Horspool Algorithm

Source : Practical fast searching in strings R. NIGEL HORSPOOL Advisor: Prof. R. C. T. Lee Speaker: H. M. Chen

Definition of String Matching Problem

Given a pattern string P of length m and a text string T of length n, we would like to know whether there exists an occurrence of P in T.

Text
Pattern

Rule 2: Character Matching Rule

For any character X in T, find the nearest X in P which is to the left of X in T.

 For each position of the window, we compare its last character() with the last character of the pattern. If they match, we scan the window backwardly against the pattern until we either find the pattern or fail on a text character.
Suffix search
Text Pattern

match
4

 Then, no matter whether there is a match or not, we shift the window so that the pattern matches . Note that is the last character of the previous window.
Suffix search
Text Pattern

match

Text Safe shift

no in this part
5

Preprocessing phase
HpBc table The value bmBc for a particular alphabet is defined as the rightmost position of that character in the pattern 1.

Example : T : GCATCGCAGAGAGTATACAGTACG P : GCAGAGAG

7 6 5 4 3 2 1

A C G *

HpBc[a]

1 6

8
6

Pseudo code
Horspool (P = p1p2pm,T = t1t2tn) Preprocessing For c Do d[c] m For j 1m-1 Do d[pj] m - j Searching pos0 While pos n-m Do j m While j > 0 And tpos+j = pj Do j j-1 If j = 0 Then report an occurrence at pos+1 pos pos +d[tpos+m] End of while
7

Preprocessing phase
for example : T : GCATCGCAGAGAGTATACAGTACG P : GCAGAGAG

Step1: For c

Do d[c] m

c {A C G T} d[A]=8 , d[C]=8 d[G]=8 , d[T]=8

Step2: For j 1m-1 Do d[pj] m j

d[A]=1 , d[C]=6 d[G]=2 , d[T]=8
8

Example(1/3)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

GCATCGCAGAGAGTATACAGTACG GCAGAGAG
pos 0 + d[t0+7] , pos 0 + d[A], pos 1

pos pos +d[tpos+m]

ACG* 1 62 8

GCATCGCAGAGAGTATACAGTACG GCAGAGAG
pos 1 + d[t1+7] , pos 1 + d[G], pos 3

GCATCGCAGAGAGTATACAGTACG GCAGAGAG
pos 3 + d[t3+7] , pos 3 + d[G], pos 5
9

Example(2/3)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

GCATCGCAGAGAGTATACAGTACG GCAGAGAG
While j > 0 And tpos+j = pj Do j j-1 If j = 0 Then report an occurrence at pos+1

ACG* 1 62 8

pos 5 + d[t5+7] , pos 5 + d[G], pos 7

GCATCGCAGAGAGTATACAGTACG GCAGAGAG
pos 7 + d[t7+7] , pos 7 + d[A], pos 8

GCATCGCAGAGAGTATACAGTACG GCAGAGAG
pos 8 + d[t8+7] , pos 8 + d[T], pos 16
10

Example(3/3)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

GCATCGCAGAGAGTATACAGTACG GCAGAGAG
pos 16 + d[t16+7] , pos 16 + d[G], pos 18 pos > n-m // pos >23-7 jump out of while loop

ACG* 1 62 8

11

Example(1/2)
for example : T : AGATACGATATATAC P : ATATA
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

A T *

HoBc[a] 2 1 5

AGATACGATATATAC ATATA
d[A] = 2

AGATACGATATATAC ATATA
G A, d[G] = 5
12

Example(2/2)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

AGATACGATATATAC ATATA
We verify backward the window and find the occurrence. We then shift by re-using the last character of the window, d[A] = 2

AT* 215

AGATACGATATATAC ATATA
We find the pattern. We shift by the last character of then window, d[A] = 2. Then, pos > n-m and the search stops.

13

Time complexity
preprocessing phase in O(m+ ) time and O() space complexity. searching phase in O(mn) time complexity. the average number of comparisons for one text character is between 1/ and 2/(+1). ( is the number of storing characters)

14

References
AHO, A.V., 1990, Algorithms for finding patterns in strings. in Handbook of Theoretical Computer Science, Volume A, Algorithms and complexity, J. van Leeuwen ed., Chapter 5, pp 255-300, Elsevier, Amsterdam. BAEZA-YATES, R.A., RGNIER, M., 1992, Average running time of the BoyerMoore-Horspool algorithm, Theoretical Computer Science 92(1):19-31. BEAUQUIER, D., BERSTEL, J., CHRTIENNE, P., 1992, lments d'algorithmique, Chapter 10, pp 337-377, Masson, Paris. CROCHEMORE, M., HANCART, C., 1999, Pattern Matching in Strings, in Algorithms and Theory of Computation Handbook, M.J. Atallah ed., Chapter 11, pp 11-1--11-28, CRC Press Inc., Boca Raton, FL. HANCART, C., 1993. Analyse exacte et en moyenne d'algorithmes de recherche d'un motif dans un texte, Ph. D. Thesis, University Paris 7, France. HORSPOOL R.N., 1980, Practical fast searching in strings, Software - Practice & Experience, 10(6):501-506. LECROQ, T., 1995, Experimental results on string matching algorithms, Software Practice & Experience 25(7):727-765. STEPHEN, G.A., 1994, String Searching Algorithms, World Scientific.

15

THANK YOU

16