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 "DefaultCellProliferativeType.hpp"
#include "CellLabel.hpp"
#include "CellAncestor.hpp"
#include "CellId.hpp"
#include "CellData.hpp"
#include "CellVecData.hpp"

#include "ApoptoticCellProperty.hpp"
#include "AbstractCellCycleModel.hpp"
#include "AbstractSrnModel.hpp"
#include "SimulationTime.hpp"
#include "CellPropertyRegistry.hpp"
#include "CellPropertyCollection.hpp"
#include "SmartPointers.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;

class Cell : private boost::noncopyable, public boost::enable_shared_from_this<Cell>
{
private:

    bool mCanDivide;

    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;
    }

protected:

    CellPropertyCollection mCellPropertyCollection;

    AbstractCellCycleModel* mpCellCycleModel;

    AbstractSrnModel* mpSrnModel;

    double mDeathTime;

    double mStartOfApoptosisTime;

    double mApoptosisTime;

    bool mUndergoingApoptosis;

    bool mIsDead;

    bool mIsLogged;

public:

    Cell(boost::shared_ptr<AbstractCellProperty> pMutationState,
         AbstractCellCycleModel* pCellCycleModel,
         AbstractSrnModel* pSrnModel=NULL,
         bool archiving=false,
         CellPropertyCollection cellPropertyCollection=CellPropertyCollection());

    ~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;

    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();

    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;
};


#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_*/