Suffix array: Difference between revisions

Revision as of 00:21, 3 October 2021

Revision as of 03:09, 5 October 2021

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Recent work by {{harvtxt|Salson|Lecroq|Léonard|Mouchard|2010}} proposes an algorithm for updating the suffix array of a text that has been edited instead of rebuilding a new suffix array from scratch. Even if the theoretical worst-case time complexity is <math>\mathcal{O}(n \log n)</math>, it appears to perform well in practice: experimental results from the authors showed that their implementation of dynamic suffix arrays is generally more efficient than rebuilding when considering the insertion of a reasonable number of letters in the original text.

In practical [[open source]] work, a commonly used routine for suffix array construction was qsufsort, based on the 1999 Larsson-Sadakane algorithm.<ref>{{cite journal |last1=Larsson |first1=N. Jesper |last2=Sadakane |first2=Kunihiko |title=Faster suffix sorting |journal=Theoretical Computer Science |date=22 November 2007 |volume=387 |issue=3 |pages=258–272 |doi=10.1016/j.tcs.2007.07.017 |language=en |issn=0304-3975|doi-access=free }}</ref> This routine has been superseded by Yuta Mori's DivSufSort, "the fastest known suffix sorting algorithm in main memory" as of 2017. It too can be modified to compute an LCP array. It uses a induced copying combined with Itoh-Tanaka.<ref>{{cite journal |last1=Fischer |first1=Johannes |last2=Kurpicz |first2=Florian |title=Dismantling DivSufSort |arxiv=1710.01896 |date=5 October 2017 |journal=Proceedings of the Prague Stringology Conference 2017}}</ref> In 2021 a faster implementation of the algorithm was presented by Ilya Grebnov <ref>{{Cite web|title=New saca and bwt library (libsais)|url=https://encode.su/threads/3579-New-saca-and-bwt-library-(libsais)|access-date=2021-10-03|website=encode.su}}</ref> which in average showed 65% performance improvement over DivSufSort implementation on Silesia Corpus.<ref>{{Citation|last=Grebnov|first=Ilya|title=libsais|date=2021-09-22|url=https://github.com/IlyaGrebnov/libsais|access-date=2021-10-02}}</ref>.

== Generalized Suffix Array ==