TysonNovakCellCycleModel.cpp

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*/

#include "TysonNovakCellCycleModel.hpp"
#include "StemCellProliferativeType.hpp"
#include "TransitCellProliferativeType.hpp"

TysonNovakCellCycleModel::TysonNovakCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractOdeBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
{
    if (!mpOdeSolver)
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<TysonNovakCellCycleModel, CvodeAdaptor>::Instance();
        mpOdeSolver->Initialise();
        // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
        mpOdeSolver->CheckForStoppingEvents();
        mpOdeSolver->SetMaxSteps(10000);
        mpOdeSolver->SetTolerances(1e-6, 1e-8);
#else
        mpOdeSolver = CellCycleModelOdeSolver<TysonNovakCellCycleModel, BackwardEulerIvpOdeSolver>::Instance();
        mpOdeSolver->SetSizeOfOdeSystem(6);
        mpOdeSolver->Initialise();
        SetDt(0.1/90.0);
#endif //CHASTE_CVODE
    }
}

TysonNovakCellCycleModel::TysonNovakCellCycleModel(const TysonNovakCellCycleModel& rModel)
    : AbstractOdeBasedCellCycleModel(rModel)
{
    /*
     * Initialize only those member variables defined in this class.
     * Create the new cell-cycle model's ODE system and use the current
     * values of the state variables in mpOdeSystem as an initial condition.
     *
     * The member variable mDivideTime is initialized in the
     * AbstractOdeBasedCellCycleModel constructor.
     *
     * The member variables mBirthTime, mReadyToDivide and mDimension
     * are initialized in the AbstractCellCycleModel constructor.
     *
     * Note that the cell proliferative type is (re)set as soon as
     * InitialiseDaughterCell() is called on the new cell-cycle model.
     */
    assert(rModel.GetOdeSystem());
    SetOdeSystem(new TysonNovak2001OdeSystem);
    SetStateVariables(rModel.GetOdeSystem()->rGetStateVariables());
}

void TysonNovakCellCycleModel::Initialise()
{
    assert(mpOdeSystem == nullptr);
    mpOdeSystem = new TysonNovak2001OdeSystem;
    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());

    AbstractOdeBasedCellCycleModel::Initialise();
}

void TysonNovakCellCycleModel::ResetForDivision()
{
    AbstractOdeBasedCellCycleModel::ResetForDivision();

    assert(mpOdeSystem != nullptr);

#ifdef CHASTE_CVODE
    mpOdeSystem->rGetStateVariables()[5] = 0.5*mpOdeSystem->rGetStateVariables()[5];
#else
    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());
#endif //CHASTE_CVODE
}

void TysonNovakCellCycleModel::InitialiseDaughterCell()
{
    if (mpCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
    {
        /*
         * 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_transit_type =
        mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<TransitCellProliferativeType>();
        mpCell->SetCellProliferativeType(p_transit_type);
    }
}

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

double TysonNovakCellCycleModel::GetAverageTransitCellCycleTime()
{
    return 1.25;
}

double TysonNovakCellCycleModel::GetAverageStemCellCycleTime()
{
    return 1.25;
}

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

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

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