VanLeeuwen2009WntSwatCellCycleOdeSystem.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 VANLEEUWEN2009WNTSWATCELLCYCLEODESYSTEM_HPP_
#define VANLEEUWEN2009WNTSWATCELLCYCLEODESYSTEM_HPP_

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

#include <cmath>
#include <iostream>

#include "AbstractOdeSystem.hpp"
#include "AbstractCellMutationState.hpp"
#include "UblasCustomFunctions.hpp"

// Needed here to avoid serialization errors
#include "ApcOneHitCellMutationState.hpp"
#include "ApcTwoHitCellMutationState.hpp"
#include "BetaCateninOneHitCellMutationState.hpp"

class VanLeeuwen2009WntSwatCellCycleOdeSystem : public AbstractOdeSystem
{
private:

    double mk2d;
    double mk3d;
    double mk34d;
    double mk43d;
    double mk23d;
    double mad;
    double mJ11d;
    double mJ12d;
    double mJ13d;
    double mJ61d;
    double mJ62d;
    double mJ63d;
    double mKm1d;
    double mkpd;
    double mphi_r;
    double mphi_i;
    double mphi_j;
    double mphi_p;
    double mk16d;
    double mk61d;
    double mPhiE2F1;

    double mSa;
    double mSca;
    double mSc;
    double mSct;
    double mSd;
    double mSt;
    double mSx;
    double mSy;
    double mDa;
    double mDca;
    double mDc;
    double mDct;
    double mDd;
    double mDdx;
    double mDt;
    double mDu;
    double mDx;
    double mDy;
    double mKc;
    double mKd;
    double mKt;
    double mPc;
    double mPu;
    double mXiD;
    double mXiDx;
    double mXiX;
    double mXiC;

    boost::shared_ptr<AbstractCellMutationState> mpMutationState;

    unsigned mHypothesis;

    double mWntLevel;

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

public:

    VanLeeuwen2009WntSwatCellCycleOdeSystem(unsigned hypothesis,
                                            double wntLevel = 0.0,
                                            boost::shared_ptr<AbstractCellMutationState> pMutationState=boost::shared_ptr<AbstractCellMutationState>(),
                                            std::vector<double> stateVariables=std::vector<double>());

    ~VanLeeuwen2009WntSwatCellCycleOdeSystem();

    void Init();

    void SetMutationState(boost::shared_ptr<AbstractCellMutationState> pMutationState);

    const boost::shared_ptr<AbstractCellMutationState> GetMutationState() const;

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

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

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

    double GetWntLevel() const;

    unsigned GetHypothesis() const;
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(VanLeeuwen2009WntSwatCellCycleOdeSystem)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const VanLeeuwen2009WntSwatCellCycleOdeSystem * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const unsigned hypothesis = t->GetHypothesis();
    ar & hypothesis;

    const double wnt_level = t->GetWntLevel();
    ar & wnt_level;

    const boost::shared_ptr<AbstractCellMutationState> p_mutation_state = t->GetMutationState();
    ar & p_mutation_state;

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

template<class Archive>
inline void load_construct_data(
    Archive & ar, VanLeeuwen2009WntSwatCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    unsigned hypothesis;
    ar & hypothesis;

    double wnt_level;
    ar & wnt_level;

    boost::shared_ptr<AbstractCellMutationState> p_mutation_state;
    ar & p_mutation_state;

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

    // Invoke inplace constructor to initialise instance
    ::new(t)VanLeeuwen2009WntSwatCellCycleOdeSystem(hypothesis, wnt_level, p_mutation_state, state_variables);
}
}
} // namespace ...

#endif /*VANLEEUWEN2009WNTSWATCELLCYCLEODESYSTEM_HPP_*/

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