#include <aligned_region.hh>

Public Types
typedef AlignedColumnIterator	iterator

Public Member Functions
	AlignedRegion (const AlignmentHandle &aln, int start, int end, int master=-1)

int	GetEnd () const

int	GetStart () const

int	GetMaster () const

void	SetMaster (int master)

void	Delete ()

void	Replace (const AlignedRegion &aln_r)

void	ShiftLeft (int n)

void	ShiftRight (int n)

int	GetLength () const

AlignmentHandle	GetAlignmentHandle () const

AlignedColumn	operator[] (int index) const

AlignedColumnIterator	begin ()

AlignedColumnIterator	end ()

bool	operator== (const AlignedRegion &rhs) const

bool	operator!= (const AlignedRegion &rhs) const

Detailed Description

represents a region in a sequence alignment

The region covers the half-closed interval start/stop.

You should never need to construct an aligned region manually. Use one of the helper methods of AlignmentHandle.

Definition at line 38 of file aligned_region.hh.

Member Typedef Documentation

◆ iterator

typedef AlignedColumnIterator iterator

Definition at line 40 of file aligned_region.hh.

Constructor & Destructor Documentation

◆ AlignedRegion()

AlignedRegion	(	const AlignmentHandle &	aln,
		int	start,
		int	end,
		int	master = `-1`
	)

Member Function Documentation

◆ begin()

AlignedColumnIterator begin ( )

iterator pointing at start of aligned region

◆ Delete()

void Delete ( )

delete interval and update length of AlignedRegion

◆ end()

AlignedColumnIterator end ( )

iterator pointing at end of aligned region.

◆ GetAlignmentHandle()

AlignmentHandle GetAlignmentHandle ( ) const

retrieve alignment handle for aligned region

◆ GetEnd()

int GetEnd ( ) const

get end of aligned region

◆ GetLength()

int GetLength ( ) const

length of the aligned region

See also: AlignmentHandle::GetLength()

◆ GetMaster()

int GetMaster ( ) const

◆ GetStart()

int GetStart ( ) const

get start of aligned region

◆ operator!=()

bool operator!= ( const AlignedRegion & rhs ) const

◆ operator==()

bool operator== ( const AlignedRegion & rhs ) const

◆ operator[]()

AlignedColumn operator[] ( int index ) const

get aligned column at given index

The indices range from 0 to GetLength()-1.

◆ Replace()

void Replace ( const AlignedRegion & aln_r )

replace region with content of AlignedRegion and set length to length of aln_r

◆ SetMaster()

void SetMaster ( int master )

◆ ShiftLeft()

void ShiftLeft ( int n )

shift the aligned region of the master sequence to the left by n characters.

◆ ShiftRight()

void ShiftRight ( int n )

shift the aligned region of the master sequence to the right by n characters.

See also

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

build-2.9.0-doc/stage/include/ost/seq/aligned_region.hh

Public Types

Public Member Functions