Cell.hpp

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*/
 
#ifndef CELL_HPP_
#define CELL_HPP_
 
#include <boost/utility.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/enable_shared_from_this.hpp>
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/shared_ptr.hpp>
 
#include "AbstractCellMutationState.hpp"
#include "AbstractCellProliferativeType.hpp"
#include "CellData.hpp"
#include "CellVecData.hpp"
#include "CellEdgeData.hpp"
 
 
#include "AbstractCellCycleModel.hpp"
#include "AbstractSrnModel.hpp"
#include "CellPropertyCollection.hpp"
 
class AbstractCellCycleModel; // Circular definition (cells need to know about cycle models and vice-versa).
class AbstractSrnModel; // Circular definition (cells need to know about subcellular reaction network models and vice-versa).
class Cell;
 
typedef boost::shared_ptr<Cell> CellPtr;
 
struct null_deleter
{
    void operator()(void const *) const
    {
    }
};
 
class Cell : private boost::noncopyable, public boost::enable_shared_from_this<Cell>
{
private:
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // These first four are also dealt with by {load,save}_construct_data
        archive & mCanDivide;
        archive & mpCellCycleModel;
        archive & mpSrnModel;
        archive & mUndergoingApoptosis;
        archive & mDeathTime;
        archive & mStartOfApoptosisTime;
        archive & mApoptosisTime;
        archive & mIsDead;
        archive & mIsLogged;
        archive & mHasSrnModel;
    }
 
protected:
 
    bool mCanDivide;
 
    CellPropertyCollection mCellPropertyCollection;
 
    AbstractCellCycleModel* mpCellCycleModel;
 
    AbstractSrnModel* mpSrnModel;
 
    double mDeathTime;
 
    double mStartOfApoptosisTime;
 
    double mApoptosisTime;
 
    bool mUndergoingApoptosis;
 
    bool mIsDead;
 
    bool mIsLogged;
 
    bool mHasSrnModel;
 
public:
 
    Cell(boost::shared_ptr<AbstractCellProperty> pMutationState,
         AbstractCellCycleModel* pCellCycleModel,
         AbstractSrnModel* pSrnModel=nullptr,
         bool archiving=false,
         CellPropertyCollection cellPropertyCollection=CellPropertyCollection());
 
    virtual ~Cell();
 
    boost::shared_ptr<AbstractCellProliferativeType> GetCellProliferativeType() const;
 
    void SetCellProliferativeType(boost::shared_ptr<AbstractCellProperty> pProliferativeType);
 
    void SetBirthTime(double birthTime);
 
    void SetCellCycleModel(AbstractCellCycleModel* pCellCycleModel);
 
    AbstractCellCycleModel* GetCellCycleModel() const;
 
    void InitialiseCellCycleModel();
 
    void SetSrnModel(AbstractSrnModel* pSrnModel);
 
    AbstractSrnModel* GetSrnModel() const;
 
    void InitialiseSrnModel();
 
    double GetAge() const;
 
    double GetBirthTime() const;
 
    double GetStartOfApoptosisTime() const;
 
    double GetApoptosisTime() const;
 
    void SetApoptosisTime(double apoptosisTime);
 
    boost::shared_ptr<AbstractCellMutationState> GetMutationState() const;
 
    boost::shared_ptr<CellData> GetCellData() const;
 
    boost::shared_ptr<CellEdgeData> GetCellEdgeData() const;
 
    bool HasCellVecData() const;
 
    boost::shared_ptr<CellVecData> GetCellVecData() const;
 
    void SetMutationState(boost::shared_ptr<AbstractCellProperty> pMutationState);
 
    CellPropertyCollection& rGetCellPropertyCollection();
 
    const CellPropertyCollection& rGetCellPropertyCollection() const;
 
    void AddCellProperty(const boost::shared_ptr<AbstractCellProperty>& rProperty);
 
    template<typename CLASS>
    void RemoveCellProperty()
    {
        bool cell_has_property = false;
 
        for (std::set<boost::shared_ptr<AbstractCellProperty> >::iterator property_iter = mCellPropertyCollection.Begin();
             property_iter != mCellPropertyCollection.End();
             ++property_iter)
        {
            if ((*property_iter)->IsType<CLASS>())
            {
                cell_has_property = true;
                (*property_iter)->DecrementCellCount();
                break;
            }
        }
 
        if (cell_has_property)
        {
            mCellPropertyCollection.RemoveProperty<CLASS>();
        }
    }
 
    template<typename CLASS>
    bool HasCellProperty() const
    {
        return mCellPropertyCollection.HasProperty<CLASS>();
    }
 
    bool ReadyToDivide();
 
    virtual CellPtr Divide();
 
    void StartApoptosis(bool setDeathTime=true);
 
    void Kill();
 
    bool HasApoptosisBegun() const;
 
    double GetTimeUntilDeath() const;
 
    bool IsDead();
 
    void SetLogged();
 
    bool IsLogged();
 
    void SetAncestor(boost::shared_ptr<AbstractCellProperty> pCellAncestor);
 
    unsigned GetAncestor() const;
 
    unsigned GetCellId() const;
 
    bool HasSrnModel() const;
};
 
 
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(Cell)
 
namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const Cell * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const boost::shared_ptr<AbstractCellMutationState> p_mutation_state = t->GetMutationState();
    ar & p_mutation_state;
    const AbstractCellCycleModel* const p_cell_cycle_model = t->GetCellCycleModel();
    ar & p_cell_cycle_model;
    const AbstractSrnModel* const p_srn_model = t->GetSrnModel();
    ar & p_srn_model;
    const CellPropertyCollection& r_cell_property_collection = t->rGetCellPropertyCollection();
    ar & r_cell_property_collection;
}
 
template<class Archive>
inline void load_construct_data(
    Archive & ar, Cell * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    boost::shared_ptr<AbstractCellMutationState> p_mutation_state;
    ar & p_mutation_state;
 
    AbstractCellCycleModel* p_cell_cycle_model;
    ar & p_cell_cycle_model;
 
    AbstractSrnModel* p_srn_model;
    ar & p_srn_model;
 
    bool archiving = true;
 
    CellPropertyCollection cell_property_collection;
    ar & cell_property_collection;
 
    // Invoke inplace constructor to initialize instance
    ::new(t)Cell(p_mutation_state, p_cell_cycle_model, p_srn_model, archiving, cell_property_collection);
}
}
} // namespace ...
 
#endif /*CELL_HPP_*/