Class Comparison

  • public class Comparison
    extends Object
    This class provides static methods for the calculation of the percentage of identity between two aligned sequences.

    Since 4.1.1 the methods for distance inference in forester are also used in BioJava, so this implementation of percentage of identity is not needed anymore. However, the code is maintained as the own BioJava implementation.

    Scooter Willis
    • Method Detail

      • PID

        public static final float PID​(String seq1,
                                      String seq2)
        this is a gapped PID calculation
        s1 - SequenceI
        s2 - SequenceI
      • PID

        public static final float PID​(String seq1,
                                      String seq2,
                                      int start,
                                      int end)
      • isGap

        public static final boolean isGap​(char c)
        Method that determines if a character means a gap in the alignment.
        c - gap character is one of the symbols in {' ','-','.'}
        true if it is a gap, false otherwise