# Copyright 2014-2020 by Christopher C. Little.
# This file is part of Abydos.
#
# Abydos is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Abydos is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Abydos. If not, see <http://www.gnu.org/licenses/>.
"""abydos.distance._ncd_bwtrle.
NCD using BWT plus RLE
"""
from deprecation import deprecated
from ._ncd_rle import NCDrle
from .. import __version__
from ..compression import BWT
__all__ = ['NCDbwtrle', 'dist_ncd_bwtrle', 'sim_ncd_bwtrle']
[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, tar):
"""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))
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the NCDbwtrle.dist method instead.',
)
def dist_ncd_bwtrle(src, tar):
"""Return the NCD between two strings using BWT plus RLE.
This is a wrapper for :py:meth:`NCDbwtrle.dist`.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression distance
Examples
--------
>>> dist_ncd_bwtrle('cat', 'hat')
0.75
>>> dist_ncd_bwtrle('Niall', 'Neil')
0.8333333333333334
>>> dist_ncd_bwtrle('aluminum', 'Catalan')
1.0
>>> dist_ncd_bwtrle('ATCG', 'TAGC')
0.8
.. versionadded:: 0.3.5
"""
return NCDbwtrle().dist(src, tar)
[docs]def sim_ncd_bwtrle(src, tar):
"""Return the NCD similarity between two strings using BWT plus RLE.
This is a wrapper for :py:meth:`NCDbwtrle.sim`.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression similarity
Examples
--------
>>> sim_ncd_bwtrle('cat', 'hat')
0.25
>>> sim_ncd_bwtrle('Niall', 'Neil')
0.16666666666666663
>>> sim_ncd_bwtrle('aluminum', 'Catalan')
0.0
>>> sim_ncd_bwtrle('ATCG', 'TAGC')
0.19999999999999996
.. versionadded:: 0.3.5
"""
return NCDbwtrle().sim(src, tar)
if __name__ == '__main__':
import doctest
doctest.testmod()