An opportunistic text indexing structure based on run length encoding

Yuya Tamakoshi; Keisuke Goto; Shunsuke Inenaga; Hideo Bannai; Masayuki Takeda

doi:10.1007/978-3-319-18173-8_29

An opportunistic text indexing structure based on run length encoding

Yuya Tamakoshi, Keisuke Goto, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda

Mathematical Informatics

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

3 Citations (Scopus)

Abstract

We present a new text indexing structure based on the run length encoding (RLE) of a text string T which, given the RLE of a query pattern P, reports all the occ occurrences of P in T in O(m+occ+log n) time, where n and m are the sizes of the RLEs of T and P, respectively. The data structure requires n(2 logN+log n+log σ)+O(n) bits of space, where N is the length of the uncompressed text string T and σ is the alphabet size. Moreover, using n(3 logN + logn + logσ) + 2σ log N/σ + O(n log log n) bits of total space, our data structure can be enhanced to answer the beginning position of the lexicographically ith smallest suffix of T for a given rank i in O(log² n) time. All these data structures can be constructed in O(n log n) time using O(n logN) bits of extra space.

Original language	English
Title of host publication	Algorithms and Complexity - 9th International Conference, CIAC 2015, Proceedings
Editors	Peter Widmayer, Vangelis Th. Paschos
Publisher	Springer Verlag
Pages	390-402
Number of pages	13
ISBN (Print)	9783319181721
DOIs	https://doi.org/10.1007/978-3-319-18173-8_29
Publication status	Published - 2015
Event	9th International Conference on Algorithms and Complexity, CIAC 2015 - Paris, France Duration: May 20 2015 → May 22 2015

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9079
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	9th International Conference on Algorithms and Complexity, CIAC 2015
Country/Territory	France
City	Paris
Period	5/20/15 → 5/22/15

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
Computer Science(all)

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10.1007/978-3-319-18173-8_29

Cite this

Tamakoshi, Y., Goto, K., Inenaga, S., Bannai, H., & Takeda, M. (2015). An opportunistic text indexing structure based on run length encoding. In P. Widmayer, & V. T. Paschos (Eds.), Algorithms and Complexity - 9th International Conference, CIAC 2015, Proceedings (pp. 390-402). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9079). Springer Verlag. https://doi.org/10.1007/978-3-319-18173-8_29

An opportunistic text indexing structure based on run length encoding. / Tamakoshi, Yuya; Goto, Keisuke; Inenaga, Shunsuke et al.
Algorithms and Complexity - 9th International Conference, CIAC 2015, Proceedings. ed. / Peter Widmayer; Vangelis Th. Paschos. Springer Verlag, 2015. p. 390-402 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9079).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Tamakoshi, Y, Goto, K, Inenaga, S, Bannai, H & Takeda, M 2015, An opportunistic text indexing structure based on run length encoding. in P Widmayer & VT Paschos (eds), Algorithms and Complexity - 9th International Conference, CIAC 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9079, Springer Verlag, pp. 390-402, 9th International Conference on Algorithms and Complexity, CIAC 2015, Paris, France, 5/20/15. https://doi.org/10.1007/978-3-319-18173-8_29

Tamakoshi Y, Goto K, Inenaga S, Bannai H, Takeda M. An opportunistic text indexing structure based on run length encoding. In Widmayer P, Paschos VT, editors, Algorithms and Complexity - 9th International Conference, CIAC 2015, Proceedings. Springer Verlag. 2015. p. 390-402. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-18173-8_29

Tamakoshi, Yuya ; Goto, Keisuke ; Inenaga, Shunsuke et al. / An opportunistic text indexing structure based on run length encoding. Algorithms and Complexity - 9th International Conference, CIAC 2015, Proceedings. editor / Peter Widmayer ; Vangelis Th. Paschos. Springer Verlag, 2015. pp. 390-402 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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AB - We present a new text indexing structure based on the run length encoding (RLE) of a text string T which, given the RLE of a query pattern P, reports all the occ occurrences of P in T in O(m+occ+log n) time, where n and m are the sizes of the RLEs of T and P, respectively. The data structure requires n(2 logN+log n+log σ)+O(n) bits of space, where N is the length of the uncompressed text string T and σ is the alphabet size. Moreover, using n(3 logN + logn + logσ) + 2σ log N/σ + O(n log log n) bits of total space, our data structure can be enhanced to answer the beginning position of the lexicographically ith smallest suffix of T for a given rank i in O(log2 n) time. All these data structures can be constructed in O(n log n) time using O(n logN) bits of extra space.

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An opportunistic text indexing structure based on run length encoding

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