Class NucleotideScores

  • All Implemented Interfaces:
    ScoreMatrix
    Direct Known Subclasses:
    Hamming, JukesCantor

    public class NucleotideScores
    extends Scores
    Version:
    $Id: NucleotideScores.java 916 2008-05-26 03:33:27Z matt_kearse $
    Author:
    Richard Moir, Alexei Drummond
    • Constructor Detail

      • NucleotideScores

        public NucleotideScores​(float match,
                                float misMatch)
        Parameters:
        match - match score
        misMatch - mismatch score
      • NucleotideScores

        public NucleotideScores​(float match,
                                float misMatch,
                                float ambiguousMatch)
      • NucleotideScores

        public NucleotideScores​(java.lang.String name,
                                float match,
                                float misMatch)
      • NucleotideScores

        public NucleotideScores​(java.lang.String name,
                                float match,
                                float mismatchTransition,
                                float mismatchTransversion)
      • NucleotideScores

        public NucleotideScores​(java.lang.String name,
                                float match,
                                float mismatchTransition,
                                float mismatchTransversion,
                                float ambiguousMatch,
                                boolean useWeightedAmbigousMatches)
      • NucleotideScores

        public NucleotideScores​(Scores scores,
                                double percentmatches)
    • Method Detail

      • getName

        public java.lang.String getName()
        Returns:
        human readable name
      • getAlphabet

        public final java.lang.String getAlphabet()
        Returns:
        a string containing the valid characters for this score matrix.
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class Scores