MultipleCaBasedCellPopulation.hpp

/*

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*/

#ifndef MULTIPLECABASEDCELLPOPULATION_HPP_
#define MULTIPLECABASEDCELLPOPULATION_HPP_

#include "AbstractOnLatticeCellPopulation.hpp"
#include "PottsMesh.hpp"
#include "VertexMesh.hpp"
#include "AbstractMultipleCaUpdateRule.hpp"

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/vector.hpp>

// Needed here to avoid serialization errors (on Boost<1.37)
#include "WildTypeCellMutationState.hpp"

template<unsigned DIM>
class AbstractMultipleCaUpdateRule; // Circular definition

template<unsigned DIM>
class MultipleCaBasedCellPopulation : public AbstractOnLatticeCellPopulation<DIM>
{
    friend class TestMultipleCaBasedCellPopulation;

private:


    unsigned mLatticeCarryingCapacity;

    out_stream mpVizLocationsFile;

    std::vector<boost::shared_ptr<AbstractMultipleCaUpdateRule<DIM> > > mUpdateRuleCollection;

    std::vector<unsigned> mAvailableSpaces;

    void SetEmptySites(const std::set<unsigned>& rEmptySiteIndices);

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
#define COVERAGE_IGNORE
        archive & boost::serialization::base_object<AbstractOnLatticeCellPopulation<DIM> >(*this);
        archive & mLatticeCarryingCapacity;
        archive & mUpdateRuleCollection;
        archive & mAvailableSpaces;

#undef COVERAGE_IGNORE
    }

    void Validate();

    void WriteVtkResultsToFile();

public:

    MultipleCaBasedCellPopulation(PottsMesh<DIM>& rMesh,
                                  std::vector<CellPtr>& rCells,
                                  const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                                  unsigned latticeCarryingCapacity=1u,
                                  bool deleteMesh=false,
                                  bool validate=false);

    MultipleCaBasedCellPopulation(PottsMesh<DIM>& rMesh);

    virtual ~MultipleCaBasedCellPopulation();

    std::vector<unsigned>& rGetAvailableSpaces();

    bool IsSiteAvailable(unsigned index);


    PottsMesh<DIM>& rGetMesh();

    const PottsMesh<DIM>& rGetMesh() const;

    Node<DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

    c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);

    void AddCellUsingLocationIndex(unsigned index, CellPtr pCell);

    void RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell);

     Node<DIM>* GetNodeCorrespondingToCell(CellPtr pCell);

    CellPtr AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell=CellPtr());

    unsigned RemoveDeadCells();

//    /**
//     * Calculated the probability of a cell moving based on the calculations provided by Owen et. al 2011
//     */
//    double CalculateProbabilityOfMoving(unsigned node_index, unsigned node_neighbour_index, double dt);

    void UpdateCellLocations(double dt);

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void Update(bool hasHadBirthsOrDeaths=true);

    void CreateOutputFiles(const std::string& rDirectory, bool cleanOutputDirectory);

    void CloseOutputFiles();

    void WriteResultsToFiles();

    void WriteCellVolumeResultsToFile();

    double GetVolumeOfCell(CellPtr pCell);

    virtual void GenerateCellResultsAndWriteToFiles();

    double GetWidth(const unsigned& rDimension);

    void AddUpdateRule(boost::shared_ptr<AbstractMultipleCaUpdateRule<DIM> > pUpdateRule);


    void RemoveAllUpdateRules();

    const std::vector<boost::shared_ptr<AbstractMultipleCaUpdateRule<DIM> > >& rGetUpdateRuleCollection() const;

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(MultipleCaBasedCellPopulation)

// No archiving yet so untested
#define COVERAGE_IGNORE
namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const MultipleCaBasedCellPopulation<DIM> * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const PottsMesh<DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, MultipleCaBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    PottsMesh<DIM>* p_mesh;
    ar >> p_mesh;

    // Invoke inplace constructor to initialise instance
    ::new(t)MultipleCaBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...
#undef COVERAGE_IGNORE

#endif /*MULTIPLECABASEDCELLPOPULATION_HPP_*/