AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp

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#include "UblasIncludes.hpp"
#include "AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp"

AbstractVanLeeuwen2009WntSwatCellCycleModel::AbstractVanLeeuwen2009WntSwatCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
   : AbstractWntOdeBasedCellCycleModel(pOdeSolver)
{
}

void AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel()
{
    assert(mpOdeSystem != NULL);
    assert(mpCell != NULL);
    double beta_catenin_level =   mpOdeSystem->rGetStateVariables()[16]
                                + mpOdeSystem->rGetStateVariables()[17]
                                + mpOdeSystem->rGetStateVariables()[18]
                                + mpOdeSystem->rGetStateVariables()[19];

    CellProliferativeType cell_type = TRANSIT;

    // For mitogenic stimulus of 1/25.0 in Wnt equations
    if (beta_catenin_level < 10.188)
    {
        cell_type = DIFFERENTIATED;
    }

    mpCell->SetCellProliferativeType(cell_type);
}

void AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise()
{
    assert(mpOdeSystem == NULL);
    assert(mpCell != NULL);

    double wnt_level = GetWntLevel();

    InitialiseOdeSystem(wnt_level, mpCell->GetMutationState());

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

    ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel();
}

void AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(double currentTime)
{
    // Pass this time step's Wnt stimulus into the solver as a constant over this timestep.
    mpOdeSystem->rGetStateVariables()[21] = GetWntLevel();

    // Use the cell's current mutation status as another input
    static_cast<VanLeeuwen2009WntSwatCellCycleOdeSystem*>(mpOdeSystem)->SetMutationState(mpCell->GetMutationState());
}

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel()
{
    return mpOdeSystem->rGetStateVariables()[13] + mpOdeSystem->rGetStateVariables()[14];
}

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel()
{
    return  mpOdeSystem->rGetStateVariables()[7] + mpOdeSystem->rGetStateVariables()[8]
          + mpOdeSystem->rGetStateVariables()[9] + mpOdeSystem->rGetStateVariables()[10]
          + mpOdeSystem->rGetStateVariables()[11];
}

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel()
{
    return mpOdeSystem->rGetStateVariables()[16] +
           mpOdeSystem->rGetStateVariables()[17] +
           mpOdeSystem->rGetStateVariables()[18] +
           mpOdeSystem->rGetStateVariables()[19];
}

void AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output

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