Interface SequenceDistance<T>

    • Method Detail

      • computeAlignment

        SequenceDistance.DistanceResult<T> computeAlignment​(T[] a,
                                                            T[] b,
                                                            SequenceDistance.Equivalence<T> eq)
        Compute the distance and a possible alignment between two sequences.
        Parameters:
        a - first sequence
        b - second sequence
        eq - equivalence relation on T
        Returns:
        a distance and optional alignment
      • computeAlignment

        SequenceDistance.DistanceResult<T> computeAlignment​(java.util.List<T> a,
                                                            java.util.List<T> b,
                                                            SequenceDistance.Equivalence<T> eq)
        Compute the distance and a possible alignment between two sequences.
        Parameters:
        a - first sequence
        b - second sequence
        eq - equivalence relation on T
        Returns:
        a distance and optional alignment
      • computeDistance

        int computeDistance​(T[] a,
                            T[] b,
                            SequenceDistance.Equivalence<T> eq)
        Computes only the distance between two sequences.
        Parameters:
        a - first sequence
        b - second sequence
        eq - equivalence relation on T
        Returns:
        the distance
      • computeDistance

        int computeDistance​(java.util.List<T> a,
                            java.util.List<T> b,
                            SequenceDistance.Equivalence<T> eq)
        Computes only the distance between two sequences.
        Parameters:
        a - first sequence
        b - second sequence
        eq - equivalence relation on T
        Returns:
        the distance