biophysics/ReadCell.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-20011 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 READCELL_H
#define READCELL_H
enum ParseStage { COMMENT, DATA, SCRIPT };

class ReadCell
{
    public:
        // ReadCell( const vector< double >& globalParms );
        ReadCell();
        
        Id read(
            const string& filename, 
            const string& cellname,
            Id parent );
    
        static void addChannelMessage( Id chan );
    private:
        bool innerRead( ifstream& fin );
        bool readData( const string& line );
        bool readScript( const string& line );
        Id buildCompartment( 
            const string& name,
            const string& parent,
            double x0, double y0, double z0,
            double x, double y, double z,
            double d,
            double& length, // Length is sent back.
            vector< string >& argv );
        bool buildChannels(
            Id compt,
            vector< string >& argv,
            double diameter,
            double length);
        Id startGraftCell( const string& cellPath );
        Id findChannel( const string& name );
        Id addChannel(
            Id compt,
            Id chan, 
            double value,
            double dia,
            double length );
        bool addCanonicalChannel(
            Id compt,
            Id chan, 
            double value,
            double dia,
            double length );
        bool addSpikeGen(
            Id compt,
            Id chan, 
            double value,
            double dia,
            double length );
        bool addCaConc(
            Id compt,
            Id chan, 
            double value,
            double dia,
            double length );
        bool addNernst(
            Id compt,
            Id chan,
            double value );
/*
        void addKinModel(
            Id compt,
            double value,
            string name,
            string method );
        void addM2C(
            Id compt,
            double value, 
            vector< string >::iterator args );
        void addC2M(
            Id compt,
            double value, 
            vector< string >::iterator args );
*/
        
        void countProtos();
        
        // For error messages
        string fileName_;
        unsigned int lineNum_;
        
        double RM_;
        double CM_;
        double RA_;
        double EREST_ACT_;
        double ELEAK_;
        double dendrDiam;
        double aveLength;
        double spineSurf;
        double spineDens;
        double spineFreq;
        double membFactor;
        bool erestFlag_;
        bool eleakFlag_;
        
        Id cell_;
        Id currCell_;
        Id lastCompt_;
        Id protoCompt_;
        
        unsigned int numCompartments_;
        unsigned int numChannels_;
        unsigned int numOthers_;
        
        unsigned int numProtoCompts_;
        unsigned int numProtoChans_;
        unsigned int numProtoOthers_;
        
        bool graftFlag_;
        bool polarFlag_;
        bool relativeCoordsFlag_;
        bool doubleEndpointFlag_;
        bool symmetricFlag_;
        
        map< string, Id > chanProtos_;
        
        Shell* shell_;
};
#endif

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