LocARNA::AlignerN::UnmodifiedScoringViewN Class Reference

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

#include <aligner_n.hh>

List of all members.

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 (bool isA, const Arc &arcX, const Arc &arcY)
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

)

[inline, explicit]

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	(	bool	isA,
		const Arc &	arcX,
		const Arc &	arcY
	)		[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

---

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

• src/LocARNA/aligner_n.hh