DeltaNotchInteriorSrnModel.cpp

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#include "DeltaNotchInteriorSrnModel.hpp"
#include "DeltaNotchEdgeSrnModel.hpp"
 
DeltaNotchInteriorSrnModel::DeltaNotchInteriorSrnModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
        : AbstractOdeSrnModel(2, pOdeSolver)
{
    if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchInteriorSrnModel, CvodeAdaptor>::Instance();
        mpOdeSolver->Initialise();
        mpOdeSolver->SetMaxSteps(10000);
#else
        mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchInteriorSrnModel, RungeKutta4IvpOdeSolver>::Instance();
        mpOdeSolver->Initialise();
        SetDt(0.001);
#endif //CHASTE_CVODE
    }
    assert(mpOdeSolver->IsSetUp());
}
 
DeltaNotchInteriorSrnModel::DeltaNotchInteriorSrnModel(const DeltaNotchInteriorSrnModel& rModel)
        : AbstractOdeSrnModel(rModel)
{
    /*
     * Set each member variable of the new SRN model that inherits
     * its value from the parent.
     *
     * Note 1: some of the new SRN model's member variables
     * will already have been correctly initialized in its constructor.
     *
     * Note 2: one or more of the new SRN model's member variables
     * may be set/overwritten as soon as InitialiseDaughterCell() is called on
     * the new SRN model.
     *
     * Note 3: Only set the variables defined in this class. Variables defined
     * in parent classes will be defined there.
     */
 
    assert(rModel.GetOdeSystem());
    AbstractOdeSystem* p_parent_system(rModel.GetOdeSystem());
    SetOdeSystem(new DeltaNotchInteriorOdeSystem(p_parent_system->rGetStateVariables()));
    for (unsigned i=0; i < p_parent_system->GetNumberOfParameters(); ++i)
    {
        mpOdeSystem->SetParameter(i, p_parent_system->GetParameter(i));
    }
}
 
AbstractSrnModel* DeltaNotchInteriorSrnModel::CreateSrnModel()
{
    return new DeltaNotchInteriorSrnModel(*this);
}
 
void DeltaNotchInteriorSrnModel::ResetForDivision()
{
    assert(mpOdeSystem != nullptr);
    assert(mpCell != nullptr);
    ScaleSrnVariables(0.5);
}
 
void DeltaNotchInteriorSrnModel::SimulateToCurrentTime()
{
    // Custom behaviour
    UpdateDeltaNotch();
 
    // Run the ODE simulation as needed
    AbstractOdeSrnModel::SimulateToCurrentTime();
}
 
void DeltaNotchInteriorSrnModel::Initialise()
{
    AbstractOdeSrnModel::Initialise(new DeltaNotchInteriorOdeSystem);
}
 
void DeltaNotchInteriorSrnModel::UpdateDeltaNotch()
{
    assert(mpOdeSystem != nullptr);
    assert(mpCell != nullptr);
 
    const double total_edge_delta = mpCell->GetCellData()->GetItem("total neighbour edge delta");
    mpOdeSystem->SetParameter("total neighbour edge delta", total_edge_delta);
 
    const double total_edge_notch = mpCell->GetCellData()->GetItem("total edge notch");
    mpOdeSystem->SetParameter("total edge notch", total_edge_notch);
}
 
double DeltaNotchInteriorSrnModel::GetNotch()
{
    assert(mpOdeSystem != nullptr);
    double notch = mpOdeSystem->rGetStateVariables()[0];
    return notch;
}
 
void DeltaNotchInteriorSrnModel::SetNotch(double value)
{
    assert(mpOdeSystem != nullptr);
    mpOdeSystem->rGetStateVariables()[0] = value;
}
 
double DeltaNotchInteriorSrnModel::GetDelta()
{
    assert(mpOdeSystem != nullptr);
    double delta = mpOdeSystem->rGetStateVariables()[1];
    return delta;
}
 
void DeltaNotchInteriorSrnModel::SetDelta(double value)
{
    assert(mpOdeSystem != nullptr);
    mpOdeSystem->rGetStateVariables()[1] = value;
}
 
double DeltaNotchInteriorSrnModel::GetTotalEdgeDelta()
{
    assert(mpOdeSystem != nullptr);
    double total_edge_delta = mpOdeSystem->GetParameter("total neighbour edge delta");
    return total_edge_delta;
}
 
double DeltaNotchInteriorSrnModel::GetTotalEdgeNotch()
{
    assert(mpOdeSystem != nullptr);
    double total_edge_notch = mpOdeSystem->GetParameter("total edge notch");
    return total_edge_notch;
}
 
void DeltaNotchInteriorSrnModel::OutputSrnModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output, so just call method on direct parent class
    AbstractOdeSrnModel::OutputSrnModelParameters(rParamsFile);
}
 
void DeltaNotchInteriorSrnModel::AddShrunkEdgeToInterior(AbstractSrnModel* pShrunkEdgeSrn)
{
    // Half of junctional Delta/Notch is endocytosed back to the cytoplasm
    auto p_shrunk_srn = static_cast<DeltaNotchEdgeSrnModel*>(pShrunkEdgeSrn);
    const double edge_notch = p_shrunk_srn->GetNotch();
    const double edge_delta = p_shrunk_srn->GetDelta();
    const double this_notch = GetNotch();
    const double this_delta = GetDelta();
 
    const double fraction = 0.5;
    SetDelta(this_delta+fraction*edge_delta);
    SetNotch(this_notch+fraction*edge_notch);
}
 
 
 
// Declare identifier for the serializer
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(DeltaNotchInteriorSrnModel)
#include "CellCycleModelOdeSolverExportWrapper.hpp"
EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(DeltaNotchInteriorSrnModel)