# 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_rle.
NCD using RLE
"""
from deprecation import deprecated
from ._distance import _Distance
from .. import __version__
from ..compression import RLE
__all__ = ['NCDrle', 'dist_ncd_rle', 'sim_ncd_rle']
[docs]class NCDrle(_Distance):
"""Normalized Compression Distance using RLE.
Cf. https://en.wikipedia.org/wiki/Run-length_encoding
Normalized compression distance (NCD) :cite:`Cilibrasi:2005`.
.. versionadded:: 0.3.6
"""
_rle = RLE()
[docs] def dist(self, src, tar):
"""Return the NCD between two strings using RLE.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression distance
Examples
--------
>>> cmp = NCDrle()
>>> cmp.dist('cat', 'hat')
1.0
>>> cmp.dist('Niall', 'Neil')
1.0
>>> cmp.dist('aluminum', 'Catalan')
1.0
>>> cmp.dist('ATCG', 'TAGC')
1.0
.. versionadded:: 0.3.5
.. versionchanged:: 0.3.6
Encapsulated in class
"""
if src == tar:
return 0.0
src_comp = self._rle.encode(src)
tar_comp = self._rle.encode(tar)
concat_comp = self._rle.encode(src + tar)
concat_comp2 = self._rle.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 NCDrle.dist method instead.',
)
def dist_ncd_rle(src, tar):
"""Return the NCD between two strings using RLE.
This is a wrapper for :py:meth:`NCDrle.dist`.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression distance
Examples
--------
>>> dist_ncd_rle('cat', 'hat')
1.0
>>> dist_ncd_rle('Niall', 'Neil')
1.0
>>> dist_ncd_rle('aluminum', 'Catalan')
1.0
>>> dist_ncd_rle('ATCG', 'TAGC')
1.0
.. versionadded:: 0.3.5
"""
return NCDrle().dist(src, tar)
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the NCDrle.sim method instead.',
)
def sim_ncd_rle(src, tar):
"""Return the NCD similarity between two strings using RLE.
This is a wrapper for :py:meth:`NCDrle.sim`.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression similarity
Examples
--------
>>> sim_ncd_rle('cat', 'hat')
0.0
>>> sim_ncd_rle('Niall', 'Neil')
0.0
>>> sim_ncd_rle('aluminum', 'Catalan')
0.0
>>> sim_ncd_rle('ATCG', 'TAGC')
0.0
.. versionadded:: 0.3.5
"""
return NCDrle().sim(src, tar)
if __name__ == '__main__':
import doctest
doctest.testmod()