jebl.evolution.align.scores
Interface ScoreMatrix

All Known Implementing Classes:

AminoAcidScores, Blosum45, Blosum50, Blosum55, Blosum60, Blosum62, Blosum65, Blosum70, Blosum75, Blosum80, Blosum85, Blosum90, Hamming, JukesCantor, NucleotideScores, Pam100, Pam110, Pam120, Pam130, Pam140, Pam150, Pam160, Pam170, Pam180, Pam190, Pam200, Pam210, Pam220, Pam230, Pam240, Pam250, Scores, SubstScoreMatrix

public interface ScoreMatrix

Author:

Alexei Drummond

Method Summary

String	getAlphabet()
String	getName()
float	getScore(char x, char y)

Method Detail

getName

String getName()

Returns:

human readable name

getScore

float getScore(char x,
               char y)

Returns:

the score for matching char x with char y

getAlphabet

String getAlphabet()

Returns:

a string containing the valid characters for this score matrix.