biophysics/CompartmentBase.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment,
** also known as GENESIS 3 base code.
**           copyright (C) 2003-2006 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/

#ifndef _COMPARTMENT_BASE_H
#define _COMPARTMENT_BASE_H

#ifdef  CYMOOSE

template<typename A>
class SrcFinfo1;


#endif     /* -----  CYMOOSE  ----- */

namespace moose
{
class CompartmentBase
{
    public:
            CompartmentBase();
            virtual ~CompartmentBase();

            // Value Field access function definitions.
            void setVm( const Eref& e, double Vm );
            double getVm( const Eref& e ) const;
            void setEm( const Eref& e, double Em );
            double getEm( const Eref& e ) const;
            void setCm( const Eref& e, double Cm );
            double getCm( const Eref& e ) const;
            void setRm( const Eref& e, double Rm );
            double getRm( const Eref& e ) const;
            void setRa( const Eref& e, double Ra );
            double getRa( const Eref& e ) const;
            double getIm( const Eref& e ) const;
            void setInject( const Eref& e, double Inject );
            double getInject( const Eref& e ) const;
            void setInitVm( const Eref& e, double initVm );
            double getInitVm( const Eref& e ) const;
            void setDiameter( double diameter );
            double getDiameter() const;
            void setLength( double length );
            double getLength() const;
            void setX0( double value );
            double getX0() const;
            void setY0( double value );
            double getY0() const;
            void setZ0( double value );
            double getZ0() const;
            void setX( double value );
            double getX() const;
            void setY( double value );
            double getY() const;
            void setZ( double value );
            double getZ() const;

            // Dest function definitions.
            void process( const Eref& e, ProcPtr p );

            void reinit( const Eref& e, ProcPtr p );

            void initProc( const Eref& e, ProcPtr p );

            void initReinit( const Eref& e, ProcPtr p );

            void handleChannel( const Eref& e, double Gk, double Ek);

            void handleRaxial( double Ra, double Vm);

            void handleAxial( double Vm);

            void injectMsg( const Eref& e, double current);

            void randInject( const Eref& e, double prob, double current);

            void cable();

            void displace( double dx, double dy, double dz );

            void setGeomAndElec( const Eref& e, 
                            double length, double dia );
            // Here we define the virtual functions for each of the above
            // wrappers.
            // Value Field access function definitions.
            virtual void vSetVm( const Eref& e, double Vm ) = 0;
            virtual double vGetVm( const Eref& e ) const = 0;
            virtual void vSetEm( const Eref& e, double Em ) = 0;
            virtual double vGetEm( const Eref& e ) const = 0;
            virtual void vSetCm( const Eref& e, double Cm ) = 0;
            virtual double vGetCm( const Eref& e ) const = 0;
            virtual void vSetRm( const Eref& e, double Rm ) = 0;
            virtual double vGetRm( const Eref& e ) const = 0;
            virtual void vSetRa( const Eref& e, double Ra ) = 0;
            virtual double vGetRa( const Eref& e ) const = 0;
            virtual double vGetIm( const Eref& e ) const = 0;
            virtual void vSetInject( const Eref& e, double Inject ) = 0;
            virtual double vGetInject( const Eref& e ) const = 0;
            virtual void vSetInitVm( const Eref& e, double initVm ) = 0;
            virtual double vGetInitVm( const Eref& e ) const = 0;

            // Dest function definitions.
            virtual void vProcess( const Eref& e, ProcPtr p ) = 0;

            virtual void vReinit( const Eref& e, ProcPtr p ) = 0;

            virtual void vInitProc( const Eref& e, ProcPtr p ) = 0;

            virtual void vInitReinit( const Eref& e, ProcPtr p ) = 0;

            virtual void vHandleChannel( const Eref& e, double Gk, double Ek) = 0;

            virtual void vHandleRaxial( double Ra, double Vm) = 0;

            virtual void vHandleAxial( double Vm) = 0;

            virtual void vInjectMsg( const Eref& e, double current) = 0;

            virtual void vRandInject( const Eref& e, double prob, double current) = 0;

            // Required for solver setup
            
            virtual void vSetSolver( const Eref& e, Id hsolve );
            

            bool rangeWarning( const string& field, double value );

            void updateLength();

            static const Cinfo* initCinfo();

            static SrcFinfo1< double >* VmOut();

            static void zombify( Element* orig, const Cinfo* zClass,
                        Id hsolve );
    private:
            double diameter_;
            double length_;
            double x0_;
            double y0_;
            double z0_;
            double x_;
            double y_;
            double z_;
};
}

// Used by solver, readcell, etc.

#endif // _COMPARTMENT_BASE_H

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