mesh/SpineEntry.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2013 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 _SPINE_ENTRY_H
#define _SPINE_ENTRY_H

class SpineEntry
{
    public:
        SpineEntry( Id shaft, Id head, unsigned int parent );
        SpineEntry();

        unsigned int parent() const;
        void setParent( unsigned int parent );

        unsigned int fid() const;

        Id shaftId() const; 
        Id headId() const; 

        void matchCubeMeshEntriesToHead( const ChemCompt* compt,
                unsigned int myIndex,
                double granularity, vector< VoxelJunction >& ret ) const;

        void matchCubeMeshEntriesToPSD( const ChemCompt* compt,
                unsigned int myIndex,
                double granularity, vector< VoxelJunction >& ret ) const;

        unsigned int matchNeuroMeshEntriesToShaft( const ChemCompt* compt,
            unsigned int myIndex,
            double& area, double& length ) const;

        double volume() const;

        void mid( double& x, double& y, double& z ) const;

        void apex( double& x, double& y, double& z ) const;

        void matchCubeMeshEntries( const ChemCompt* other, 
            unsigned int myIndex,
            double granularity, vector< VoxelJunction >& ret );

        double rootArea() const;
        double headArea() const;
        double diffusionLength() const;

        void setVolume( double volume );

        void positionShaftBase( double x, double y, double z );

        vector< double > psdCoords() const;

    private:
        CylBase root_; 
        CylBase shaft_; 
        CylBase head_; 

        unsigned int parent_; 

        Id shaftId_; 
        Id headId_; 
};

#endif  // _SPINE_ENTRY_H

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