Cell.hpp

/*
 
Copyright (c) 2005-2024, University of Oxford.
All rights reserved.
 
University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.
 
This file is part of Chaste.
 
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.
 
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#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_*/