Package jebl.evolution.align.scores

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