ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp

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#include "ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp"
#include "Exception.hpp"
#include "StemCellProliferativeType.hpp"
#include "TransitCellProliferativeType.hpp"
#include "DifferentiatedCellProliferativeType.hpp"

ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel()
    : AbstractSimpleGenerationBasedCellCycleModel(),
      mRate(1.0/mTransitCellG1Duration)
{
}

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

    /*
     * 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) 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.
     *
     * Note 3: the member variable mDimension remains unset, since this cell-cycle
     * model does not need to know the spatial dimension, so if we were to call
     * SetDimension() on the new cell-cycle model an exception would be triggered;
     * hence we do not set this member variable.
     */
    p_model->SetBirthTime(mBirthTime);
    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->SetGeneration(mGeneration);
    p_model->SetMaxTransitGenerations(mMaxTransitGenerations);
    p_model->SetRate(mRate);

    return p_model;
}

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetG1Duration()
{
    RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();

    if (    mpCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>()
            || mpCell->GetCellProliferativeType()->IsType<TransitCellProliferativeType>() )
    {
        // Generate an exponential random number with mScale
        mG1Duration = p_gen->ExponentialRandomDeviate(mRate);
    }
    else if (mpCell->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>())
    {
        mG1Duration = DBL_MAX;
    }
    else
    {
        NEVER_REACHED;
    }
}

double ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::GetRate()
{
    return mRate;
}

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetRate(double rate)
{
    mRate = rate;

    // These are now set to the average value of the G1Duration
    SetTransitCellG1Duration(1.0/rate);
    SetStemCellG1Duration(1.0/rate);
}

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetStemCellG1Duration(double stemCellG1Duration)
{
    assert(stemCellG1Duration > 0.0);
    mStemCellG1Duration = stemCellG1Duration;

    mRate = 1.0/stemCellG1Duration;
}

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetTransitCellG1Duration(double transitCellG1Duration)
{
    assert(transitCellG1Duration > 0.0);
    mTransitCellG1Duration = transitCellG1Duration;

    mRate = 1.0/transitCellG1Duration;
}

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
     *rParamsFile << "\t\t\t<Rate>" << mRate << "</Rate>\n";

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

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