Alarcon2004OxygenBasedCellCycleOdeSystem.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
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This file is part of Chaste.

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 * 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
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   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
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*/

#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_*/