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Representing the suffix tree with the CDAWG

Published 24 May 2017 in cs.DS | (1705.08640v1)

Abstract: Given a string TT, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with eTe_T arcs, taking overall O(eT+eT‾)O(e_T+e_{{\overline{T}}}) words of space, where T‾{\overline{T}} is the reverse of TT, and supporting some key operations in time between O(1)O(1) and O(log⁡log⁡n)O(\log{\log{n}}) in the worst case. This representation is especially appealing for highly repetitive strings, like collections of similar genomes or of version-controlled documents, in which eTe_T grows sublinearly in the length of TT in practice. In this paper we augment such representation, supporting a number of additional queries in worst-case time between O(1)O(1) and O(log⁡n)O(\log{n}) in the RAM model, without increasing space complexity asymptotically. Our technique, based on a heavy path decomposition of the suffix tree, enables also a representation of the suffix array, of the inverse suffix array, and of TT itself, that takes O(eT)O(e_T) words of space, and that supports random access in O(log⁡n)O(\log{n}) time. Furthermore, we establish a connection between the reversed CDAWG of TT and a context-free grammar that produces TT and only TT, which might have independent interest.

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