Class ExactMatchDistance

  • All Implemented Interfaces:
    SequenceDistanceMeasurer, SequenceDistanceMeasurerDouble

    public final class ExactMatchDistance
    extends Object
    implements SequenceDistanceMeasurer

    ExactMatch distance (or Hamming Distance) of a pair of non-binary strings (or more generally sequences) is the number of sequence (or string) positions where the two sequences differ. This class supports comparison of Java String objects, as well as comparisons of arrays of any of Java's eight primitive types, and arrays of any object type. It is the count of the number of positions for which the two sequences contain different elements.

    Most other implementations of Hamming distance require the two strings to be of the same length. Ours does not. If the two sequences (i.e., arrays or Strings) are of different lengths, then the difference in length affects distance. E.g., although "abbd" is a distance of 1 from "abcd" since they differ in one position, "abbd" is a distance of 4 from "abcdefg" (the one difference, plus the three extra characters).

    Runtime: O(n), where n is the length of the shorter of the two sequences.

    If your sequences are guaranteed not to have duplicates, and to contain the same set of elements, then consider instead using the ExactMatchDistance class, which assumes permutations of the integers from 0 to N-1.

    Exact match distance was introduced specifically for permutations in:
    S. Ronald, "More distance functions for order-based encodings," in Proc. IEEE CEC. IEEE Press, 1998, pp. 558–563.

    • Constructor Detail

      • ExactMatchDistance

        public ExactMatchDistance()
        Constructs the distance measurer as specified in the class documentation.
    • Method Detail

      • distance

        public int distance​(int[] s1,
                            int[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(long[] s1,
                            long[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(short[] s1,
                            short[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(byte[] s1,
                            byte[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(char[] s1,
                            char[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(boolean[] s1,
                            boolean[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(double[] s1,
                            double[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(float[] s1,
                            float[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public int distance​(Object[] s1,
                            Object[] s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two arrays of objects. The objects in the arrays must be of a class that has overridden the Object.equals method.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Parameters:
        s1 - First array.
        s2 - Second array.
        Returns:
        distance between s1 and s2
      • distance

        public <T> int distance​(List<T> s1,
                                List<T> s2)
        Description copied from interface: SequenceDistanceMeasurer
        Measures the distance between two lists of objects. The objects in the lists must be of a class that has overridden the Object.equals method.
        Specified by:
        distance in interface SequenceDistanceMeasurer
        Type Parameters:
        T - Type of List elements.
        Parameters:
        s1 - First list.
        s2 - Second list.
        Returns:
        distance between s1 and s2