CellCycleModelOdeHandler.cpp

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*/

#include "CellCycleModelOdeHandler.hpp"

CellCycleModelOdeHandler::CellCycleModelOdeHandler(double lastTime,
                                                   boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : mDt(DOUBLE_UNSET),
      mpOdeSystem(nullptr),
      mpOdeSolver(pOdeSolver),
      mLastTime(lastTime),
      mFinishedRunningOdes(false)
{
}

CellCycleModelOdeHandler::~CellCycleModelOdeHandler()
{
    if (mpOdeSystem != nullptr)
    {
        delete mpOdeSystem;
    }
}

CellCycleModelOdeHandler::CellCycleModelOdeHandler(const CellCycleModelOdeHandler& rHandler)
    : mDt(rHandler.mDt),
      mpOdeSystem(rHandler.mpOdeSystem),
      mpOdeSolver(rHandler.mpOdeSolver),
      mLastTime(rHandler.mLastTime),
      mFinishedRunningOdes(rHandler.mFinishedRunningOdes)
{
}

void CellCycleModelOdeHandler::SetOdeSystem(AbstractOdeSystem* pOdeSystem)
{
    mpOdeSystem = pOdeSystem;
}

AbstractOdeSystem* CellCycleModelOdeHandler::GetOdeSystem() const
{
    return mpOdeSystem;
}

const boost::shared_ptr<AbstractCellCycleModelOdeSolver> CellCycleModelOdeHandler::GetOdeSolver() const
{
    return mpOdeSolver;
}

void CellCycleModelOdeHandler::SetDt(double timeStep)
{
    mDt = timeStep;
}

double CellCycleModelOdeHandler::GetDt()
{
    if (mDt == DOUBLE_UNSET)
    {
        if (mpOdeSolver->IsAdaptive())
        {
            mDt = SimulationTime::Instance()->GetTimeStep();
        }
        else
        {
            mDt = 0.0001; // Some models need this, so let's pick a safe default
        }
    }
    return mDt;
}

bool CellCycleModelOdeHandler::SolveOdeToTime(double currentTime)
{
    bool stopping_event_occurred = false;
    if (mLastTime < currentTime)
    {
        AdjustOdeParameters(currentTime);

        mpOdeSolver->SolveAndUpdateStateVariable(mpOdeSystem, mLastTime, currentTime, GetDt());

        stopping_event_occurred = mpOdeSolver->StoppingEventOccurred();
        if (stopping_event_occurred)
        {
            mLastTime = mpOdeSolver->GetStoppingTime();
        }
        else
        {
            mLastTime = currentTime;
        }
    }
    return stopping_event_occurred;
}

void CellCycleModelOdeHandler::AdjustOdeParameters(double currentTime)
{
}

void CellCycleModelOdeHandler::SetLastTime(double lastTime)
{
    mLastTime = lastTime;
}

void CellCycleModelOdeHandler::SetStateVariables(const std::vector<double>& rStateVariables)
{
    assert(mpOdeSystem);
    mpOdeSystem->SetStateVariables(rStateVariables);
}

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

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