Combinatorial Pattern Matching

Volume 3109 of the series Lecture Notes in Computer Science pp 420-433

Compressed Compact Suffix Arrays

  • Veli MäkinenAffiliated withDepartment of Computer Science, University of Helsinki
  • , Gonzalo NavarroAffiliated withDepartment of Computer Science, University of Chile

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The compact suffix array (CSA) is a space-efficient full-text index, which is fast in practice to search for patterns in a static text. Compared to other compressed suffix arrays (Grossi and Vitter, Sadakane, Ferragina and Manzini), the CSA is significantly larger (2.7 times the text size, as opposed to 0.6–0.8 of compressed suffix arrays). The space of the CSA includes that of the text, which the CSA needs separately available. Compressed suffix arrays, on the other hand, include the text, that is, they are self-indexes. Although compressed suffix arrays are very fast to determine the number of occurrences of a pattern, they are in practice very slow to report even a few occurrence positions or text contexts. In this aspect the CSA is much faster. In this paper we contribute to this space-time trade off by introducing the Compressed CSA (CCSA), a self-index that improves the space usage of the CSA in exchange for search speed. We show that the occ occurrence positions of a pattern of length m in a text of length n can be reported in O((m+occ)log n) time using the CCSA, whose representation needs O(n(1+H k log n)) bits for any k, H k being the k-th order empirical entropy of the text. In practice the CCSA takes 1.6 times the text size (and includes the text). This is still larger than current compressed suffix arrays, and similar in size to the LZ-index of Navarro. Search times are by far better than for self-indexes that take less space than the text, and competitive against the LZ-index and versions of compressed suffix arrays tailored to take 1.6 times the text size.