AlignedRegion Class Reference

represents a region in a sequence alignment More...

#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.

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Member Typedef Documentation

typedef AlignedColumnIterator iterator

Definition at line 40 of file aligned_region.hh.

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Constructor & Destructor Documentation

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

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Member Function Documentation

AlignedColumnIterator begin

(

)

iterator pointing at start of aligned region

void Delete

(

)

delete interval and update length of AlignedRegion

AlignedColumnIterator end

(

)

iterator pointing at end of aligned region.

AlignmentHandle GetAlignmentHandle

(

)

const

retrieve alignment handle for aligned region

int GetEnd

(

)

const

get end of aligned region

int GetLength

(

)

const

length of the aligned region

See also:

AlignmentHandle::GetLength()

int GetMaster

(

)

const

int GetStart

(

)

const

get start of aligned region

bool operator!=

(

const AlignedRegion &

rhs

)

const

bool operator==

(

const AlignedRegion &

rhs

)

const

AlignedColumn operator[]

(

int

index

)

const

get aligned column at given index

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

void Replace

(

const AlignedRegion &

aln_r

)

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

void SetMaster

(

int

master

)

void ShiftLeft

(

int

n

)

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

void ShiftRight

(

int

n

)

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

See also:

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

• stage/include/ost/seq/aligned_region.hh