kinetics/ReadKkit.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2010 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 _READ_KKIT_H
#define _READ_KKIT_H

class ReadKkit
{
    public: 
        enum ParseMode {
            DATA,
            INIT,
            COMMENT,
            LINE_CONTINUE
        };

        ReadKkit();

        // Field assignment stuff
        double getMaxTime() const;
        double getPlotDt() const;
        double getDefaultVol() const;
        string getBasePath() const;
        unsigned int getVersion() const;
        bool getMoveOntoCompartment() const;
        void setMoveOntoCompartment( bool v );

        // Undump operations
        
        void innerRead( ifstream& fin );
        ParseMode readInit( const string& line );
        Id read( const string& filename, const string& cellname, 
            Id parent, const string& solverClass = "Stoich" );
        void readData( const string& line );
        void undump( const vector< string >& args );

        // void setupGslRun();

        void run();
        void dumpPlots( const string& filename );

        // Building up the model
        Id buildCompartment( const vector< string >& args );
        Id buildPool( const vector< string >& args );
        Id buildReac( const vector< string >& args );
        Id buildEnz( const vector< string >& args );
        Id buildPlot( const vector< string >& args );
        Id buildTable( const vector< string >& args );
        unsigned int loadTab(  const vector< string >& args );
        Id buildGroup( const vector< string >& args );
        Id buildText( const vector< string >& args );
        Id buildGraph( const vector< string >& args );
        Id buildGeometry( const vector< string >& args );
        Id buildStim( const vector< string >& args );
        Id buildChan( const vector< string >& args );
        Id buildInfo( Id parent, map< string, int >& m, 
            const vector< string >& args );
        void buildSumTotal( const string& src, const string& dest );
        Id findSumTotSrc( const string& src );

        // Special ops in the model definition
        void addmsg( const vector< string >& args );
        void setupSlaveMsg( const string& src, const string& dest );
        void innerAddMsg( 
            const string& src, const map< string, Id >& m1, 
                const string& srcMsg,
            const string& dest, const map< string, Id >& m2, 
                const string& destMsg,
            bool isBackward = 0 );
        void call( const vector< string >& args );
        void objdump( const vector< string >& args );
        void textload( const vector< string >& args );
        void separateVols( Id pool, double vol );
        void assignPoolCompartments();

        void assignReacCompartments();
        void assignEnzCompartments();
        void assignMMenzCompartments();

        void convertParametersToConcUnits();

        void convertPoolAmountToConcUnits();

        void convertReacRatesToConcUnits();

        void convertMMenzRatesToConcUnits();

        void convertEnzRatesToConcUnits();

        // Utility functions
        
        string pathTail( const string& path, string& head ) const;

        string cleanPath( const string& path ) const;

    private:
        string basePath_; 
        Id baseId_; 

        double fastdt_; 
        double simdt_;  
        double controldt_;  
        double plotdt_;     
        double maxtime_;    
        double transientTime_;  
        bool useVariableDt_;    
        double defaultVol_;     
        unsigned int version_;  
        unsigned int initdumpVersion_;  

        bool moveOntoCompartment_;  

        unsigned int numCompartments_;
        unsigned int numPools_;
        unsigned int numReacs_;
        unsigned int numEnz_;
        unsigned int numMMenz_;
        unsigned int numPlot_;
        unsigned int numStim_;
        unsigned int numOthers_;

        unsigned int lineNum_;

        map< string, int > poolMap_;
        map< string, int > reacMap_;
        map< string, int > enzMap_;
        map< string, int > groupMap_;
        map< string, int > tableMap_;
        map< string, int > stimMap_;
        map< string, Id > poolIds_;
        map< string, Id > reacIds_;
        map< string, Id > enzIds_;
        map< string, Id > mmEnzIds_;
        map< string, Id > plotIds_;
        map< string, Id > tabIds_;
        map< string, Id > stimIds_;
        map< string, Id > chanIds_;

        /*
        vector< Id > pools_;
        vector< double > poolVols_;
        */

        vector< double > vols_;

        Id lastTab_;
        vector< double > tabEntries_;

        vector< vector< Id > > volCategories_;
        vector< Id > compartments_;
        vector< pair< Id, Id > > enzCplxMols_;

        map< Id, int > poolFlags_;

        map< Id, double > poolVols_; // Need for enz complexes.

        Shell* shell_;

        static const double EPSILON;
};

#endif // READ_KKIT_H

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