com.milaboratory.core.alignment

Interface AlignmentScoring<S extends Sequence<S>>

All Superinterfaces:

Serializable

All Known Implementing Classes:

AbstractAlignmentScoring, AffineGapAlignmentScoring, LinearGapAlignmentScoring

public interface AlignmentScoring<S extends Sequence<S>>
extends Serializable

AlignmentScoring - interface which is to be implemented by any scoring system

Method Summary

Methods

Modifier and Type	Method and Description
Alphabet<S>	getAlphabet()
int	getMaximalMatchScore()
int	getMaximalMismatchScore()
int	getMinimalMatchScore()
int	getMinimalMismatchScore()
int	getScore(byte from, byte to)

Method Detail

getScore

int getScore(byte from,
           byte to)

getAlphabet

Alphabet<S> getAlphabet()

getMinimalMatchScore

int getMinimalMatchScore()

getMaximalMatchScore

int getMaximalMatchScore()

getMinimalMismatchScore

int getMinimalMismatchScore()

getMaximalMismatchScore

int getMaximalMismatchScore()