DeltaNotchCellCycleModel.cpp

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#include "UblasIncludes.hpp"
#include "DeltaNotchCellCycleModel.hpp"
#include "CellCycleModelOdeSolver.hpp"
#include "CvodeAdaptor.hpp"
#include "Exception.hpp"



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

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

    // Create the new cell-cycle model's ODE system
    double mean_neighbouring_delta = GetMeanNeighbouringDelta();
    p_model->SetOdeSystem(new DeltaNotchOdeSystem);
    p_model->GetOdeSystem()->SetParameter("Mean Delta", mean_neighbouring_delta);

    // Use the current values of the state variables in mpOdeSystem as an initial condition for the new cell-cycle model's ODE system
    assert(mpOdeSystem);
    p_model->SetStateVariables(mpOdeSystem->rGetStateVariables());

    // Set the values of the new cell-cycle model's member variables
    p_model->SetBirthTime(mBirthTime);
    p_model->SetLastTime(mLastTime);
    p_model->SetDimension(mDimension);
    p_model->SetGeneration(mGeneration);
    p_model->SetMaxTransitGenerations(mMaxTransitGenerations);

    return p_model;
}

void DeltaNotchCellCycleModel::UpdateCellCyclePhase()
{
    assert(SimulationTime::Instance()->IsStartTimeSetUp());
    UpdateDeltaNotch();
    SolveOdeToTime(SimulationTime::Instance()->GetTime());
    AbstractSimpleCellCycleModel::UpdateCellCyclePhase();
}

void DeltaNotchCellCycleModel::Initialise()
{
    assert(mpOdeSystem == NULL);
    assert(mpCell != NULL);

    mpOdeSystem = new DeltaNotchOdeSystem;
    if (mInitialConditions == std::vector<double>())
    {
        mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());
    }
    else
    {
        mpOdeSystem->SetStateVariables(mInitialConditions);
    }

    StochasticDurationGenerationBasedCellCycleModel::Initialise();

    SetLastTime(mBirthTime);
}

void DeltaNotchCellCycleModel::SetInitialConditions(std::vector<double> initialConditions)
{
    assert(initialConditions.size() == 2);
    mInitialConditions = initialConditions;
}

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

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

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

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

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

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

    // Call direct parent class
    StochasticDurationGenerationBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}

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