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Semi-dynamic Compact Index for Short Patterns and Succinct van Emde Boas Tree

  • Yoshiaki Matsuoka
  • Tomohiro I
  • Shunsuke Inenaga
  • Hideo Bannai
  • Masayuki Takeda
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9133)

Abstract

We present a compact semi-dynamic text index which allows us to find short patterns efficiently. For parameters \(k\le q \le \log _\sigma n - \log _\sigma \log _\sigma n\) and alphabet size \(\sigma = O(\mathrm {polylog}(n))\), all \( occ \) occurrences of a pattern of length at most \(q-k+1\) can be obtained in \(O(k \times occ + \log _\sigma n)\) time, where \(n\) is the length of the text. Adding characters to the end of the text is supported in amortized constant time. Our index requires \((n/k) \log (n/k) + n \log \sigma + o(n)\) bits of space, which is compact (i.e., \(O(n \log \sigma )\)) when \(k = \varTheta (\log _{\sigma } n)\). As a byproduct, we present a succinct van Emde Boas tree which supports insertion, deletion, predecessor, and successor on a dynamic set of integers over the universe \([0, m-1]\) in \(O(\log \log m)\) time and requires only \(m + o(m)\) bits of space.

Keywords

Transition Graph Suffix Tree Alphabet Size Suffix Array Short Pattern 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Yoshiaki Matsuoka
    • 1
  • Tomohiro I
    • 2
  • Shunsuke Inenaga
    • 1
  • Hideo Bannai
    • 1
  • Masayuki Takeda
    • 1
  1. 1.Department of InformaticsKyushu UniversityFukuokaJapan
  2. 2.Department of Computer ScienceTU DortmundDortmundGermany

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