StochasticWntCellCycleModel.cpp

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#include "StochasticWntCellCycleModel.hpp"

StochasticWntCellCycleModel::StochasticWntCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : WntCellCycleModel(pOdeSolver)
{
    if (!pOdeSolver)
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<StochasticWntCellCycleModel, CvodeAdaptor>::Instance();
        mpOdeSolver->Initialise();
        // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
        mpOdeSolver->CheckForStoppingEvents();
        mpOdeSolver->SetMaxSteps(10000);
#else
        mpOdeSolver = CellCycleModelOdeSolver<StochasticWntCellCycleModel, RungeKutta4IvpOdeSolver>::Instance();
        mpOdeSolver->Initialise();
#endif //CHASTE_CVODE
    }
}

StochasticWntCellCycleModel::~StochasticWntCellCycleModel()
{}

StochasticWntCellCycleModel::StochasticWntCellCycleModel(const StochasticWntCellCycleModel& rModel)
   : WntCellCycleModel(rModel),
     mStochasticG2Duration(rModel.mStochasticG2Duration)
{
    /*
     * Initialize only the member variable defined in this class.
     *
     * The new cell-cycle model's ODE system is created and initialized
     * in the WntCellCycleModel constructor.
     *
     * 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.
     *
     * Note that mStochasticG2Duration is (re)set as soon as
     * InitialiseDaughterCell() is called on the new cell-cycle model.
     */
}

void StochasticWntCellCycleModel::GenerateStochasticG2Duration()
{
    RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();

    double mean = AbstractPhaseBasedCellCycleModel::GetG2Duration();
    double standard_deviation = 0.9;
    mStochasticG2Duration = p_gen->NormalRandomDeviate(mean, standard_deviation);

    // Check that the normal random deviate has not returned a small or negative G2 duration
    if (mStochasticG2Duration < mMinimumGapDuration)
    {
        mStochasticG2Duration = mMinimumGapDuration;
    }
}

void StochasticWntCellCycleModel::InitialiseDaughterCell()
{
    WntCellCycleModel::InitialiseDaughterCell();
    GenerateStochasticG2Duration();
}

void StochasticWntCellCycleModel::Initialise()
{
    WntCellCycleModel::Initialise();
    GenerateStochasticG2Duration();
}

void StochasticWntCellCycleModel::ResetForDivision()
{
    AbstractWntOdeBasedCellCycleModel::ResetForDivision();
    GenerateStochasticG2Duration();
}

double StochasticWntCellCycleModel::GetG2Duration() const
{
    return mStochasticG2Duration;
}

AbstractCellCycleModel* StochasticWntCellCycleModel::CreateCellCycleModel()
{
   return new StochasticWntCellCycleModel(*this);
}

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

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(StochasticWntCellCycleModel)
#include "CellCycleModelOdeSolverExportWrapper.hpp"
EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(StochasticWntCellCycleModel)