New text indexing functionalities of the compressed suffix arrays

Abstract

New text indexing functionalities of the compressed suffix arrays are proposed. The compressed suffix array proposed by Grossi and Vitter is a space-efficient data structure for text indexing. It occupies only O( n) bits for a text of length n; however it also uses the text itself that occupies n log 2| A| bits for the alphabet A . In this paper we modify the data structure so that pattern matching can be done without any access to the text. In addition to the original functions of the compressed suffix array, we add new operations search, decompress and inverse to the compressed suffix arrays. We show that the new index can find occ occurrences of any substring P of the text in O(| P|log n+ occlog ϵ n) time for any fixed 1⩾ ϵ>0 without access to the text. The index also can decompress a part of the text of length m in O( m+log ϵ n) time. For a text of length n on an alphabet A such that | A|= polylog(n) , our new index occupies only O(nH 0+n loglog| A|) bits where H 0⩽ log| A| is the order-0 entropy of the text. Especially for ϵ=1 the size is nH 0+O(n loglog| A|) bits. Therefore the index will be smaller than the text, which means we can perform fast queries from compressed texts.