java - Fast algorithm for searching for substrings in a string

Question

I'd like an efficient algorithm (or library) that I can use in Java to search for substrings in a string.

What I would like to do is:

Given an input string - INSTR:

"BCDEFGH"

And a set of candidate strings - CAND:

"AB", "CDE", "FG", "H", "IJ"

Find any CAND strings that match as substrings within INSTR

In this example I would match "CDE", "FG", and "H" (but not "AB" and "IJ")

There could be many thousand candidate strings (in CAND), but more importantly I will be doing this search many millions of times so I need it to be FAST.

I'd like to work with char arrays. Also, I'm not intested in architectural solutions, like distributing the search - just the most efficient function/algorithm for doing it locally.

Additionally, all the strings in CAND and INSTR will all be relatively small (< 50 chars) - i.e. the target string INSTR is NOT long relative to the candidate strings.

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Update I should have mentioned, the set of CAND strings is invariant across all values of INSTR.

Update I only need to know that there was a match - and i don't need to know what the match was.

Final Update I opted to try AhoCorsick and Rabin-Karp, due to simplicity of implementation. Because I have variable length patterns I used a modified Rabin-Karp that hashes the first n characters of each pattern, where n is the length of the smallest pattern, N was then the length of my rolling substring search window. For the Aho Corsick I used this

In my test i searched for 1000 patterns in two documents news paper articles, averaged across 1000 iterations etc... Normalised times to complete were:

AhoCorsick: 1

RabinKarp: 1.8

Naive Search (check each pattern & use string.contains): 50

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*Some resources describing the algos mentioned in the answers below:

http://www.seas.gwu.edu/~simhaweb/cs151/lectures/module5/module5.html

http://www.cs.princeton.edu/courses/archive/spr09/cos226/lectures/18SubstringSearch-2x2.pdf

http://www-igm.univ-mlv.fr/~lecroq/string/index.html*

Answer 1

Read up on the Aho-Corasick algorithm and the Rabin-Karp algorithm.

If the input is not too large, you don't want to repeat the search many times and you do not have many patterns, it might be a good idea to use a single pattern algorithm several times. The Wikipedia article on search algorithms gives many algorithms with running and preprocessing times.

Implementations:

• https://hkn.eecs.berkeley.edu/~dyoo/java/index.html
• http://algs4.cs.princeton.edu/53substring/RabinKarp.java.html
• https://github.com/hankcs/AhoCorasickDoubleArrayTrie
• https://github.com/RokLenarcic/AhoCorasick
• https://github.com/robert-bor/aho-corasick

Presentations:

• http://www.slideshare.net/taka111/ahocorasick-string-matching-algorithm-15078438