AbstractCardiacCellInterface.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 ABSTRACTCARDIACCELLINTERFACE_HPP_
#define ABSTRACTCARDIACCELLINTERFACE_HPP_

#include <boost/shared_ptr.hpp>

#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"

#include "AbstractIvpOdeSolver.hpp"
#include "AbstractStimulusFunction.hpp"
#include "OdeSolution.hpp"
#include "AbstractLookupTableCollection.hpp"

class AbstractCardiacCellInterface
{
public:
    AbstractCardiacCellInterface(boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
                                 unsigned voltageIndex,
                                 boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    virtual ~AbstractCardiacCellInterface();

    virtual void SetTimestep(double dt)=0;

    virtual void SolveAndUpdateState(double tStart, double tEnd)=0;

    virtual OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)=0;

    virtual void ComputeExceptVoltage(double tStart, double tEnd)=0;

    virtual double GetIIonic(const std::vector<double>* pStateVariables=NULL)=0;

    virtual void SetVoltage(double voltage)=0;

    virtual double GetVoltage()=0;

    unsigned GetVoltageIndex();

    void SetStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus);

    double GetStimulus(double time);

    void SetIntracellularStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus);

    double GetIntracellularStimulus(double time);

    double GetIntracellularAreaStimulus(double time);

    void SetUsedInTissueSimulation(bool tissue=true);

    virtual void UseCellMLDefaultStimulus();

    bool HasCellMLDefaultStimulus();

    virtual AbstractLookupTableCollection* GetLookupTableCollection()
    {
        return NULL;
    }

    boost::shared_ptr<AbstractStimulusFunction> GetStimulusFunction();

    const boost::shared_ptr<AbstractStimulusFunction> GetStimulusFunction() const;

    const boost::shared_ptr<AbstractIvpOdeSolver> GetSolver() const;

    virtual void SetVoltageDerivativeToZero(bool clamp=true);

protected:
    unsigned mVoltageIndex;

    boost::shared_ptr<AbstractIvpOdeSolver> mpOdeSolver;

    boost::shared_ptr<AbstractStimulusFunction> mpIntracellularStimulus;

    bool mSetVoltageDerivativeToZero;

    bool mIsUsedInTissue;

    bool mHasDefaultStimulusFromCellML;

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

CLASS_IS_ABSTRACT(AbstractCardiacCellInterface)


#endif /*ABSTRACTCARDIACCELLINTERFACE_HPP_*/