Class NucleotideScores

java.lang.Object
jebl.evolution.align.scores.Scores
jebl.evolution.align.scores.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
  • Field Details

  • Constructor Details

    • NucleotideScores

      public NucleotideScores(NucleotideScores scores)
    • 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(String name, float match, float misMatch)
    • NucleotideScores

      public NucleotideScores(String name, float match, float mismatchTransition, float mismatchTransversion)
    • NucleotideScores

      public NucleotideScores(String name, float match, float mismatchTransition, float mismatchTransversion, float ambiguousMatch, boolean useWeightedAmbigousMatches)
    • NucleotideScores

      public NucleotideScores(Scores scores, double percentmatches)
  • Method Details

    • getName

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

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

      public String toString()
      Overrides:
      toString in class Scores