A Fast Generic Sequence Matching Algorithm

A string matching—andmore generally, sequence matching—algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is better than that of the fastest versions of the Boyer-Moore algorithm. The algorithm retains its efficiency advantages in a wide variety of sequence matching problems of practical interest, including traditional string matching; large-alphabet problems (as in Unicode strings); and small-alphabet, long-pattern problems (as in DNA searches). Since it is expressed as a generic algorithm for searching in sequences over an arbitrary type T , it is well suited for use in generic software libraries such as the C++ Standard Template Library. The algorithm was obtained by adding to the Knuth-MorrisPratt algorithm one of the pattern-shifting techniques from the BoyerMoore algorithm, with provision for use of hashing in this technique. In situations in which a hash function or random access to the sequences is not available, the algorithm falls back to an optimized version of the Knuth-Morris-Pratt algorithm. key words String search String matching Pattern matching Sequence matching Generic algorithms Knuth-Morris-Pratt algorithm BoyerMoore algorithm DNA pattern matching C++ Standard Template Library STL Ada Literate programming