AbstractCellCycleModel.cpp

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*/

#include "AbstractCellCycleModel.hpp"

AbstractCellCycleModel::AbstractCellCycleModel()
    : mBirthTime(SimulationTime::Instance()->GetTime()),
      mCurrentCellCyclePhase(M_PHASE),
      mG1Duration(DOUBLE_UNSET),
      mReadyToDivide(false),
      mDimension(UNSIGNED_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)
{
}

AbstractCellCycleModel::~AbstractCellCycleModel()
{
}

void AbstractCellCycleModel::Initialise()
{
}

void AbstractCellCycleModel::InitialiseDaughterCell()
{
}

void AbstractCellCycleModel::SetCell(CellPtr pCell)
{
    mpCell = pCell;
}

CellPtr AbstractCellCycleModel::GetCell()
{
    assert(mpCell != NULL);
    return mpCell;
}

void AbstractCellCycleModel::SetBirthTime(double birthTime)
{
    mBirthTime = birthTime;
}

double AbstractCellCycleModel::GetBirthTime() const
{
    return mBirthTime;
}

double AbstractCellCycleModel::GetAge()
{
    return SimulationTime::Instance()->GetTime() - mBirthTime;
}

CellCyclePhase AbstractCellCycleModel::GetCurrentCellCyclePhase()
{
    return mCurrentCellCyclePhase;
}

void AbstractCellCycleModel::ResetForDivision()
{
    assert(mReadyToDivide);
    mCurrentCellCyclePhase = M_PHASE;
    mReadyToDivide = false;
}

double AbstractCellCycleModel::GetG1Duration()
{
    return mG1Duration;
}

// Getter methods

double AbstractCellCycleModel::GetStemCellG1Duration()
{
    return mStemCellG1Duration;
}

double AbstractCellCycleModel::GetTransitCellG1Duration()
{
    return mTransitCellG1Duration;
}

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

double AbstractCellCycleModel::GetSDuration()
{
    return mSDuration;
}

double AbstractCellCycleModel::GetG2Duration()
{
    return mG2Duration;
}

double AbstractCellCycleModel::GetMDuration()
{
    return mMDuration;
}

// Setter methods

void AbstractCellCycleModel::SetStemCellG1Duration(double stemCellG1Duration)
{
    assert(stemCellG1Duration > 0.0);
    mStemCellG1Duration = stemCellG1Duration;
}
void AbstractCellCycleModel::SetTransitCellG1Duration(double transitCellG1Duration)
{
    assert(transitCellG1Duration > 0.0);
    mTransitCellG1Duration = transitCellG1Duration;
}
void AbstractCellCycleModel::SetSDuration(double SDuration)
{
    assert(SDuration > 0.0);
    mSDuration = SDuration;
}
void AbstractCellCycleModel::SetG2Duration(double G2Duration)
{
    assert(G2Duration > 0.0);
    mG2Duration = G2Duration;
}
void AbstractCellCycleModel::SetMDuration(double MDuration)
{
    assert(MDuration > 0.0);
    mMDuration = MDuration;
}

bool AbstractCellCycleModel::ReadyToDivide()
{
    assert(mpCell != NULL);

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

void AbstractCellCycleModel::SetDimension(unsigned dimension)
{
    if (dimension != 1 && dimension !=2 && dimension != 3)
    {
        EXCEPTION("Dimension must be 1, 2 or 3");
    }
    mDimension = dimension;
}

unsigned AbstractCellCycleModel::GetDimension()
{
    return mDimension;
}

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

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

bool AbstractCellCycleModel::CanCellTerminallyDifferentiate()
{
    return true;
}

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

double AbstractCellCycleModel::GetMinimumGapDuration()
{
    return mMinimumGapDuration;
}

void AbstractCellCycleModel::OutputCellCycleModelInfo(out_stream& rParamsFile)
{
    std::string cell_cycle_model_type = GetIdentifier();

    *rParamsFile << "\t\t<" << cell_cycle_model_type << ">\n";
    OutputCellCycleModelParameters(rParamsFile);
    *rParamsFile << "\t\t</" << cell_cycle_model_type << ">\n";
}

void AbstractCellCycleModel::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";
}