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:

List of all members.

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_

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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.

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Constructor & Destructor Documentation

bpp::SequenceWalker::SequenceWalker

(

const Sequence &

seq

)

[inline]

Definition at line 62 of file SequenceWalker.h.

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

bpp::SequenceWalker::SequenceWalker

(

const SequenceWalker &

walker

)

[inline]

Definition at line 69 of file SequenceWalker.h.

virtual bpp::SequenceWalker::~SequenceWalker

(

)

[inline, virtual]

Definition at line 78 of file SequenceWalker.h.

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Member Function Documentation

size_t SequenceWalker::getAlignmentPosition

(

size_t

seqPos

)

throw (Exception)

Definition at line 49 of file SequenceWalker.cpp.

size_t SequenceWalker::getSequencePosition

(

size_t

alnPos

)

throw (Exception)

Definition at line 81 of file SequenceWalker.cpp.

SequenceWalker& bpp::SequenceWalker::operator=

(

const SequenceWalker &

walker

)

[inline]

Definition at line 71 of file SequenceWalker.h.

References alnPos_, gap_, seq_, and seqPos_.

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Member Data Documentation

size_t bpp::SequenceWalker::alnPos_ [private]

Definition at line 58 of file SequenceWalker.h.

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

int bpp::SequenceWalker::gap_ [private]

Definition at line 59 of file SequenceWalker.h.

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

const Sequence* bpp::SequenceWalker::seq_ [private]

Definition at line 57 of file SequenceWalker.h.

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

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