Alarcon2004OxygenBasedCellCycleModel.cpp

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*/

#include "Alarcon2004OxygenBasedCellCycleModel.hpp"

#include "CellLabel.hpp"
#include "Exception.hpp"

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

void Alarcon2004OxygenBasedCellCycleModel::ResetForDivision()
{
    AbstractOdeBasedCellCycleModel::ResetForDivision();
    assert(mpOdeSystem != NULL);

    // 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];
    }
}

AbstractCellCycleModel* Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel()
{
    // Create a new cell-cycle model
    Alarcon2004OxygenBasedCellCycleModel* p_model = new Alarcon2004OxygenBasedCellCycleModel(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);
    bool is_labelled = mpCell->HasCellProperty<CellLabel>();
    p_model->SetOdeSystem(new Alarcon2004OxygenBasedCellCycleOdeSystem(mpCell->GetCellData()->GetItem("oxygen"), is_labelled));
    p_model->SetStateVariables(mpOdeSystem->rGetStateVariables());

    return p_model;
}

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

    bool is_labelled = mpCell->HasCellProperty<CellLabel>();

    mpOdeSystem = new Alarcon2004OxygenBasedCellCycleOdeSystem(mpCell->GetCellData()->GetItem("oxygen"), is_labelled);

    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());
}

void Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters(double currentTime)
{
    // Pass this time step's oxygen concentration into the solver as a constant over this timestep

    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

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

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