AngiogenesisSolver.hpp

/*

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#ifndef ANGIOGENESISSOLVER_HPP_
#define ANGIOGENESISSOLVER_HPP_

#include <vector>
#include <string>
#include "SmartPointers.hpp"
#include "VesselNetwork.hpp"
#include "Part.hpp"
#include "RegularGrid.hpp"
#include "AbstractSproutingRule.hpp"
#include "AbstractMigrationRule.hpp"
#include "AbstractCellPopulation.hpp"

template<unsigned DIM>
class AngiogenesisSolver
{
    boost::shared_ptr<VesselNetwork<DIM> > mpNetwork;

    units::quantity<unit::length> mNodeAnastamosisRadius;

    boost::shared_ptr<AbstractMigrationRule<DIM> > mpMigrationRule;

    boost::shared_ptr<AbstractSproutingRule<DIM> > mpSproutingRule;

    boost::shared_ptr<Part<DIM> > mpBoundingDomain;

    boost::shared_ptr<OutputFileHandler> mpFileHandler;

    boost::shared_ptr<RegularGrid<DIM> > mpVesselGrid;

    boost::shared_ptr<AbstractCellPopulation<DIM> > mpCellPopulation;

    units::quantity<unit::length> mCellPopulationReferenceLength;

    std::vector<boost::shared_ptr<Cell> > mTipCells;

    std::map<boost::shared_ptr<Cell> , boost::shared_ptr<VesselNode<DIM> > > mCellNodeMap;

public:

    AngiogenesisSolver();

    virtual ~AngiogenesisSolver();

    static boost::shared_ptr<AngiogenesisSolver<DIM> > Create();

    virtual void Increment();

    bool IsSproutingRuleSet();

    void Run(bool writeOutput = false);

    void SetAnastamosisRadius(units::quantity<unit::length> radius);

    void SetBoundingDomain(boost::shared_ptr<Part<DIM> > pDomain);

    void SetCellPopulation(boost::shared_ptr<AbstractCellPopulation<DIM> > pCellPopulation, units::quantity<unit::length> cellPopulationReferenceLength);

    void SetMigrationRule(boost::shared_ptr<AbstractMigrationRule<DIM> > pMigrationRule);

    void SetOutputFileHandler(boost::shared_ptr<OutputFileHandler> pHandler);

    void SetSproutingRule(boost::shared_ptr<AbstractSproutingRule<DIM> > pSproutingRule);

    void SetVesselGrid(boost::shared_ptr<RegularGrid<DIM> >pVesselGrid);

    void SetVesselNetwork(boost::shared_ptr<VesselNetwork<DIM> > pNetwork);

protected:

    virtual void DoSprouting();

    virtual void DoAnastamosis();

    virtual void UpdateNodalPositions(bool sprouting = false);
};

#endif /* ANGIOGENESISSOLVER_HPP_ */