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Stringology-Rust

automatic test

This project contains some simple and easy-to-use tools for studying of strings whose characters are drawn from the byte alphabet. It currently consists of

  • analytic tools
    • lyndonfactorization : counts the number of Lyndon factors. Outputs all ending positions of Lyndon factors when setting the environment variable RUST_LOG=debug
    • count_r : counts the number of runs in the BWT obtained by the suffix array
    • count_sigma : counts the number of different characters
    • count_z : counts the number of overlapping LZ77 factors
    • entropy : counts the k-th order empirical entropy
    • entropykmer : counts the k-th order empirical entropy via k-mers, k \in [1..7]
  • word generators with program word
    • thuemorse : computes the n-th Thue-Morse word
    • fibonacci : computes the n-th Fibonacci word
    • perioddoubling computes the n-th period-doubling sequence
    • debruijn : computes a binary de Bruijin word of order n
      • FibonacciLyndonFactor : the n-th Lyndon factor of the infinite Fibonacci word
  • lyndonwords to generate all Lyndon words up to a specific length for a given alphabet size
  • transforms
    • reverse : reverse the input byte-wise

Usage

Compile and run with cargo of rust-lang:

cargo build
cargo run --bin count_sigma -- --file ./data/tudocomp/einstein.en.txt

compute the 5th Fibonacci word

cargo run --bin word -- -n fibonacci -k 5

Datasets can be found at http://dolomit.cs.tu-dortmund.de/tudocomp/

The output format of the analytic tools is compatible with sqlplot.

CAVEATS

  • The BWT computation requires that the zero byte does not occur in your input. To enforce that, you can use the escape program to escape all zero bytes. For instance, escape -f 0 -t 255 -e 254 | count_r escapes 0 with the escape byte 254 to byte 255, and pipes the input to count_r counting the number of BWT runs.