Alarcon2004OxygenBasedCellCycleModel.cpp

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#include "Alarcon2004OxygenBasedCellCycleModel.hpp"

#include "CellLabel.hpp"

Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractOdeBasedPhaseBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
{
    if (!mpOdeSolver)
    {
        mpOdeSolver = CellCycleModelOdeSolver<Alarcon2004OxygenBasedCellCycleModel, RungeKutta4IvpOdeSolver>::Instance();
        mpOdeSolver->Initialise();
    }
    SetDt(0.0001);
}

Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel(const Alarcon2004OxygenBasedCellCycleModel& rModel)
    : AbstractOdeBasedPhaseBasedCellCycleModel(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 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.
     */

    assert(rModel.GetOdeSystem());
    bool is_labelled = rModel.mpCell->HasCellProperty<CellLabel>();
    SetOdeSystem(new Alarcon2004OxygenBasedCellCycleOdeSystem(rModel.mpCell->GetCellData()->GetItem("oxygen"), is_labelled));
    SetStateVariables(rModel.GetOdeSystem()->rGetStateVariables());
}

AbstractCellCycleModel* Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel()
{
    return new Alarcon2004OxygenBasedCellCycleModel(*this);
}

void Alarcon2004OxygenBasedCellCycleModel::ResetForDivision()
{
    AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision();
    assert(mpOdeSystem != nullptr);

    // This model needs the protein concentrations and phase resetting to G0/G1.
    // Keep the oxygen concentration the same but reset everything else
    std::vector<double> init_conds = mpOdeSystem->GetInitialConditions();
    for (unsigned i=0; i<5; i++)
    {
        mpOdeSystem->rGetStateVariables()[i] = init_conds[i];
    }
}

void Alarcon2004OxygenBasedCellCycleModel::Initialise()
{
    assert(mpOdeSystem == nullptr);
    assert(mpCell != nullptr);

    bool is_labelled = mpCell->HasCellProperty<CellLabel>();
    mpOdeSystem = new Alarcon2004OxygenBasedCellCycleOdeSystem(mpCell->GetCellData()->GetItem("oxygen"), is_labelled);
    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());

    AbstractOdeBasedPhaseBasedCellCycleModel::Initialise();
}

void Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters(double currentTime)
{
    // Pass this time step's oxygen concentration into the solver as a constant over this time step
    mpOdeSystem->rGetStateVariables()[5] = mpCell->GetCellData()->GetItem("oxygen");

    // Use whether the cell is currently labelled as another input
    bool is_labelled = mpCell->HasCellProperty<CellLabel>();
    static_cast<Alarcon2004OxygenBasedCellCycleOdeSystem*>(mpOdeSystem)->SetIsLabelled(is_labelled);
}

void Alarcon2004OxygenBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output, so just call method on direct parent class
    AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(Alarcon2004OxygenBasedCellCycleModel)
#include "CellCycleModelOdeSolverExportWrapper.hpp"
EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(Alarcon2004OxygenBasedCellCycleModel)