LocARNA::AlignerN::UnmodifiedScoringViewN Class Reference

Provides the standard view on the scoring. More...

#include <aligner_n.hh>

Collaboration diagram for LocARNA::AlignerN::UnmodifiedScoringViewN:

Public Member Functions
	UnmodifiedScoringViewN (const AlignerN *alignerN)
const Scoring *	scoring () const
infty_score_t	D (const Arc &a, const Arc &b) const
infty_score_t	D (const Arc &arcX, const Arc &arcY, bool isA)
infty_score_t	D (const ArcMatch &am) const

Protected Attributes
const AlignerN *	alignerN_
	aligner object for that the view is provided

Detailed Description

Provides the standard view on the scoring.

See also

ModifiedScoringView

Note

We use a template-based scheme to switch between use of the unmodified score and the modified score without run-time penalty for the standard case the mechanism is used for methods compute_M_entry and trace_noex

Constructor & Destructor Documentation

LocARNA::AlignerN::UnmodifiedScoringViewN::UnmodifiedScoringViewN ( const AlignerN *  alignerN )

inlineexplicit

Construct for AlignerN object

Parameters

alignerN

The aligner object

Member Function Documentation

infty_score_t LocARNA::AlignerN::UnmodifiedScoringViewN::D ( const Arc &  a, const Arc &  b  ) const

inline

View on matrix D

Parameters

a	arc in A
b	arc in B

Returns

D matrix entry for match of a and b

infty_score_t LocARNA::AlignerN::UnmodifiedScoringViewN::D ( const Arc &  arcX, const Arc &  arcY, bool  isA  )

inline

View on matrix D

Parameters

arcX	arc in A/B determined by isA
arcY	arc in B/A determined by isA
isA	swap arcX/Y parameters

Returns

D matrix entry for match of arcX<->arcY

infty_score_t LocARNA::AlignerN::UnmodifiedScoringViewN::D ( const ArcMatch &  am ) const

inline

View on matrix D

Parameters

am

arc match

Returns

D matrix entry for arc match am

const Scoring* LocARNA::AlignerN::UnmodifiedScoringViewN::scoring ( ) const

inline

Get scoring object

Returns

(unmodified) scoring object of aligner

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

• src/LocARNA/aligner_n.hh