Class Overlap<S extends BinarySequence>

  • Direct Known Subclasses:
    OverlapDnaSeq

    public abstract class Overlap<S extends BinarySequence>
    extends java.lang.Object
    Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.
    Author:
    pcingola
    • Constructor Summary

      Constructors 
      Constructor Description
      Overlap()  
    • Constructor Detail

      • Overlap

        public Overlap()
    • Method Detail

      • getBestOffset

        public int getBestOffset()
      • getBestScore

        public int getBestScore()
      • overlap

        public abstract int overlap​(S seq1,
                                    S seq2)
        Calculate the best overlap between two sequences
        Parameters:
        seq1 -
        seq1 -
        Returns: