CylBase.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2012 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 _CYL_BASE_H
#define _CYL_BASE_H

class CylBase
{
    public:
        CylBase( double x, double y, double z,
                        double dia, double length, unsigned int numDivs );
        CylBase();

        void setX( double v );
        double getX() const;
        void setY( double v );
        double getY() const;
        void setZ( double v );
        double getZ() const;
        void setDia( double v );
        double getDia() const;
        void setLength( double v );
        double getLength() const;
        void setNumDivs( unsigned int v );
        unsigned int getNumDivs() const;
        void setIsCylinder( bool v );
        bool getIsCylinder() const;

        double volume( const CylBase& parent ) const;

        double voxelVolume( const CylBase& parent, unsigned int fid ) const;

        vector< double > getCoordinates( const CylBase& parent,
                        unsigned int entry ) const;

        double getDiffusionArea(
            const CylBase& parent, unsigned int index ) const;

        double getMiddleArea(
            const CylBase& parent, unsigned int index ) const;

        double getVoxelLength() const;

        // Selects a grid size for generating intersection with CubeMesh.
        double selectGridSize( double h, double dia1, double granularity )
                const;

        void matchCubeMeshEntries( const ChemCompt* other,
            const CylBase& parent,
            unsigned int startIndex,
            double granularity,
            vector< VoxelJunction >& ret,
           bool useCylinderCurve, bool useCylinderCap ) const;

        double nearest( double x, double y, double z,
                const CylBase& parent,
                double& linePos, double& r ) const;

        double nearest( double x, double y, double z,
                const CylBase& parent,
                unsigned int& index ) const;

    private:
        double x_;
        double y_;
        double z_;

        double dia_; 
        double length_; 
        unsigned int numDivs_;  
        bool isCylinder_;   
};

#endif  // _CYL_BASE_H