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 Sequence &seq)
	SequenceWalker (const SequenceWalker &walker)
SequenceWalker &	operator= (const SequenceWalker &walker)
virtual	~SequenceWalker ()
size_t	getAlignmentPosition (size_t seqPos) throw (Exception)
size_t	getSequencePosition (size_t alnPos) throw (Exception)

Private Attributes
const Sequence *	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 54 of file SequenceWalker.h.

Constructor & Destructor Documentation

SequenceWalker() [1/2]

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

inline

Definition at line 62 of file SequenceWalker.h.

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

SequenceWalker() [2/2]

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

inline

Definition at line 69 of file SequenceWalker.h.

~SequenceWalker()

virtual bpp::SequenceWalker::~SequenceWalker ( )

inlinevirtual

Definition at line 78 of file SequenceWalker.h.

Member Function Documentation

getAlignmentPosition()

size_t SequenceWalker::getAlignmentPosition	(	size_t	seqPos	)
throw	(	Exception
	)

Definition at line 49 of file SequenceWalker.cpp.

getSequencePosition()

size_t SequenceWalker::getSequencePosition	(	size_t	alnPos	)
throw	(	Exception
	)

Definition at line 81 of file SequenceWalker.cpp.

operator=()

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

inline

Definition at line 71 of file SequenceWalker.h.

References alnPos_, gap_, seq_, and seqPos_.

Member Data Documentation

alnPos_

size_t bpp::SequenceWalker::alnPos_

private

Definition at line 58 of file SequenceWalker.h.

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

gap_

int bpp::SequenceWalker::gap_

private

Definition at line 59 of file SequenceWalker.h.

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

seq_

const Sequence* bpp::SequenceWalker::seq_

private

Definition at line 57 of file SequenceWalker.h.

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

seqPos_

size_t bpp::SequenceWalker::seqPos_

private

Definition at line 58 of file SequenceWalker.h.

Referenced by operator=().

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

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