Cell.hpp

/*

Copyright (C) University of Oxford, 2005-2011

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.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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 "CellProliferativeTypes.hpp"
#include "AbstractCellMutationState.hpp"
#include "CellLabel.hpp"
#include "ApoptoticCellProperty.hpp"
#include "AbstractCellCycleModel.hpp"
#include "SimulationTime.hpp"
#include "CellPropertyRegistry.hpp"
#include "CellPropertyCollection.hpp"

class AbstractCellCycleModel; // Circular definition (cells need to know about cycle models and vice-versa).

class Cell;

typedef boost::shared_ptr<Cell> CellPtr;

class Cell : 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 & mUndergoingApoptosis;
        archive & mDeathTime;
        archive & mStartOfApoptosisTime;
        archive & mApoptosisTime;
        archive & mIsDead;
        archive & mIsLogged;
        archive & mAncestor;
        archive & mCellId;
        archive & mMaxCellId;
    }

protected:

    CellPropertyCollection mCellPropertyCollection;

    AbstractCellCycleModel* mpCellCycleModel;

    unsigned mAncestor;

    unsigned mCellId;

    static unsigned mMaxCellId;

    double mDeathTime;

    double mStartOfApoptosisTime;

    double mApoptosisTime;

    bool mUndergoingApoptosis;

    bool mIsDead;

    bool mIsLogged;

public:

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

    ~Cell();

    void SetBirthTime(double birthTime);

    void SetCellCycleModel(AbstractCellCycleModel* pCellCycleModel);

    AbstractCellCycleModel* GetCellCycleModel() const;

    void InitialiseCellCycleModel();

    double GetAge() const;

    double GetBirthTime() const;

    double GetStartOfApoptosisTime() const;

    double GetApoptosisTime() const;

    void SetApoptosisTime(double apoptosisTime);

    boost::shared_ptr<AbstractCellMutationState> GetMutationState() 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(unsigned ancestorIndex);

    unsigned GetAncestor() const;

    unsigned GetCellId() const;

    static void ResetMaxCellId();
};


#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 BOOST_PFTO 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 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;

    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, archiving, cell_property_collection);
}
}
} // namespace ...

#endif /*CELL_HPP_*/