseBasedCellCycleModel::AbstractPhaseBasedCellCycleModel(const AbstractPhaseBasedCellCycleModel& rModel)
    : AbstractCellCycleModel(rModel),
      mCurrentCellCyclePhase(rModel.mCurrentCellCyclePhase),
      mG1Duration(rModel.mG1Duration),
      mMinimumGapDuration(rModel.mMinimumGapDuration),
      mStemCellG1Duration(rModel.mStemCellG1Duration),
      mTransitCellG1Duration(rModel.mTransitCellG1Duration),
      mSDuration(rModel.mSDuration),
      mG2Duration(rModel.mG2Duration),
      mMDuration(rModel.mMDuration)
{
    /*
     * Initialize only those member variables defined in this class.
     *
     * The member variables mBirthTime, mReadyToDivide and mDimension
     * are initialized in the AbstractCellCycleModel constructor.
     */
}

void AbstractPhaseBasedCellCycleModel::ResetForDivision()
{
    AbstractCellCycleModel::ResetForDivision();
    mCurrentCellCyclePhase = M_PHASE;
}

bool AbstractPhaseBasedCellCycleModel::ReadyToDivide()
{
    assert(mpCell != nullptr);

    if (!mReadyToDivide)
    {
        UpdateCellCyclePhase();
        if ((mCurrentCellCyclePhase != G_ZERO_PHASE) &&
            (GetAge() >= GetMDuration() + GetG1Duration() + GetSDuration() + GetG2Duration()))
        {
            mReadyToDivide = true;
        }
    }
    return mReadyToDivide;
}

double AbstractPhaseBasedCellCycleModel::GetG1Duration() const
{
    return mG1Duration;
}

double AbstractPhaseBasedCellCycleModel::GetStemCellG1Duration() const
{
    return mStemCellG1Duration;
}

double AbstractPhaseBasedCellCycleModel::GetTransitCellG1Duration() const
{
    return mTransitCellG1Duration;
}

double AbstractPhaseBasedCellCycleModel::GetSG2MDuration() const
{
    return mSDuration + mG2Duration + mMDuration;
}

double AbstractPhaseBasedCellCycleModel::GetSDuration() const
{
    return mSDuration;
}

double AbstractPhaseBasedCellCycleModel::GetG2Duration() const
{
    return mG2Duration;
}

double AbstractPhaseBasedCellCycleModel::GetMDuration() const
{
    return mMDuration;
}

CellCyclePhase AbstractPhaseBasedCellCycleModel::GetCurrentCellCyclePhase() const
{
    return mCurrentCellCyclePhase;
}

double AbstractPhaseBasedCellCycleModel::GetAverageTransitCellCycleTime()
{
    return mTransitCellG1Duration + GetSG2MDuration();
}

double AbstractPhaseBasedCellCycleModel::GetAverageStemCellCycleTime()
{
    return mStemCellG1Duration + GetSG2MDuration();
}

double AbstractPhaseBasedCellCycleModel::GetMinimumGapDuration() const
{
    return mMinimumGapDuration;
}

void AbstractPhaseBasedCellCycleModel::SetStemCellG1Duration(double stemCellG1Duration)
{
    assert(stemCellG1Duration >= 0.0);
    mStemCellG1Duration = stemCellG1Duration;
}

void AbstractPhaseBasedCellCycleModel::SetTransitCellG1Duration(double transitCellG1Duration)
{
    assert(transitCellG1Duration >= 0.0);
    mTransitCellG1Duration = transitCellG1Duration;
}

void AbstractPhaseBasedCellCycleModel::SetSDuration(double SDuration)
{
    assert(SDuration >= 0.0);
    mSDuration = SDuration;
}

void AbstractPhaseBasedCellCycleModel::SetG2Duration(double G2Duration)
{
    assert(G2Duration >= 0.0);
    mG2Duration = G2Duration;
}

void AbstractPhaseBasedCellCycleModel::SetMDuration(double MDuration)
{
    assert(MDuration >= 0.0);
    mMDuration = MDuration;
}

void AbstractPhaseBasedCellCycleModel::SetMinimumGapDuration(double minimumGapDuration)
{
    assert(minimumGapDuration > 0.0);
    mMinimumGapDuration = minimumGapDuration;
}

void AbstractPhaseBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<StemCellG1Duration>" << mStemCellG1Duration << "</StemCellG1Duration>\n";
    *rParamsFile << "\t\t\t<TransitCellG1Duration>" << mTransitCellG1Duration << "</TransitCellG1Duration>\n";
    *rParamsFile << "\t\t\t<SDuration>" << mSDuration << "</SDuration>\n";
    *rParamsFile << "\t\t\t<G2Duration>" << mG2Duration << "</G2Duration>\n";
    *rParamsFile << "\t\t\t<MDuration>" << mMDuration << "</MDuration>\n";

    // Call method on direct parent class
    AbstractCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}