bpp::SequenceWalker Class Reference

A helper class to easily convert coordinates between sequence and alignments. More...

#include <Bpp/Seq/SequenceWalker.h>

Collaboration diagram for bpp::SequenceWalker:

Public Member Functions
	SequenceWalker (const SequenceInterface &seq)
	SequenceWalker (const SequenceWalker &walker)
SequenceWalker &	operator= (const SequenceWalker &walker)
virtual	~SequenceWalker ()
size_t	getAlignmentPosition (size_t seqPos)
size_t	getSequencePosition (size_t alnPos)

Private Attributes
const SequenceInterface *	seq_
size_t	seqPos_
size_t	alnPos_
int	gap_

Detailed Description

A helper class to easily convert coordinates between sequence and alignments.

Coordinates are 0-based. The walker will be more efficient if coordinates are called in pre-ordered way.

Definition at line 19 of file SequenceWalker.h.

Constructor & Destructor Documentation

SequenceWalker() [1/2]

bpp::SequenceWalker::SequenceWalker ( const SequenceInterface &  seq )

inline

Definition at line 27 of file SequenceWalker.h.

References alnPos_, gap_, seq_, and bpp::CruxSymbolListInterface::size().

SequenceWalker() [2/2]

bpp::SequenceWalker::SequenceWalker ( const SequenceWalker &  walker )

inline

Definition at line 36 of file SequenceWalker.h.

~SequenceWalker()

virtual bpp::SequenceWalker::~SequenceWalker ( )

inlinevirtual

Definition at line 46 of file SequenceWalker.h.

Member Function Documentation

getAlignmentPosition()

size_t SequenceWalker::getAlignmentPosition

(

size_t

seqPos

)

Definition at line 16 of file SequenceWalker.cpp.

getSequencePosition()

size_t SequenceWalker::getSequencePosition

(

size_t

alnPos

)

Definition at line 56 of file SequenceWalker.cpp.

operator=()

SequenceWalker& bpp::SequenceWalker::operator= ( const SequenceWalker &  walker )

inline

Definition at line 38 of file SequenceWalker.h.

References alnPos_, gap_, seq_, and seqPos_.

Member Data Documentation

alnPos_

size_t bpp::SequenceWalker::alnPos_

private

Definition at line 23 of file SequenceWalker.h.

Referenced by operator=(), and SequenceWalker().

gap_

int bpp::SequenceWalker::gap_

private

Definition at line 24 of file SequenceWalker.h.

Referenced by operator=(), and SequenceWalker().

seq_

const SequenceInterface* bpp::SequenceWalker::seq_

private

Definition at line 22 of file SequenceWalker.h.

Referenced by operator=(), and SequenceWalker().

seqPos_

size_t bpp::SequenceWalker::seqPos_

private

Definition at line 23 of file SequenceWalker.h.

Referenced by operator=().

---

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

• Bpp/Seq/SequenceWalker.h
• Bpp/Seq/SequenceWalker.cpp