LocARNA::AlignerN::ModifiedScoringViewN Class Reference

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

#include <aligner_n.hh>

Collaboration diagram for LocARNA::AlignerN::ModifiedScoringViewN:

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.

See also

UnmodifiedScoringView

Constructor & Destructor Documentation

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

inlineexplicit

Construct for AlignerN object

Parameters

alignerN

The aligner object

Note

scoring object in aligner has to be modified by lambda already

Member Function Documentation

size_t LocARNA::AlignerN::ModifiedScoringViewN::arc_length ( const Arc &  a ) const

inlineprotected

Computes length of an arc

Parameters

a

the arc

Returns

length of arc a

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

Returns

modified D matrix entry for match of a and b

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

inline

View on matrix D

Parameters

am

arc match

Returns

modified D matrix entry for arc match am

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

inline

Get scoring object

Returns

modified scoring object of aligner

void LocARNA::AlignerN::ModifiedScoringViewN::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_n.hh