biophysics/SwcSegment.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2015 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 SWC_SEGMENT_H
#define SWC_SEGMENT_H

class SwcSegment
{
    public:
        SwcSegment()
                : myIndex_( 0 ), type_( 0 ), radius_( 0.0 ),
                length_( 0.0 ), L_( 0.0 ),
                parent_( ~0U ), 
                geometricalDistanceFromSoma_( 0.0 ),
                electrotonicDistanceFromSoma_( 0.0 )
        {;}

        SwcSegment( const string& line );

        SwcSegment( int i,  short type, 
                        double x, double y, double z, 
                        double r, int parent );
        bool OK() const
        {
            return type_!=BadSegment && type_!=UNDEF && type_!=CUSTOM;
        }

        void setBad() {
            type_ = BadSegment;
        }


        unsigned int parent() const {
            return parent_;
        }

        void setParent( unsigned int pa ) {
            parent_ = pa;
        }

        unsigned int myIndex() const {
            return myIndex_;
        }

        void addChild( unsigned int kid ) {
            kids_.push_back( kid );
        }

        void figureOutType();

        const vector< int >& kids() const
        {
            return kids_;
        }

        void replaceKids( const vector< int >& kids )
        {
            kids_ = kids;
        }

        unsigned short type() const {
            return type_;
        }

        double radius() const {
            return radius_;
        }
        double length() const {
            return length_;
        }

        double L() const {
            return L_;
        }

        double distance( const SwcSegment& other ) const  {
            return v_.distance( other.v_ );
        }

        const Vec& vec() const {
            return v_;
        }

        void setGeometricalDistanceFromSoma( const SwcSegment& soma )
        {
            geometricalDistanceFromSoma_ = v_.distance( soma.v_ );
        }

        void setCumulativeDistance( double len, double L,
                        double pSoma, double eSoma )
        {
            length_ = len;
            L_ = L;
            pathDistanceFromSoma_ = pSoma;
            electrotonicDistanceFromSoma_ = eSoma;
        }

        double getPathDistFromSoma() const  {
            return pathDistanceFromSoma_;
        }
        
        double getGeomDistFromSoma() const  {
            return geometricalDistanceFromSoma_;
        }
        
        double getElecDistFromSoma() const  {
            return electrotonicDistanceFromSoma_;
        }

        // This is the original SWC set.
        static const short UNDEF;
        static const short SOMA;
        static const short AXON;
        static const short DEND;
        static const short APICAL;
        static const short FORK; // Assumed to be on regular dend
        static const short END; // Assumed to be on regular dend
        static const short CUSTOM;
        // Here are a few more
        static const short BadSegment;
        static const short AXON_FORK;
        static const short AXON_END;
        static const short APICAL_FORK;
        static const short APICAL_END;

        static const string typeName[];

    protected:
        unsigned int myIndex_; 

        short type_; 
        Vec v_; 
        double radius_; 
        double length_; 
        double L_;      
        unsigned int parent_; 

        double pathDistanceFromSoma_; 

        double geometricalDistanceFromSoma_; 

        double electrotonicDistanceFromSoma_; 

        vector< int > kids_; // Indices of all children of segment.
};

class SwcBranch: public SwcSegment
{
    public:
        SwcBranch( int i,  const SwcSegment& start, double len, double L,
                const vector< int >& cable );

        void printDiagnostics() const;

        double r0; 
        double r1; 

        double geomLength;

        double pathLength;


        double electroLength;

        vector< int > segs_; 
};

#endif // SWC_SEGMENT_H

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