Alarcon2004OxygenBasedCellCycleOdeSystem.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 _ALARCON2004OXYGENBASEDCELLCYCLEODESYSTEM_HPP_
#define _ALARCON2004OXYGENBASEDCELLCYCLEODESYSTEM_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include <cmath>

#include "AbstractOdeSystem.hpp"

class Alarcon2004OxygenBasedCellCycleOdeSystem : public AbstractOdeSystem
{
private:

    double ma1;
    double ma2;
    double ma3;
    double ma4;
    double mb3;
    double mb4;
    double mc1;
    double mc2;
    double md1;
    double md2;
    double mJ3;
    double mJ4;
    double mEta;
    double mMstar;
    double mB;
    double mxThreshold;
    double myThreshold;

    double mOxygenConcentration;

    bool mIsLabelled;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOdeSystem>(*this);
    }

public:

    Alarcon2004OxygenBasedCellCycleOdeSystem(double oxygenConcentration,
                                             bool isLabelled,
                                             std::vector<double> stateVariables=std::vector<double>());

    ~Alarcon2004OxygenBasedCellCycleOdeSystem();

    void Init();

    void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY);

    bool CalculateStoppingEvent(double time, const std::vector<double>& rY);

    void SetIsLabelled(bool isLabelled);

    bool IsLabelled() const;

    double GetOxygenConcentration() const;
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(Alarcon2004OxygenBasedCellCycleOdeSystem)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const Alarcon2004OxygenBasedCellCycleOdeSystem * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const double oxygen_concentration = t->GetOxygenConcentration();
    ar & oxygen_concentration;

    const bool is_labelled = t->IsLabelled();
    ar & is_labelled;

    const std::vector<double> state_variables = t->rGetConstStateVariables();
    ar & state_variables;
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, Alarcon2004OxygenBasedCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    double oxygen_concentration;
    ar & oxygen_concentration;

    bool is_labelled;
    ar & is_labelled;

    std::vector<double> state_variables;
    ar & state_variables;

    // Invoke inplace constructor to initialise instance
    ::new(t)Alarcon2004OxygenBasedCellCycleOdeSystem(oxygen_concentration, is_labelled, state_variables);
}
}
} // namespace ...

#endif /*_ALARCON2004OXYGENBASEDCELLCYCLEODESYSTEM_HPP_*/