Class KnuthMorrisPrattSearch

  • public final class KnuthMorrisPrattSearch
    extends Object
    An object to find exact subsequences within a sequence.

    Reference: KNUTH D.E., MORRIS (Jr) J.H., PRATT V.R., 1977, Fast pattern matching in strings, SIAM Journal on Computing 6(1):323-350. USAGE:

    When the object is constructed the findMatches() method would be called. This will return an int[] giving the offsets (ie the location of the first symbol of each match in the text). The getKMPNextTable() returns the table of border lengths used in the algorithm. This method is protected as it is unlikely it will be needed except for debugging.

    The algorithm finds exact matches therefore ambiguity symbols will match only themselves. The class cannot perform regular expressions. The class operates on all alphabets thus if searching for a DNA pattern you should compile both the pattern and its reverse complement.

    WARNING the behaviour of a pattern containing gaps is undefined. It's not recommended that you try it.

    Copyright: Copyright (c) 2002

    Company: AgResearch

    Mark Schreiber
    • Constructor Detail

      • KnuthMorrisPrattSearch

        public KnuthMorrisPrattSearch​(SymbolList pattern)
        Constructs a KMP matcher to find exact occurances of pattern in text using the Knuth-Morris-Pratt algorithm.

        A new class should be constructed for each occurance of pattern.

        pattern - the pattern to search for
    • Method Detail

      • findMatches

        public int[] findMatches​(SymbolList text)
        This will return an int[] giving the offsets of the matches in text (ie the location of the first symbol of each match in the text).
        text - the text or sequence to search for the pattern
        an int[] giving the offsets to the matches or a zero length array if there are no matches.
      • getKmpNextTable

        protected int[] getKmpNextTable()
        Returns the table of border lengths
        an int[] of border lenghts
      • main

        public static void main​(String[] args)
                         throws Exception
        Demo and Test method
        args - no arguments required
        Exception - if the test fails