AbstractOdeBasedCellCycleModel.cpp

/*

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#include "AbstractOdeBasedCellCycleModel.hpp"
#include <iostream>
#include <cassert>
#include "Exception.hpp"

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel(double lastTime,
                                                               boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : CellCycleModelOdeHandler(lastTime, pOdeSolver),
      mDivideTime(lastTime),
      mFinishedRunningOdes(false),
      mG2PhaseStartTime(DBL_MAX)
{
    AbstractCellCycleModel::SetBirthTime(lastTime);
}

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel()
{
}

void AbstractOdeBasedCellCycleModel::SetBirthTime(double birthTime)
{
    AbstractCellCycleModel::SetBirthTime(birthTime);
    mLastTime = birthTime;
    mDivideTime = birthTime;
}

std::vector<double> AbstractOdeBasedCellCycleModel::GetProteinConcentrations() const
{
    assert(mpOdeSystem != NULL);
    return mpOdeSystem->rGetStateVariables();
}

void AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(double lastTime, std::vector<double> proteinConcentrations)
{
    assert(mpOdeSystem != NULL);
    assert(proteinConcentrations.size()==mpOdeSystem->rGetStateVariables().size());
    mLastTime = lastTime;
    mpOdeSystem->SetStateVariables(proteinConcentrations);
}

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

    double current_time = SimulationTime::Instance()->GetTime();

    // Update the phase from M to G1 when necessary
    if (mCurrentCellCyclePhase == M_PHASE)
    {
        double m_duration = GetMDuration();
        if (GetAge() >= m_duration)
        {
            mCurrentCellCyclePhase = G_ONE_PHASE;
            mLastTime = m_duration + mBirthTime;
        }
        else
        {
            // Still dividing; don't run ODEs
            return;
        }
    }

    if (current_time > mLastTime)
    {
        if (!mFinishedRunningOdes)
        {
            // Update whether a stopping event has occurred
            mFinishedRunningOdes = SolveOdeToTime(current_time);

            // Check no concentrations have gone negative
            for (unsigned i=0; i<mpOdeSystem->GetNumberOfStateVariables(); i++)
            {
                if (mpOdeSystem->rGetStateVariables()[i] < -DBL_EPSILON)
                {
                    #define COVERAGE_IGNORE
                    EXCEPTION("A protein concentration " << i << " has gone negative (" <<
                              mpOdeSystem->rGetStateVariables()[i] << ")\n"
                              << "Chaste predicts that the CellCycleModel numerical method is probably unstable.");
                    #undef COVERAGE_IGNORE
                }
            }

            if (mFinishedRunningOdes)
            {
                // Update durations of each phase
                mG1Duration = GetOdeStopTime() - mBirthTime - GetMDuration();
                mG2PhaseStartTime = GetOdeStopTime() + GetSDuration();
                mDivideTime = mG2PhaseStartTime + GetG2Duration();

                // Update phase
                if (current_time >= mG2PhaseStartTime)
                {
                    mCurrentCellCyclePhase = G_TWO_PHASE;
                }
                else
                {
                    mCurrentCellCyclePhase = S_PHASE;
                }
            }
        }
        else
        {
            // ODE model finished, just increasing time until division...
            if (current_time >= mG2PhaseStartTime)
            {
                mCurrentCellCyclePhase = G_TWO_PHASE;
            }
        }
    }
}

void AbstractOdeBasedCellCycleModel::ResetForDivision()
{
    assert(mFinishedRunningOdes);
    AbstractCellCycleModel::ResetForDivision();
    mBirthTime = mDivideTime;
    mLastTime = mDivideTime;
    mFinishedRunningOdes = false;
    mG1Duration = DBL_MAX;
    mDivideTime = DBL_MAX;
}

double AbstractOdeBasedCellCycleModel::GetOdeStopTime()
{
    double stop_time = DOUBLE_UNSET;
    if (mpOdeSolver->StoppingEventOccurred())
    {
        stop_time = mpOdeSolver->GetStoppingTime();
    }
    return stop_time;
}

void AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes(bool finishedRunningOdes)
{
    mFinishedRunningOdes = finishedRunningOdes;
}

void AbstractOdeBasedCellCycleModel::SetDivideTime(double divideTime)
{
    mDivideTime = divideTime;
}

void AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime(double g2PhaseStartTime)
{
    mG2PhaseStartTime = g2PhaseStartTime;
}

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

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