Paquet : libxxsds-dynamic-dev (1.0~alpha.1+git20210426.548c6f7-1)

[ Paquet source : xxsds-dynamic  ]

succinct and compressed fully-dynamic data structures library

This library offers space- and time-efficient implementations of some basic succinct/compressed dynamic data structures. It only ships header files, i.e. is inclusion only.

DYNAMIC features:

 * A succinct Searchable Partial Sums with Indels (SPSI) structure
   representing a list of integers s_1, s_2, ..., s_m. Space: about
    1.2 * m * ( log(M/m) + log log m )
   bits, where
    M = m + s_1 + s_2 + ... + s_m.
   The structure supports also update operations (i.e. s_i = s_i + delta).
 * A Succinct dynamic bitvector supporting rank/select/access/Indel
   (RSAI) operations. Space: about 1.2 * n bits.
 * A gap-compressed dynamic bitvector supporting rank/select/access/Indel
   operations. Space: about 1.2 * b * ( log(n/b) + log log b ) bits,
   b being the number of bits set and n being the bitvector length. All
   operations take log(b) time.
 * A dynamic sparse vector (of integers) with access/Indel operations.
 * A dynamic string supporting rank/select/access/Indel operations. The
   user can choose at construction time between
   fixed-length/gamma/Huffman encoding of the alphabet. All operations
   take log(n) * log(sigma) time (or log(n) * H0 with Huffman encoding).
 * A run-length encoded dynamic string supporting
   rank/select/access/insert operations (removes are not yet
   implemented). Space: approximately
    R*(1.2 * log(sigma) + 2.4 * (log(n/R)+log log R) )
   bits, where R is the number of runs in the string. All operations
   take log(R) time.
 * A dynamic (left-extend only) entropy/run-length compressed BWT
 * A dynamic (left-extend only) entropy/run-length compressed
   FM-index. This structure consists in the above BWT + a dynamic suffix
   array sampling

Algorithms

 * Two algorithms to build LZ77 in repetition-aware RAM working
   space. Both algorithms use a run-length encoded BWT with sparse
   Suffix array sampling. The first algorithm stores 2 SA samples per
   BWT run. The second algorithm (much more space efficient) stores
   1 SA sample per LZ factor. From the papers "Computing LZ77 in
   Run-Compressed Space", Alberto Policriti and Nicola Prezza, DCC2016
   and " LZ77 Computation Based on the Run-Length Encoded BWT", Alberto
   Policriti and Nicola Prezza (Algorithmica)
 * An algorithm to build the BWT in run-compressed space
 * An algorithm to build LZ77 in nH0(2+o(1)) space and n * log n *
   H0 time. From the paper "Fast Online Lempel-Ziv Factorization in
   Compressed Space", Alberto Policriti and Nicola Prezza, SPIRE2015
 * An algorithm to build the BWT in high-order compressed space. The
   algorithm runs in O(n * H_k * log log n) average-case time (e.g. good
   for DNA) and O(n * H_k * log n) worst-case time. From the paper
   "Average linear time and compressed space construction of the
   Burrows-Wheeler transform" Policriti A., Gigante N. and Prezza N.,
   LATA 2015 (the paper discusses a theoretically faster variant)

The SPSI structure is the building block on which all other structures are based. This structure is implemented with cache-efficient B-trees.

Étiquettes: Développement de logiciel: Bibliothèques, Rôle: Bibliothèque de programmation

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