TysonNovakCellCycleModel.cpp

/*

Copyright (C) University of Oxford, 2005-2010

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#include "TysonNovakCellCycleModel.hpp"

TysonNovakCellCycleModel::TysonNovakCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractOdeBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
{
    if (!mpOdeSolver)
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<TysonNovakCellCycleModel, CvodeAdaptor>::Instance();
        mpOdeSolver->Initialise();
        // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
        mpOdeSolver->CheckForStoppingEvents();
        mpOdeSolver->SetMaxSteps(10000);
        mpOdeSolver->SetTolerances(1e-6, 1e-8);
#else
        mpOdeSolver = CellCycleModelOdeSolver<TysonNovakCellCycleModel, BackwardEulerIvpOdeSolver>::Instance();
        mpOdeSolver->SetSizeOfOdeSystem(6);
        mpOdeSolver->Initialise();
        SetDt(0.1/60.0);
#endif //CHASTE_CVODE
    }
}

void TysonNovakCellCycleModel::Initialise()
{
    assert(mpOdeSystem == NULL);
    mpOdeSystem = new TysonNovak2001OdeSystem;
    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());

    AbstractCellCycleModel::Initialise();
}

void TysonNovakCellCycleModel::ResetForDivision()
{
    AbstractOdeBasedCellCycleModel::ResetForDivision();

    assert(mpOdeSystem != NULL);

#ifdef CHASTE_CVODE
    mpOdeSystem->rGetStateVariables()[5] = 0.5*mpOdeSystem->rGetStateVariables()[5];
#else
    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());
#endif //CHASTE_CVODE
}

void TysonNovakCellCycleModel::InitialiseDaughterCell()
{
    if (mCellProliferativeType == STEM)
    {
        mCellProliferativeType = TRANSIT;
    }
}

AbstractCellCycleModel* TysonNovakCellCycleModel::CreateCellCycleModel()
{
    // Create a new cell cycle model
    TysonNovakCellCycleModel* p_model = new TysonNovakCellCycleModel(mpOdeSolver);

    // 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->SetOdeSystem(new TysonNovak2001OdeSystem);
    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->SetDivideTime(mDivideTime);
    p_model->SetFinishedRunningOdes(mFinishedRunningOdes);
    p_model->SetG2PhaseStartTime(mG2PhaseStartTime);
    p_model->SetCellProliferativeType(mCellProliferativeType);

    return p_model;
}

double TysonNovakCellCycleModel::GetSDuration()
{
    return 0.0;
}

double TysonNovakCellCycleModel::GetG2Duration()
{
    return 0.0;
}

double TysonNovakCellCycleModel::GetMDuration()
{
    return 0.0;
}

double TysonNovakCellCycleModel::GetAverageTransitCellCycleTime()
{
    return 1.25;
}

double TysonNovakCellCycleModel::GetAverageStemCellCycleTime()
{
    return 1.25;
}


bool TysonNovakCellCycleModel::CanCellTerminallyDifferentiate()
{
    return false;
}

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

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