LocARNA::AlignerImpl::ModifiedScoringView Class Reference

Provides a modified view on the scoring. More...

#include <aligner_impl.hh>

List of all members.

Public Member Functions
	ModifiedScoringView (const AlignerImpl *aligner_impl)
void	set_lambda (score_t lambda)
const Scoring *	scoring () const
infty_score_t	D (const Arc &a, const Arc &b) const
infty_score_t	D (const ArcMatch &am) const

---

Detailed Description

Provides a modified view on the scoring.

This view is used when computing length normalized local alignment.

See also:

UnmodifiedScoringView

---

Constructor & Destructor Documentation

LocARNA::AlignerImpl::ModifiedScoringView::ModifiedScoringView

(

const AlignerImpl *

aligner_impl

)

[inline, explicit]

Construct for Aligner object

Parameters:

aligner_impl

The aligner implementation object

Note:

scoring object in aligner has to be modified by lambda already

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Member Function Documentation

infty_score_t LocARNA::AlignerImpl::ModifiedScoringView::D	(	const Arc &	a,
		const Arc &	b
	)		const [inline]

View on matrix D

Parameters:

a	arc in A
b	arc in B

Returns:

modified D matrix entry for match of a and b

infty_score_t LocARNA::AlignerImpl::ModifiedScoringView::D

(

const ArcMatch &

am

)

const [inline]

View on matrix D

Parameters:

am

arc match

Returns:

modified D matrix entry for arc match am

const Scoring* LocARNA::AlignerImpl::ModifiedScoringView::scoring

(

)

const [inline]

Get scoring object

Returns:

modified scoring object of aligner

void LocARNA::AlignerImpl::ModifiedScoringView::set_lambda

(

score_t

lambda

)

[inline]

Change modification factor lambda

Parameters:

lambda

modification factor

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

• src/LocARNA/aligner_impl.hh