AbstractCardiacCellInterface.hpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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*/

#ifndef ABSTRACTCARDIACCELLINTERFACE_HPP_
#define ABSTRACTCARDIACCELLINTERFACE_HPP_

#include <boost/shared_ptr.hpp>

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

#include "AbstractIvpOdeSolver.hpp"
#include "RegularStimulus.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 unsigned GetNumberOfStateVariables() const=0;

    virtual unsigned GetNumberOfParameters() const=0;

    virtual std::vector<double> GetStdVecStateVariables()=0;

    virtual const std::vector<std::string>& rGetStateVariableNames() const=0;


    virtual void SetStateVariables(const std::vector<double>& rVariables)=0;

    virtual void SetStateVariable(unsigned index, double newValue)=0;

    virtual void SetStateVariable(const std::string& rName, double newValue)=0;

    virtual double GetAnyVariable(const std::string& rName, double time)=0;

    virtual double GetParameter(const std::string& rParameterName)=0;

    virtual double GetParameter(unsigned parameterIndex)=0;

    virtual void SetParameter(const std::string& rParameterName, double value)=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 boost::shared_ptr<RegularStimulus> 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;

    void SetSolver(boost::shared_ptr<AbstractIvpOdeSolver> pSolver);

    virtual void SetVoltageDerivativeToZero(bool clamp=true);

    void SetFixedVoltage(double voltage);

    virtual void SetStretch(double stretch)
    {
    }

    virtual double GetIntracellularCalciumConcentration();

protected:
    unsigned mVoltageIndex;

    boost::shared_ptr<AbstractIvpOdeSolver> mpOdeSolver;

    boost::shared_ptr<AbstractStimulusFunction> mpIntracellularStimulus;

    bool mSetVoltageDerivativeToZero;

    bool mIsUsedInTissue;

    bool mHasDefaultStimulusFromCellML;

    double mFixedVoltage;

private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // For version 0 these were archived by AbstractCardiacCell, now
        // we have AbstractCvodeCells too, so doing it here.
        if (version > 0)
        {
            archive & mSetVoltageDerivativeToZero;
            archive & mIsUsedInTissue;
            archive & mHasDefaultStimulusFromCellML;
            // archive & mFixedVoltage; - this doesn't need archiving as it is reset every PDE time step if used.
        }
        // archive & mVoltageIndex; - always set by constructor - called by concrete class
        // archive & mpOdeSolver; - always set by constructor - called by concrete class
        // archive & mpIntracellularStimulus; - always set by constructor - called by concrete class
    }
};

CLASS_IS_ABSTRACT(AbstractCardiacCellInterface)
BOOST_CLASS_VERSION(AbstractCardiacCellInterface, 1)

#endif /*ABSTRACTCARDIACCELLINTERFACE_HPP_*/