• DOI:10.1007/978-3-319-67428-5_14
• Corpus ID: 24148451

Fast Label Extraction in the CDAWG

@article{Belazzougui2017FastLE,
  title={Fast Label Extraction in the CDAWG},
  author={Djamal Belazzougui and Fabio Cunial},
  journal={ArXiv},
  year={2017},
  volume={abs/1707.08197}
}

• Djamal Belazzougui, F. Cunial
• Published 25 July 2017
• Computer Science
• ArXiv

The compact directed acyclic word graph (CDAWG) of a string $T$ of length $n$ takes space proportional just to the number $e$ of right extensions of the maximal repeats of $T$, and it is thus an appealing index for highly repetitive datasets, like collections of genomes from similar species, in which $e$ grows significantly more slowly than $n$. We reduce from $O(m\log{\log{n}})$ to $O(m)$ the time needed to count the number of occurrences of a pattern of length $m$, using an existing data structure that takes an amount of space proportional to the size of the CDAWG. This implies a reduction from $O(m\log{\log{n}}+\mathtt{occ})$ to $O(m+\mathtt{occ})$ in the time needed to locate all the $\mathtt{occ}$ occurrences of the pattern. We also reduce from $O(k\log{\log{n}})$ to $O(k)$ the time needed to read the $k$ characters of the label of an edge of the suffix tree of $T$, and we reduce from $O(m\log{\log{n}})$ to $O(m)$ the time needed to compute the matching statistics between a query of length $m$ and $T$, 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.