Source code for abydos.distance._ncd_bwtrle

# Copyright 2014-2020 by Christopher C. Little.
# This file is part of Abydos.
#
# Abydos is free software: you can redistribute it and/or modify
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"""abydos.distance._ncd_bwtrle.

NCD using BWT plus RLE
"""

from ._ncd_rle import NCDrle
from ..compression import BWT

__all__ = ['NCDbwtrle']


[docs]class NCDbwtrle(NCDrle): """Normalized Compression Distance using BWT plus RLE. Cf. https://en.wikipedia.org/wiki/Burrows-Wheeler_transform Normalized compression distance (NCD) :cite:`Cilibrasi:2005`. .. versionadded:: 0.3.6 """ _bwt = BWT()
[docs] def dist(self, src: str, tar: str) -> float: """Return the NCD between two strings using BWT plus RLE. Parameters ---------- src : str Source string for comparison tar : str Target string for comparison Returns ------- float Compression distance Examples -------- >>> cmp = NCDbwtrle() >>> cmp.dist('cat', 'hat') 0.75 >>> cmp.dist('Niall', 'Neil') 0.8333333333333334 >>> cmp.dist('aluminum', 'Catalan') 1.0 >>> cmp.dist('ATCG', 'TAGC') 0.8 .. versionadded:: 0.3.5 .. versionchanged:: 0.3.6 Encapsulated in class """ if src == tar: return 0.0 src_comp = self._rle.encode(self._bwt.encode(src)) tar_comp = self._rle.encode(self._bwt.encode(tar)) concat_comp = self._rle.encode(self._bwt.encode(src + tar)) concat_comp2 = self._rle.encode(self._bwt.encode(tar + src)) return ( min(len(concat_comp), len(concat_comp2)) - min(len(src_comp), len(tar_comp)) ) / max(len(src_comp), len(tar_comp))
if __name__ == '__main__': import doctest doctest.testmod()