LocARNA::AlignerImpl::ModifiedScoringView Class Reference

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

#include <aligner_impl.hh>

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

ModifiedScoringView()

LocARNA::AlignerImpl::ModifiedScoringView::ModifiedScoringView ( const AlignerImpl *  aligner_impl )

inlineexplicit

Construct for Aligner object

Parameters

aligner_impl

The aligner implementation object

Note

scoring object in aligner has to be modified by lambda already

Member Function Documentation

D() [1/2]

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

D() [2/2]

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

scoring()

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

inline

Get scoring object

Returns

pointer to modified scoring object of aligner

set_lambda()

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