bpp::SeqRange Class Reference

a coordinate range on a sequence. Stores coordinates as a Range<size_t> object, but also keep the strand information. More...

#include <Bpp/Seq/Feature/SequenceFeature.h>

Inheritance diagram for bpp::SeqRange:

Collaboration diagram for bpp::SeqRange:

Public Member Functions
	SeqRange (size_t a, size_t b, char strand='.')
SeqRange *	clone () const
virtual char	getStrand () const
virtual bool	isNegativeStrand () const
virtual bool	isStranded () const
virtual void	invert ()

Private Attributes
char	strand_

Detailed Description

a coordinate range on a sequence. Stores coordinates as a Range<size_t> object, but also keep the strand information.

Definition at line 75 of file SequenceFeature.h.

Constructor & Destructor Documentation

SeqRange()

bpp::SeqRange::SeqRange ( size_t  a, size_t  b, char  strand = '.'  )

inline

Parameters

a	First position
b	Second position
strand	The strand information. Can take one of the four values: '+' for positive strand, '-' for negative, '.' if not stranded or '?' if strandedness is relevant but unknown.

Definition at line 87 of file SequenceFeature.h.

References strand_.

Referenced by clone().

Member Function Documentation

clone()

SeqRange* bpp::SeqRange::clone ( ) const

inline

Definition at line 93 of file SequenceFeature.h.

References SeqRange().

getStrand()

virtual char bpp::SeqRange::getStrand ( ) const

inlinevirtual

Definition at line 96 of file SequenceFeature.h.

References strand_.

invert()

virtual void bpp::SeqRange::invert ( )

inlinevirtual

Definition at line 100 of file SequenceFeature.h.

References isNegativeStrand(), isStranded(), and strand_.

Referenced by bpp::BasicSequenceFeature::invert().

isNegativeStrand()

virtual bool bpp::SeqRange::isNegativeStrand ( ) const

inlinevirtual

Definition at line 98 of file SequenceFeature.h.

References strand_.

Referenced by bpp::SequenceFeatureTools::extract(), invert(), and bpp::BasicSequenceFeature::isNegativeStrand().

isStranded()

virtual bool bpp::SeqRange::isStranded ( ) const

inlinevirtual

Definition at line 99 of file SequenceFeature.h.

References strand_.

Referenced by invert(), and bpp::BasicSequenceFeature::isStranded().

Member Data Documentation

strand_

char bpp::SeqRange::strand_

private

Definition at line 79 of file SequenceFeature.h.

Referenced by getStrand(), invert(), isNegativeStrand(), isStranded(), and SeqRange().

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The documentation for this class was generated from the following file:

• Bpp/Seq/Feature/SequenceFeature.h