SingleOdeWntCellCycleModel.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 SINGLEODEWNTCELLCYCLEMODEL_HPP_
#define SINGLEODEWNTCELLCYCLEMODEL_HPP_

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

#include <cfloat>

#include "SimpleWntCellCycleModel.hpp"
#include "Mirams2010WntOdeSystem.hpp"
#include "RungeKutta4IvpOdeSolver.hpp"
#include "CvodeAdaptor.hpp"

class SingleOdeWntCellCycleModel : public SimpleWntCellCycleModel
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        assert(mpOdeSystem);
        archive & boost::serialization::base_object<SimpleWntCellCycleModel>(*this);
        boost::shared_ptr<AbstractCellMutationState> p_mutation_state = static_cast<Mirams2010WntOdeSystem*>(mpOdeSystem)->GetMutationState();
        archive & p_mutation_state;
        archive & mBetaCateninDivisionThreshold;
        archive & mLastTime;
        archive & mpOdeSystem->rGetStateVariables();
    }
    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        /*
         * The ODE system is set up by the archiving constructor, so we can set the mutation state
         * here. This is a horrible hack, but avoids having to regenerate test archives.
         */
        assert(mpOdeSystem);
        archive & boost::serialization::base_object<SimpleWntCellCycleModel>(*this);
        boost::shared_ptr<AbstractCellMutationState> p_mutation_state;
        archive & p_mutation_state;
        static_cast<Mirams2010WntOdeSystem*>(mpOdeSystem)->SetMutationState(p_mutation_state);

        archive & mBetaCateninDivisionThreshold;
        archive & mLastTime;
        archive & mpOdeSystem->rGetStateVariables();
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

    
    Mirams2010WntOdeSystem* mpOdeSystem;

    double mBetaCateninDivisionThreshold;

    void ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel();

    void UpdateBetaCateninLevel();

#ifdef CHASTE_CVODE

    static CvodeAdaptor msSolver;
#else

    static RungeKutta4IvpOdeSolver msSolver;
#endif //CHASTE_CVODE

    double mLastTime;

public:

    SingleOdeWntCellCycleModel()
      :   mpOdeSystem(NULL),
          mLastTime(DBL_MAX) // Ensure this is set properly before we try to use it.
    {
#ifdef CHASTE_CVODE
        msSolver.SetMaxSteps(10000);
#endif // CHASTE_CVODE
    };

    SingleOdeWntCellCycleModel(std::vector<double>& rProteinConcs,
                               boost::shared_ptr<AbstractCellMutationState> pMutationState,
                               unsigned& rDimension,
                               bool useTypeDependentG1 = false);

    ~SingleOdeWntCellCycleModel();

    SingleOdeWntCellCycleModel(const SingleOdeWntCellCycleModel& rOtherModel);

    void Initialise();

     void UpdateCellCyclePhase();

    AbstractCellCycleModel* CreateCellCycleModel();

    double GetBetaCateninConcentration();

    void SetBetaCateninDivisionThreshold(double betaCateninDivisionThreshold);

    double GetBetaCateninDivisionThreshold();
};

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

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const SingleOdeWntCellCycleModel * t, const unsigned int file_version)
{
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, SingleOdeWntCellCycleModel * t, const unsigned int file_version)
{
    std::vector<double> state_vars;
    for (unsigned i=0; i<3; i++)
    {
        state_vars.push_back(0.0);
    }

    boost::shared_ptr<AbstractCellMutationState> p_mutation_state;
    unsigned dimension = 1;
    ::new(t)SingleOdeWntCellCycleModel(state_vars, p_mutation_state, dimension);
}
}
} // namespace

#endif /*SINGLEODEWNTCELLCYCLEMODEL_HPP_*/