AbstractSimpleGenerationalCellCycleModel.cpp

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*/

#include "AbstractSimpleGenerationalCellCycleModel.hpp"
#include "DifferentiatedCellProliferativeType.hpp"
#include "StemCellProliferativeType.hpp"
#include "TransitCellProliferativeType.hpp"

AbstractSimpleGenerationalCellCycleModel::AbstractSimpleGenerationalCellCycleModel()
    : AbstractSimplePhaseBasedCellCycleModel(),
      mGeneration(0),
      mMaxTransitGenerations(3) // taken from Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)
{
}

AbstractSimpleGenerationalCellCycleModel::~AbstractSimpleGenerationalCellCycleModel()
{
}

AbstractSimpleGenerationalCellCycleModel::AbstractSimpleGenerationalCellCycleModel(const AbstractSimpleGenerationalCellCycleModel& rModel)
    : AbstractSimplePhaseBasedCellCycleModel(rModel),
      mGeneration(rModel.mGeneration),
      mMaxTransitGenerations(rModel.mMaxTransitGenerations)
{
    /*
     * Initialize only those member variables defined in this class.
     *
     * The member variables mCurrentCellCyclePhase, mG1Duration,
     * mMinimumGapDuration, mStemCellG1Duration, mTransitCellG1Duration,
     * mSDuration, mG2Duration and mMDuration are initialized in the
     * AbstractPhaseBasedCellCycleModel constructor.
     *
     * The member variables mBirthTime, mReadyToDivide and mDimension
     * are initialized in the AbstractCellCycleModel constructor.
     *
     * Note that mG1Duration is (re)set as soon as InitialiseDaughterCell()
     * is called on the new cell-cycle model.
     */
}

void AbstractSimpleGenerationalCellCycleModel::ResetForDivision()
{
    mGeneration++;
    if (mpCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
    {
    /*
    * Run this check first to allow for mMaxTransitGenerations = 0
    */
        mGeneration = 0;
    }
    if (mGeneration > mMaxTransitGenerations)
    {
        /*
         * This method is usually called within a CellBasedSimulation, after the CellPopulation
         * has called CellPropertyRegistry::TakeOwnership(). This means that were we to call
         * CellPropertyRegistry::Instance() here when setting the CellProliferativeType, we
         * would be creating a new CellPropertyRegistry. In this case the cell proliferative
         * type counts, as returned by AbstractCellPopulation::GetCellProliferativeTypeCount(),
         * would be incorrect. We must therefore access the CellProliferativeType via the cell's
         * CellPropertyCollection.
         */
        boost::shared_ptr<AbstractCellProperty> p_diff_type =
            mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<DifferentiatedCellProliferativeType>();
        mpCell->SetCellProliferativeType(p_diff_type);
    }
    AbstractSimplePhaseBasedCellCycleModel::ResetForDivision();
}

void AbstractSimpleGenerationalCellCycleModel::InitialiseDaughterCell()
{
    /*
     * If the parent cell is a stem cell then its generation was reset
     * to zero when ResetForDivision() was called. The daughter cell's
     * generation must therefore be incremented here.
     */
    if (mGeneration == 0)
    {
        mGeneration = 1;
    }
    /*
     * In generation-based cell-cycle models, the daughter cell
     * is always of type transit or differentiated.
     */
    boost::shared_ptr<AbstractCellProperty> p_transit_type =
        mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<TransitCellProliferativeType>();
    mpCell->SetCellProliferativeType(p_transit_type);

    if (mGeneration > mMaxTransitGenerations)
    {
        boost::shared_ptr<AbstractCellProperty> p_diff_type =
            mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<DifferentiatedCellProliferativeType>();
        mpCell->SetCellProliferativeType(p_diff_type);
    }
    AbstractSimplePhaseBasedCellCycleModel::InitialiseDaughterCell();
}

void AbstractSimpleGenerationalCellCycleModel::SetGeneration(unsigned generation)
{
    mGeneration = generation;
}

unsigned AbstractSimpleGenerationalCellCycleModel::GetGeneration() const
{
    return mGeneration;
}

void AbstractSimpleGenerationalCellCycleModel::SetMaxTransitGenerations(unsigned maxTransitGenerations)
{
    mMaxTransitGenerations = maxTransitGenerations;
}

unsigned AbstractSimpleGenerationalCellCycleModel::GetMaxTransitGenerations() const
{
    return mMaxTransitGenerations;
}

void AbstractSimpleGenerationalCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<MaxTransitGenerations>" << mMaxTransitGenerations << "</MaxTransitGenerations>\n";

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