LocARNA::AlignerRestriction Class Reference

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

#include <aligner_restriction.hh>

Public Member Functions
	AlignerRestriction (int startA, int startB, int endA, int endB)
	end position in B More...
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

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

• src/LocARNA/aligner_restriction.hh