CellCycleModelProteinConcentrationsWriter.cpp

/*

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*/

#include "CellCycleModelProteinConcentrationsWriter.hpp"
#include "AbstractCellPopulation.hpp"
#include "CellCycleModelOdeHandler.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellCycleModelProteinConcentrationsWriter<ELEMENT_DIM, SPACE_DIM>::CellCycleModelProteinConcentrationsWriter()
    : AbstractCellWriter<ELEMENT_DIM, SPACE_DIM>("proteinconcentrations.dat")
{
    this->mVtkCellDataName = "Protein concentrations";
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double CellCycleModelProteinConcentrationsWriter<ELEMENT_DIM, SPACE_DIM>::GetCellDataForVtkOutput(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
    /*
     * At present it is not possible to output all cell variables via this method, we just return zero.
     * If the user requires cell variables to be output to VTK, the easiest way to do this is to store
     * them in the cell's CellData using a modifier object, since any CellData is automatically output
     * to VTK (if CHASTE_VTK is turned on).
     */
    return 0.0;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellCycleModelProteinConcentrationsWriter<ELEMENT_DIM, SPACE_DIM>::VisitCell(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
    CellCycleModelOdeHandler* p_model = dynamic_cast<CellCycleModelOdeHandler*>(pCell->GetCellCycleModel());

    if (p_model)
    {
        // Write location index corresponding to cell
        *this->mpOutStream << pCellPopulation->GetLocationIndexUsingCell(pCell) << " ";

        // Write cell variables
        std::vector<double> proteins = p_model->GetProteinConcentrations();
        for (unsigned i=0; i<proteins.size(); i++)
        {
            *this->mpOutStream << proteins[i] << " ";
        }
    }

    else
    {
        EXCEPTION("CellCycleModelProteinConcentrationsWriter cannot be used with a cell-cycle model that does not inherit from CellCycleModelOdeHandler");
    }
}

// Explicit instantiation
template class CellCycleModelProteinConcentrationsWriter<1,1>;
template class CellCycleModelProteinConcentrationsWriter<1,2>;
template class CellCycleModelProteinConcentrationsWriter<2,2>;
template class CellCycleModelProteinConcentrationsWriter<1,3>;
template class CellCycleModelProteinConcentrationsWriter<2,3>;
template class CellCycleModelProteinConcentrationsWriter<3,3>;

#include "SerializationExportWrapperForCpp.hpp"
// Declare identifier for the serializer
EXPORT_TEMPLATE_CLASS_ALL_DIMS(CellCycleModelProteinConcentrationsWriter)