WntCellCycleOdeSystem.hpp

/*

Copyright (c) 2005-2015, 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 WNTCELLCYCLEODESYSTEM_HPP_
#define WNTCELLCYCLEODESYSTEM_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"

class WntCellCycleOdeSystem : 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 ma2d;
    double ma3d;
    double ma4d;
    double ma5d;
    double mk16d;
    double mk61d;
    double mPhiE2F1;

    boost::shared_ptr<AbstractCellMutationState> mpMutationState;

    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:

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

    ~WntCellCycleOdeSystem();

    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;
};

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

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const WntCellCycleOdeSystem * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    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, WntCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    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)WntCellCycleOdeSystem(wnt_level, p_mutation_state, state_variables);
}
}
} // namespace ...

#endif /*WNTCELLCYCLEODESYSTEM_HPP_*/