LocARNA-1.9.2
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Public Member Functions | Protected Attributes
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 Scoringscoring () 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 AlignerNalignerN_
 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

Construct for AlignerN object

Parameters:
alignerNThe 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:
aarc in A
barc 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:
arcXarc in A/B determined by isA
arcYarc in B/A determined by isA
isAswap arcX/Y parameters
Returns:
D matrix entry for match of arcX<->arcY

View on matrix D

Parameters:
amarc match
Returns:
D matrix entry for arc match am

Get scoring object

Returns:
(unmodified) scoring object of aligner

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