SimpleMatchMismatchScoring
in package
implements
SubstitutionScoringInterface
Awards a fixed score for identical symbols and another fixed score for anything else, case insensitive. Suitable for DNA and RNA, and usable as a crude default for amino acids when no substitution matrix is available.
Class SimpleMatchMismatchScoring
Tags
Table of Contents
Interfaces
- SubstitutionScoringInterface
- Interface SubstitutionScoringInterface - lets a pairwise aligner stay ignorant of how two symbols are scored against each other, whether by a flat match/mismatch rule or a substitution matrix such as PAM250.
Properties
- $matchScore : int
- $mismatchScore : int
Methods
- __construct() : mixed
- SimpleMatchMismatchScoring constructor.
- score() : int
Properties
$matchScore
private
int
$matchScore
$mismatchScore
private
int
$mismatchScore
Methods
__construct()
SimpleMatchMismatchScoring constructor.
public
__construct([int $iMatchScore = 1 ][, int $iMismatchScore = -1 ]) : mixed
Parameters
- $iMatchScore : int = 1
-
Awarded when both symbols are identical
- $iMismatchScore : int = -1
-
Awarded when they differ
score()
public
score(string $sFirstSymbol, string $sSecondSymbol) : int
Parameters
- $sFirstSymbol : string
- $sSecondSymbol : string