biophysics/MarkovRateTable.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2011 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 _MARKOVRATETABLE_H
#define _MARKOVRATETABLE_H

//Class : MarkovRateTable
//Author : Vishaka Datta S, 2011, NCBS
//
//Presents a unified interface to deal with transition rates that are dependent
//on one or two parameters, or are constant.
//Ther Interpol2D class is used for carrying out 2-D rate lookups. The one 
//parameter lookup functions are based on the lookup tables used in the HHGate
//class.
//
//The class consists of a table of pointers to the VectorTable class and the
//Interpol2D class. Since these classes are user-defined and possess
//constructors, destructors, etc., using a union is not possible (but would've
//been more efficient).
//
//For a given rate entry (i,j) either one of these pointers may be set, but not 
//both. If both pointers are null, the rate is assumed to be zero i.e. there
//is no transition from state i to state j. 
//
//In case a rate is constant, it is stored in a VectorTable class whose lookup 
//table is of size 1. 
//

template <class T> 
vector< vector< T > > resize( vector< vector< T > >table, unsigned int n, T init )
{
    table.resize( n );  

    for ( unsigned int i = 0; i < n; ++i ) 
        table[i].resize( n, init );     

    return table;
}

class MarkovRateTable {
    public :    
    MarkovRateTable(); 

    ~MarkovRateTable();

    //One parameter rate table set and get functions.
    VectorTable* getVtChildTable( unsigned int, unsigned int ) const; 
    void innerSetVtChildTable( unsigned int, unsigned int, VectorTable, unsigned int );
    //Two parameter rate table set and get functions.
    Interpol2D* getInt2dChildTable( unsigned int, unsigned int ) const;
    void innerSetInt2dChildTable( unsigned int, unsigned int, Interpol2D );
    
    //Lookup functions.
    double lookup1dValue( unsigned int, unsigned int, double );
    double lookup1dIndex( unsigned int, unsigned int, unsigned int );
    double lookup2dValue( unsigned int, unsigned int, double, double );
    double lookup2dIndex( unsigned int, unsigned int, unsigned int, unsigned int );

    //Rate update and initialization functions.
    void updateRates(); 
    void initConstantRates();

    vector< unsigned int > getListOf1dRates();
    vector< unsigned int > getListOf2dRates();
    vector< unsigned int > getListOfLigandRates();
    vector< unsigned int > getListOfVoltageRates();
    vector< unsigned int > getListOfConstantRates();

    //Overloading the >> operator. This is done so that VectorTable and 
    //Interpol2D classes can be used to declare OpFuncs.
    friend istream& operator>>( istream&, MarkovRateTable& );   

    //*ValueFinfo related functions.
    vector< vector< double > > getQ() const;    
    unsigned int getSize() const;

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

    //Helper functions
    
    //Returns true if the (i,j)'th rate is zero i.e. no transitions between states
    //i and j. When this is the case, both the  (i,j)'th pointers in vtTables_
    // and int2dTables_ are not set i.e. both are zero.
    bool isRateZero( unsigned int, unsigned int ) const ;

    //Returns true if the (i,j)'th rate is a constant. This is true when the
    //vtTables_[i][j] pointer points to a 1D lookup table of size 1.
    bool isRateConstant( unsigned int, unsigned int ) const ;

    //Returns true if the (i,j)'th rate is varies with only one parameter. 
    bool isRate1d( unsigned int, unsigned int ) const ;  

    //Returns true if the (i,j)'th rate is dependent on ligand concentration and
    //not membrane voltage, and is set with a 1D lookup table. 
    bool isRateLigandDep( unsigned int, unsigned int) const;

    //Returns true if the (i,j)'th rate varies with two parameters.
    bool isRate2d( unsigned int, unsigned int ) const ;

    //Returns true if a table is being accessed at an invalid address.
    bool areIndicesOutOfBounds( unsigned int, unsigned int ) const ;

    //These functions return general information about the whole rate table
    //itself. Useful for the MarkovSolver class.

    //Returns true if all the rates in the transition matrix are constant.
    bool areAllRatesConstant(); 

    //Returns true if at least one of the rates are 1D i.e. vary with only 
    //one parameter.
    bool areAnyRates1d();
    bool areAllRates1d();

    //Returns true if at least one of the rates are 2D i.e. vary with two
    //parameters.
    bool areAnyRates2d();
    bool areAllRates2d();

    //Returns true if at least one of the rates are ligand dependent.
    bool areAnyRatesLigandDep();
    bool areAllRatesLigandDep();

    //Returns true if at least one of the rates are voltage dependent.
    bool areAnyRatesVoltageDep();
    bool areAllRatesVoltageDep();

    static const Cinfo* initCinfo();

    //MsgDest functions.
    void process( const Eref&, ProcPtr );   
    void reinit( const Eref&, ProcPtr );    

    //Initialization of object.
    void init( unsigned int );

    //Handling incoming messages containing voltage and concentration information.
    void handleVm( double );    
    void handleLigandConc( double );

    //Setting rate tables for 1-D and 2-D rate transitions.
    void setVtChildTable( unsigned int, unsigned int, Id, unsigned int );
    void setInt2dChildTable( unsigned int, unsigned int, Id );

    //Setting a constant rate. 
    void setConstantRate( unsigned int, unsigned int, double ); 

    private : 
    //Family of 1D lookup table pointers. Each entry is a pointer to a 1-D 
    //lookup table (VectorTable type) that contains the values of the rates of 
    //transition at a given voltage or ligand concentration.
    vector< vector< VectorTable* > > vtTables_;  
    
    //Family of 2D lookup table pointers. Each entry is a pointer to a 2-D
    //lookup table of type Interpol2D. These lookup tables deal with rates that
    //vary with voltage and ligand concentration. 
    vector< vector< Interpol2D* > > int2dTables_; 
    
    //In the case of 1-D lookup tables, this matrix determines which rates are
    //ligand dependent. When the (i,j)'th value is "true", the ligand
    //concentration is used instead of voltage for rate lookups. 
    vector< vector< unsigned int > > useLigandConc_; 

    //Maintains a list of the indices of 1D,2D,constant rates, voltage and
    //ligand dependent rates. Makes updating rates a whole lot easier and 
    //more elegant than blindly scanning through the entire rate matrix 
    //each time.
    vector< unsigned int > listOf1dRates_;
    vector< unsigned int > listOf2dRates_;
    vector< unsigned int > listOfConstantRates_;
    vector< unsigned int > listOfLigandRates_;
    vector< unsigned int > listOfVoltageRates_;
    
    //The instantaneous rate matrix. 
    vector< vector< double > > Q_;

    //Membrane voltage and ligand concentration. Needed for rate lookups. 
    //Admittedly, this is a bit of a deviation from the usual scheme where
    //channels are the only destinations for Vm and conc. 
    double Vm_;
    double ligandConc_;

    //Time step of simulation. The rates are specified in sec^(-1). All the rates 
    //have to be proportionally scaled for an arbitrary time step.
    //Is not a MOOSE field, and does not need an explicit setup call either.  
    //It is set during the call to reinit. 

    unsigned int size_;

    //Check to see if the table has been initialized.
    bool isInitialized() const;
};
#endif

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