Class Scores

java.lang.Object
jebl.evolution.align.scores.Scores
All Implemented Interfaces:
ScoreMatrix
Direct Known Subclasses:
AminoAcidScores, NucleotideScores, SubstScoreMatrix

public abstract class Scores extends Object implements ScoreMatrix
Base class for all score matrices in the package.
Version:
$Id: Scores.java 916 2008-05-26 03:33:27Z matt_kearse $ Based on code originally by Peter Setsoft. See package.html.
Author:
Alexei Drummond
  • Field Details

    • score

      public float[][] score
  • Constructor Details

    • Scores

      public Scores()
  • Method Details

    • getScore

      public final float getScore(char x, char y)
      Specified by:
      getScore in interface ScoreMatrix
      Returns:
      the score for matching char x with char y
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • forMatrix

      public static Scores forMatrix(ScoreMatrix scoreMatrix)
      Parameters:
      scoreMatrix - A ScoreMatrix with only low ascii characters (< chr(127)) in the alphabet
      Returns:
      A Scores instance corresponding to scoreMatrix.
    • duplicate

      public static Scores duplicate(Scores scores)
    • includeGaps

      public static Scores includeGaps(Scores scores, float gapVersusResidueCost, float gapVersusGapCost)
      Parameters:
      scores -
      gapVersusResidueCost - should be a negative value
      gapVersusGapCost - should be a positive value
    • includeAdditionalCharacters

      public static Scores includeAdditionalCharacters(Scores scores, String characters)
      includes additional characters in the score matrix which will all have scored zero when compared to other characters. Current system does not handle special characters well, such as ? Or "R" for NucleotideSequences, which represents a "A" or "G". Currently, we just add all characters to the allowed set of characters, and they are scored as zero cost when comparing to other characters, including themselves. One-day, we should probably introduce better scoring system so that "R" is a positive score compared to "A" or "G", but a negative score compared to "C" or "T". example usage: scores = Scores.includeAdditionalCharacters(scores, "?ABCDEFGHIJKLMNOPQRSTUVWXYZ");
      Parameters:
      scores -
      characters -
      Returns:
      a new score matrix.
    • getMatrixString

      public String getMatrixString()
      Returns:
      this score matrix as a string.