English

Fast Label Extraction in the CDAWG

Data Structures and Algorithms 2017-09-27 v2

Abstract

The compact directed acyclic word graph (CDAWG) of a string TT of length nn takes space proportional just to the number ee of right extensions of the maximal repeats of TT, and it is thus an appealing index for highly repetitive datasets, like collections of genomes from similar species, in which ee grows significantly more slowly than nn. We reduce from O(mloglogn)O(m\log{\log{n}}) to O(m)O(m) the time needed to count the number of occurrences of a pattern of length mm, using an existing data structure that takes an amount of space proportional to the size of the CDAWG. This implies a reduction from O(mloglogn+occ)O(m\log{\log{n}}+\mathtt{occ}) to O(m+occ)O(m+\mathtt{occ}) in the time needed to locate all the occ\mathtt{occ} occurrences of the pattern. We also reduce from O(kloglogn)O(k\log{\log{n}}) to O(k)O(k) the time needed to read the kk characters of the label of an edge of the suffix tree of TT, and we reduce from O(mloglogn)O(m\log{\log{n}}) to O(m)O(m) the time needed to compute the matching statistics between a query of length mm and TT, using an existing representation of the suffix tree based on the CDAWG. All such improvements derive from extracting the label of a vertex or of an arc of the CDAWG using a straight-line program induced by the reversed CDAWG.

Keywords

Cite

@article{arxiv.1707.08197,
  title  = {Fast Label Extraction in the CDAWG},
  author = {Djamal Belazzougui and Fabio Cunial},
  journal= {arXiv preprint arXiv:1707.08197},
  year   = {2017}
}

Comments

16 pages, 1 figure. In proceedings of the 24th International Symposium on String Processing and Information Retrieval (SPIRE 2017). arXiv admin note: text overlap with arXiv:1705.08640

R2 v1 2026-06-22T20:57:24.793Z