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

#include <aligner_n.hh>

Public Member Functions
	ModifiedScoringViewN (const AlignerN *alignerN)
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
Protected Member Functions
size_t	arc_length (const Arc &a) const
Protected Attributes
const AlignerN *	alignerN_
	aligner object for that the view is provided
score_t	lambda_
	factor for modifying scoring

Detailed Description

Provides a modified view on the scoring.

This view is used when computing length normalized local alignment.

Constructor & Destructor Documentation

LocARNA::AlignerN::ModifiedScoringViewN::ModifiedScoringViewN ( const AlignerN * alignerN ) [inline, explicit]

Construct for AlignerN object

Parameters:

alignerN The aligner object

size_t LocARNA::AlignerN::ModifiedScoringViewN::arc_length ( const Arc & a ) const [inline, protected]

Computes length of an arc

Parameters:

a the arc

infty_score_t LocARNA::AlignerN::ModifiedScoringViewN::D	(	const Arc &	a,
		const Arc &	b
	)		const `[inline]`

View on matrix D

Parameters:

a	arc in A
b	arc in B

infty_score_t LocARNA::AlignerN::ModifiedScoringViewN::D ( const ArcMatch & am ) const [inline]

View on matrix D

Parameters:

am arc match

const Scoring* LocARNA::AlignerN::ModifiedScoringViewN::scoring ( ) const [inline]

Get scoring object

void LocARNA::AlignerN::ModifiedScoringViewN::set_lambda ( score_t lambda ) [inline]

Change modification factor lambda

Parameters:

lambda modification factor

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