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Computing All Distinct Squares in Linear Time for Integer Alphabets

Authors Hideo Bannai, Shunsuke Inenaga, Dominik Köppl



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Hideo Bannai
Shunsuke Inenaga
Dominik Köppl

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Hideo Bannai, Shunsuke Inenaga, and Dominik Köppl. Computing All Distinct Squares in Linear Time for Integer Alphabets. In 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 78, pp. 22:1-22:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2017)
https://doi.org/10.4230/LIPIcs.CPM.2017.22

Abstract

Given a string on an integer alphabet, we present an algorithm that computes the set of all distinct squares belonging to this string in time linear to the string length. As an application, we show how to compute the tree topology of the minimal augmented suffix tree in linear time. Asides from that, we elaborate an algorithm computing the longest previous table in a succinct representation using compressed working space.
Keywords
  • tandem repeats
  • distinct squares
  • counting algorithms

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