AbstractSrnModel.hpp

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*/
 
#ifndef ABSTRACTSRNMODEL_HPP_
#define ABSTRACTSRNMODEL_HPP_
 
#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
#include "Identifiable.hpp"
 
#include <boost/serialization/base_object.hpp>
 
#include <vector>
 
#include "Cell.hpp"
#include "Exception.hpp"
#include "OutputFileHandler.hpp"
#include "SimulationTime.hpp"
 
class Cell; // Circular definition (cells need to know about SRN models and vice-versa)
typedef boost::shared_ptr<Cell> CellPtr;
 
class AbstractSrnModel : public Identifiable
{
private:
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // Make sure the SimulationTime singleton gets saved too
        SerializableSingleton<SimulationTime>* p_time_wrapper = SimulationTime::Instance()->GetSerializationWrapper();
        archive & p_time_wrapper;
 
        // DO NOT archive & mpCell; -- The SrnModel is only ever archived from the Cell
        // which knows this and it is handled in the load_construct of Cell.
        archive & mSimulatedToTime;
        archive & mEdgeLocalIndex;
        archive & mIsEdgeBasedModel;
    }
 
    AbstractSrnModel& operator=(const AbstractSrnModel&);
 
protected:
 
    CellPtr mpCell;
 
    double mSimulatedToTime;
 
    unsigned mEdgeLocalIndex = UNSIGNED_UNSET;
 
    bool mIsEdgeBasedModel = false;
 
    AbstractSrnModel(const AbstractSrnModel& rModel);
 
public:
 
    AbstractSrnModel();
 
    virtual ~AbstractSrnModel();
 
    virtual void SetCell(CellPtr pCell);
 
    virtual void Initialise();
 
    virtual void InitialiseDaughterCell();
 
    CellPtr GetCell();
 
    void SetSimulatedToTime(double simulatedToTime);
 
    double GetSimulatedToTime() const;
 
    virtual void SimulateToCurrentTime()=0;
 
    virtual void ResetForDivision();
 
    virtual AbstractSrnModel* CreateSrnModel()=0;
 
    void OutputSrnModelInfo(out_stream& rParamsFile);
 
    virtual void OutputSrnModelParameters(out_stream& rParamsFile);
 
    void SetEdgeLocalIndex(unsigned index);
 
    unsigned GetEdgeLocalIndex();
 
    bool HasEdgeModel() const;
 
    void SetEdgeModelIndicator(const bool isEdgeModel);
 
    virtual void ScaleSrnVariables(const double theta);
 
    virtual void AddSrnQuantities(AbstractSrnModel* pOtherSrn,
                                  const double scale = 1.0);
 
    virtual void AddShrunkEdgeSrn(AbstractSrnModel* pShrunkEdgeSrn);
 
    virtual void AddMergedEdgeSrn(AbstractSrnModel* pMergedEdgeSrn);
 
    virtual void AddShrunkEdgeToInterior(AbstractSrnModel* pShrunkEdgeSrn);
 
    virtual void SplitEdgeSrn(const double relativePosition);
};
 
CLASS_IS_ABSTRACT(AbstractSrnModel)
 
#endif /* ABSTRACTSRNMODEL_HPP_ */