Package 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
Version:
$Id: ScoreMatrix.java 360 2006-06-22 07:42:48Z pepster $
Author:
Alexei Drummond

  • Method Details

    • 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.