AbstractWntOdeBasedCellCycleModel.cpp

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#include "AbstractWntOdeBasedCellCycleModel.hpp"
#include "Exception.hpp"

AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractOdeBasedPhaseBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
{
}

AbstractWntOdeBasedCellCycleModel::~AbstractWntOdeBasedCellCycleModel()
{
}

AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel(const AbstractWntOdeBasedCellCycleModel& rModel)
   : AbstractOdeBasedPhaseBasedCellCycleModel(rModel)
{
    /*
     * The member variables mDivideTime and mG2PhaseStartTime are
     * initialized in the AbstractOdeBasedPhaseBasedCellCycleModel
     * constructor.
     *
     * 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.
     */
}

double AbstractWntOdeBasedCellCycleModel::GetWntLevel() const
{
    assert(mpCell != nullptr);
    double level = 0;

    switch (mDimension)
    {
        case 1:
        {
            const unsigned DIM = 1;
            level = WntConcentration<DIM>::Instance()->GetWntLevel(mpCell);
            break;
        }
        case 2:
        {
            const unsigned DIM = 2;
            level = WntConcentration<DIM>::Instance()->GetWntLevel(mpCell);
            break;
        }
        case 3:
        {
            const unsigned DIM = 3;
            level = WntConcentration<DIM>::Instance()->GetWntLevel(mpCell);
            break;
        }
        default:
            NEVER_REACHED;
    }

    return level;
}

void AbstractWntOdeBasedCellCycleModel::ResetForDivision()
{
    AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision();

    assert(mpOdeSystem != nullptr);

    // This model needs the protein concentrations and phase resetting to G0/G1.
    // Keep the Wnt pathway in the same state but reset the cell cycle part
    // Cell cycle is proteins 0 to 4 (first 5 ODEs)
    std::vector<double> init_conds = mpOdeSystem->GetInitialConditions();
    for (unsigned i=0; i<5; i++)
    {
       mpOdeSystem->rGetStateVariables()[i] = init_conds[i];
    }
}

void AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase()
{
    AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase();
    if (SimulationTime::Instance()->GetTime() == mLastTime
        || GetOdeStopTime() == mLastTime)
    {
        // Should only be called if we're still running ODEs
        UpdateCellProliferativeType();
    }
}

void AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType()
{
    assert(mpOdeSystem != nullptr);
    assert(mpCell != nullptr);
    ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel();
}

double AbstractWntOdeBasedCellCycleModel::GetAverageTransitCellCycleTime()
{
    return 16.0;
}

double AbstractWntOdeBasedCellCycleModel::GetAverageStemCellCycleTime()
{
    return 16.0;
}

bool AbstractWntOdeBasedCellCycleModel::CanCellTerminallyDifferentiate()
{
    return false;
}

void AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output, so just call method on direct parent class
    AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}