LocARNA::AlignerRestriction Class Reference

Restricts range of an alignment in Aligner. More...

#include <aligner_restriction.hh>

List of all members.

Public Member Functions
	AlignerRestriction (int startA, int startB, int endA, int endB)
	end position in B
size_t	startA () const
size_t	endA () const
size_t	startB () const
size_t	endB () const
void	set_startA (size_t p)
void	set_endA (size_t p)
void	set_startB (size_t p)
void	set_endB (size_t p)

---

Detailed Description

Restricts range of an alignment in Aligner.

Contains information for restricting Aligner to sub-sequences startA..endA amd startB..endB.

Take care when using aligner restrictions for multiple Alignments with the same aligner object. The D-matrix is only computed once, so this works as long as the first Aligner::align() is called with the most general restriction (e.g. no restriction at all)!

See also:

Aligner

---

Constructor & Destructor Documentation

LocARNA::AlignerRestriction::AlignerRestriction	(	int	startA,
		int	startB,
		int	endA,
		int	endB
	)		[inline]

end position in B

Constructs with start and end positions of subsequences

Parameters:

startA	start position in A
startB	start position in B
endA	end position in A
endB	end position in B

---

Member Function Documentation

size_t LocARNA::AlignerRestriction::endA

(

)

const [inline]

Read access to member

Returns:

end position in A

size_t LocARNA::AlignerRestriction::endB

(

)

const [inline]

Read access to member

Returns:

end position in B

void LocARNA::AlignerRestriction::set_endA

(

size_t

p

)

[inline]

Write access to member

Parameters:

p	end position in A

void LocARNA::AlignerRestriction::set_endB

(

size_t

p

)

[inline]

Write access to member

Parameters:

p	end position in B

void LocARNA::AlignerRestriction::set_startA

(

size_t

p

)

[inline]

Write access to member

Parameters:

p	start position in A

void LocARNA::AlignerRestriction::set_startB

(

size_t

p

)

[inline]

Write access to member

Parameters:

p	start position in B

size_t LocARNA::AlignerRestriction::startA

(

)

const [inline]

Read access to member

Returns:

start position in A

size_t LocARNA::AlignerRestriction::startB

(

)

const [inline]

Read access to member

Returns:

start position in B

---

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

• src/LocARNA/aligner_restriction.hh