VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp

/*

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*/

#include "VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp"

VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractVanLeeuwen2009WntSwatCellCycleModel(pOdeSolver)
{
    if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, 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<VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, RungeKutta4IvpOdeSolver>::Instance();
        mpOdeSolver->Initialise();
        SetDt(0.00005);
#endif //CHASTE_CVODE
    }
}

void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::InitialiseOdeSystem(double wntConcentration, boost::shared_ptr<AbstractCellMutationState> pMutationState)
{
    mpOdeSystem = new VanLeeuwen2009WntSwatCellCycleOdeSystem(1, wntConcentration,  pMutationState);
}

AbstractCellCycleModel* VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel()
{
    // Create a new cell-cycle model
    VanLeeuwen2009WntSwatCellCycleModelHypothesisOne* p_model = new VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(mpOdeSolver);

    /*
     * Set each member variable of the new cell-cycle model that inherits
     * its value from the parent.
     *
     * Note 1: some of the new cell-cycle model's member variables (namely
     * mBirthTime, mCurrentCellCyclePhase, mReadyToDivide, mDt, mpOdeSolver)
     * will already have been correctly initialized in its constructor.
     *
     * Note 2: one or more of the new cell-cycle model's member variables
     * may be set/overwritten as soon as InitialiseDaughterCell() is called on
     * the new cell-cycle model.
     */
    p_model->SetBirthTime(mBirthTime);
    p_model->SetDimension(mDimension);
    p_model->SetMinimumGapDuration(mMinimumGapDuration);
    p_model->SetStemCellG1Duration(mStemCellG1Duration);
    p_model->SetTransitCellG1Duration(mTransitCellG1Duration);
    p_model->SetSDuration(mSDuration);
    p_model->SetG2Duration(mG2Duration);
    p_model->SetMDuration(mMDuration);
    p_model->SetDivideTime(mDivideTime);
    p_model->SetFinishedRunningOdes(mFinishedRunningOdes);
    p_model->SetG2PhaseStartTime(mG2PhaseStartTime);
    p_model->SetLastTime(mLastTime);

    /*
     * Create the new cell-cycle model's ODE system and use the current values
     * of the state variables in mpOdeSystem as an initial condition.
     */
    assert(mpOdeSystem);
    double wnt_level = GetWntLevel();
    p_model->InitialiseOdeSystem(wnt_level, mpCell->GetMutationState());
    p_model->SetStateVariables(mpOdeSystem->rGetStateVariables());

    return p_model;
}

void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output

    // Call method on direct parent class
    AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}

// Declare identifier for the serializer
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(VanLeeuwen2009WntSwatCellCycleModelHypothesisOne)
#include "CellCycleModelOdeSolverExportWrapper.hpp"
EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(VanLeeuwen2009WntSwatCellCycleModelHypothesisOne)