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gnLocation.h

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// File:            gnLocation.h
// Purpose:         Standard Location for Feature
// Description:     Feature location
// Changes:        
// Version:         libGenome 0.1.0 
// Author:          Aaron Darling 
// Last Edited:     April 15, 2001, 10:34:50pm 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        Proprietary 
#ifndef _gnLocation_h_
#define _gnLocation_h_

#include "gn/gnDefs.h"
#include <string>
#include <iostream>
#include "gn/gnClone.h"


class GNDLLEXPORT gnLocation : public gnClone
{
public:
        enum intersectRestriction{
                determinedRegions,
                undeterminedRegions,
                allRegions
        };
        
        enum gnLocationType{
                LT_Standard,    //standard == join multiple locations.
                LT_BetweenBases,
                LT_Complement,
                LT_Order,
                LT_Group,
                LT_OneOf,
                LT_Nothing
        };

        static const gnSeqI Defined = 0;
        static const gnSeqI Unknown = GNSEQI_END;

public:
        gnLocation();
        gnLocation( const gnLocation& s);
        gnLocation( const gnSeqI start, const gnSeqI end, const gnLocationType type = LT_Standard, string contigName = "");
        gnLocation( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, gnSeqI endLength, const gnLocationType type = LT_Standard, string contigName = "");

        gnLocation* Clone() const;

        void Clear();
        boolean CropTo( const gnLocation &l );
        boolean CropStart( const gnSeqI start );
        boolean CropEnd( const gnSeqI end );

        boolean Intersects( const gnLocation &l, const intersectRestriction ir = allRegions ) const;
        boolean Contains( const gnLocation& l, const intersectRestriction cr = allRegions ) const;
        boolean MovePositive( const gnSeqI diff );
        boolean MoveNegative( const gnSeqI diff );
        boolean MoveTo( const int direction, const gnSeqI diff );

        gnSeqI GetEnd() const;
        gnSeqI GetEndLength() const;
        gnSeqI GetLast() const;
        gnSeqI GetStart() const;
        gnSeqI GetStartLength() const;
        gnSeqI GetFirst() const;

        gnLocationType GetType() const;

        void GetBounds( gnSeqI &s, gnSeqI &sl, gnSeqI &e, gnSeqI &el ) const;

        bool IsEndBoundLonger() const;
        bool IsStartBoundLonger() const;
        bool IsEndBoundShorter() const;
        bool IsStartBoundShorter() const;

        void SetEnd( const gnSeqI end );
        void SetEnd( const gnSeqI end, const gnSeqI endLength );
        void SetEndLength( const gnSeqI endLength );

        void SetStart( const gnSeqI start );
        void SetStart( const gnSeqI start, const gnSeqI startLength );
        void SetStartLength( const gnSeqI startLength );
        void SetType( const gnLocationType lt );
        void SetBounds( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, const gnSeqI endLength);
        void SetBounds( const gnSeqI start, const gnSeqI end);

        gnLocation GetUnion( const gnLocation &l ) const;
        
        gnLocation GetIntersection( const gnLocation &l, const intersectRestriction ir ) const;
        
private:
        string m_name;
        gnSeqI m_start;
        gnSeqI m_startLength;
        gnSeqI m_end;
        gnSeqI m_endLength;
        
        gnLocationType m_type;

}; // class gnLocation

// GET END
inline
gnSeqI gnLocation::GetEnd() const
{
        return m_end;
}
inline
gnSeqI gnLocation::GetEndLength() const
{
        return m_endLength;
}
inline
gnSeqI gnLocation::GetLast() const
{
        return m_end + m_endLength;
}
// GET START
inline
gnSeqI gnLocation::GetStart() const
{
        return m_start;
}
inline
gnSeqI gnLocation::GetStartLength() const
{
        return m_startLength;
}
inline
gnSeqI gnLocation::GetFirst() const
{
        return m_start > m_startLength ? m_start - m_startLength : 0;
}

inline
gnLocation::gnLocationType gnLocation::GetType() const
{
        return m_type;
}

inline
bool gnLocation::IsEndBoundLonger() const
{
        return m_endLength > 0;
}
inline
bool gnLocation::IsStartBoundLonger() const
{
        return m_startLength > 0;
}
inline
bool gnLocation::IsEndBoundShorter() const
{
        return m_endLength < 0;
}
inline
bool gnLocation::IsStartBoundShorter() const
{
        return m_startLength < 0;
}

inline
void gnLocation::SetEnd( const gnSeqI end )
{
        m_end = end;
}
inline
void gnLocation::SetEnd( const gnSeqI end, const gnSeqI endLength )
{
        m_end = end;
        m_endLength = endLength;
}
inline
void gnLocation::SetEndLength( const gnSeqI endLength )
{
        m_endLength = endLength;
}
inline
void gnLocation::SetStart( const gnSeqI start )
{
        m_start = start;
}
inline
void gnLocation::SetStart( const gnSeqI start, const gnSeqI startLength )
{
        m_start = start;
        m_startLength = startLength;
}
inline
void gnLocation::SetStartLength( const gnSeqI startLength )
{
        m_startLength = startLength;
}

inline
void gnLocation::SetType( const gnLocationType lt )
{
        m_type = lt;
}


#endif
        // _gnLocation_h_

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