DeltaNotchSrnModel.cpp

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#include "DeltaNotchSrnModel.hpp"
#include "AbstractOdeSrnModel.hpp"

DeltaNotchSrnModel::DeltaNotchSrnModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractOdeSrnModel(2, pOdeSolver)
{
    if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchSrnModel, CvodeAdaptor>::Instance();
        mpOdeSolver->Initialise();
        mpOdeSolver->SetMaxSteps(10000);
#else
        mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchSrnModel, RungeKutta4IvpOdeSolver>::Instance();
        mpOdeSolver->Initialise();
        SetDt(0.001);
#endif //CHASTE_CVODE
    }
    assert(mpOdeSolver->IsSetUp());
}

AbstractSrnModel* DeltaNotchSrnModel::CreateSrnModel()
{
    // Create a new srn model
    DeltaNotchSrnModel* p_model = new DeltaNotchSrnModel(this->mpOdeSolver);

    // Create the new srn model's ODE system
    p_model->SetOdeSystem(new DeltaNotchOdeSystem);

    // Call super to set current values of the state variables in mpOdeSystem as an initial condition for the new srn model's ODE system
    return AbstractOdeSrnModel::CreateSrnModel(p_model);
}

void DeltaNotchSrnModel::SimulateToCurrentTime()
{
    // Custom behaviour
    UpdateDeltaNotch();

    // Run the ODE simulation as needed
    AbstractOdeSrnModel::SimulateToCurrentTime();
}

void DeltaNotchSrnModel::Initialise()
{
    AbstractOdeSrnModel::Initialise(new DeltaNotchOdeSystem);
}

void DeltaNotchSrnModel::UpdateDeltaNotch()
{
    assert(mpOdeSystem != NULL);
    assert(mpCell != NULL);

    double mean_delta = mpCell->GetCellData()->GetItem("mean delta");
    mpOdeSystem->SetParameter("Mean Delta", mean_delta);
}

double DeltaNotchSrnModel::GetNotch()
{
    assert(mpOdeSystem != NULL);
    double notch = mpOdeSystem->rGetStateVariables()[0];
    return notch;
}

double DeltaNotchSrnModel::GetDelta()
{
    assert(mpOdeSystem != NULL);
    double delta = mpOdeSystem->rGetStateVariables()[1];
    return delta;
}

double DeltaNotchSrnModel::GetMeanNeighbouringDelta()
{
    assert(mpOdeSystem != NULL);
    double mean_neighbouring_delta = mpOdeSystem->GetParameter("Mean Delta");
    return mean_neighbouring_delta;
}

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

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