biophysics/MarkovChannel.h

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#ifndef _MARKOVCHANNEL_H
#define _MARKOVCHANNEL_H

//This class deals with ion channels which can be found in one of multiple 
//states, some of which are conducting. This implementation assumes the 
//occurence of first order kinetics to calculate the probabilities of the
//channel of being found in all states. Further, the rates of transition 
//between these states can be constant, voltage-dependent, ligand dependent 
//(only one ligand species) or both. The current flow obtained from the channel
//is calculated in a deterministic method by solving the system of
//differential equations obtained from the assumptions above.
//The implicit assumption is that there are a number of ion channels present in
//the system. */

class MarkovChannel : public ChanCommon
{
    public:
    //Default constructor. Use is not recommended as most of the class members
    //cannot be initialized. 
    MarkovChannel();

    //Constructor to be used when number of states and number of open states are
    //known. Use of this constructor is recommended as all the other members of
    //the class can be initialized with the information provided. 
    static const Cinfo* initCinfo();

    MarkovChannel( unsigned int, unsigned int);
    ~MarkovChannel( );

    double getVm( ) const;  
    void setVm( double );
    
    double getLigandConc( ) const;
    void setLigandConc( double );

    unsigned int getNumStates( ) const;
    void setNumStates( unsigned int );

    unsigned int getNumOpenStates( ) const;
    void setNumOpenStates( unsigned int );

    vector< string > getStateLabels( ) const;
    void setStateLabels( vector< string > );

    //If the (i,j)'th is true, ligand concentration will be used instead of
    //voltage.
    vector< vector< bool > > getLigandGated( ) const;
    void setLigandGated ( vector< vector< bool > > );

    //Probabilities of the channel occupying all possible states.
    vector< double > getState ( ) const;
    void setState(  vector< double >  );

    //The initial state of the channel. State of the channel is reset to this
    //vector during a call to reinit().
    vector< double > getInitialState() const;
    void setInitialState( vector< double > );

    //Conductances associated with each open/conducting state.
    vector< double > getGbars( ) const;
    void setGbars( vector< double > );

    //MsgDest functions
    
    void vProcess( const Eref&, const ProcPtr);
    void vReinit( const Eref&, const ProcPtr);
    void handleLigandConc( double );
    void handleState( vector< double > );

    private:
    double g_;                                              //Expected conductance of the channel.  
    double ligandConc_;                             //Ligand concentration.
    unsigned int numStates_;                    //Total number of states.
    unsigned int numOpenStates_;            //Number of open (conducting) states.

    vector< string > stateLabels_;
    vector< double > state_;                    //Probabilities of occupancy of each state.
    vector< double > initialState_;
    vector< double > Gbars_;        //Conductance associated with each open state.
};

#endif

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