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 (const Range< size_t > range, char strand='.')
SeqRange *	clone () const
virtual char	getStrand () const
virtual bool	isNegativeStrand () const
virtual bool	isStranded () const
virtual void	invert ()
bool	operator== (const Range< T > &r) const
bool	operator!= (const Range< T > &r) const
bool	operator< (const Range< T > &r) const
virtual Range &	operator+= (const T &val)
virtual Range	operator+ (const T &val)
virtual Range &	operator-= (const T &val)
virtual Range	operator- (const T &val)
T	begin () const
T	end () const
T	length () const
bool	overlap (const Range &r) const
bool	isContiguous (const Range &r) const
bool	contains (const Range &r) const
void	expandWith (const Range &r)
void	sliceWith (const Range &r)
bool	isEmpty () const
std::string	toString () const

Private Attributes
char	strand_
T	begin_
T	end_

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() [1/2]

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().

SeqRange() [2/2]

bpp::SeqRange::SeqRange ( const Range< size_t >  range, char  strand = '.'  )

inline

Parameters

range	A range object
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 97 of file SequenceFeature.h.

References strand_.

Member Function Documentation

clone()

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

inlinevirtual

Implements bpp::Clonable.

Definition at line 103 of file SequenceFeature.h.

References SeqRange().

getStrand()

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

inlinevirtual

Definition at line 106 of file SequenceFeature.h.

References strand_.

Referenced by bpp::CoordinateTranslatorMafIterator::analyseCurrentBlock_(), and bpp::FeatureExtractorMafIterator::analyseCurrentBlock_().

invert()

virtual void bpp::SeqRange::invert ( )

inlinevirtual

Definition at line 110 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 108 of file SequenceFeature.h.

References strand_.

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

isStranded()

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

inlinevirtual

Definition at line 109 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().

---

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

• Bpp/Seq/Feature/SequenceFeature.h