abydos/distance/_chord.py
# Copyright 2018-2020 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._chord.
Chord distance
"""
from typing import Any, Optional
from ._token_distance import _TokenDistance
from ..tokenizer import _Tokenizer
__all__ = ['Chord']
class Chord(_TokenDistance):
r"""Chord distance.
For two sets X and Y drawn from an alphabet S, the chord distance
:cite:`Orloci:1967` is
.. math::
sim_{chord}(X, Y) =
\sqrt{\sum_{i \in S}\Big(\frac{X_i}{\sqrt{\sum_{j \in X} X_j^2}} -
\frac{Y_i}{\sqrt{\sum_{j \in Y} Y_j^2}}\Big)^2}
.. versionadded:: 0.4.0
"""
def __init__(
self,
tokenizer: Optional[_Tokenizer] = None,
intersection_type: str = 'crisp',
**kwargs: Any
) -> None:
"""Initialize Chord instance.
Parameters
----------
tokenizer : _Tokenizer
A tokenizer instance from the :py:mod:`abydos.tokenizer` package
intersection_type : str
Specifies the intersection type, and set type as a result:
See :ref:`intersection_type <intersection_type>` description in
:py:class:`_TokenDistance` for details.
**kwargs
Arbitrary keyword arguments
Other Parameters
----------------
qval : int
The length of each q-gram. Using this parameter and tokenizer=None
will cause the instance to use the QGram tokenizer with this
q value.
metric : _Distance
A string distance measure class for use in the ``soft`` and
``fuzzy`` variants.
threshold : float
A threshold value, similarities above which are counted as
members of the intersection for the ``fuzzy`` variant.
.. versionadded:: 0.4.0
"""
super(Chord, self).__init__(
tokenizer=tokenizer, intersection_type=intersection_type, **kwargs
)
def dist_abs(self, src: str, tar: str) -> float:
"""Return the Chord distance of two strings.
Parameters
----------
src : str
Source string (or QGrams/Counter objects) for comparison
tar : str
Target string (or QGrams/Counter objects) for comparison
Returns
-------
float
Chord distance
Examples
--------
>>> cmp = Chord()
>>> cmp.dist_abs('cat', 'hat')
1.0
>>> cmp.dist_abs('Niall', 'Neil')
1.126811100699571
>>> cmp.dist_abs('aluminum', 'Catalan')
1.336712116966249
>>> cmp.dist_abs('ATCG', 'TAGC')
1.414213562373095
.. versionadded:: 0.4.0
"""
self._tokenize(src, tar)
alphabet = self._total().keys()
den1 = max(
1, sum(val * val for val in self._src_tokens.values()) ** 0.5
)
den2 = max(
1, sum(val * val for val in self._tar_tokens.values()) ** 0.5
)
return round(
sum(
(self._src_tokens[i] / den1 - self._tar_tokens[i] / den2) ** 2
for i in alphabet
)
** 0.5,
15,
)
def dist(self, src: str, tar: str) -> float:
"""Return the normalized Chord distance of two strings.
Parameters
----------
src : str
Source string (or QGrams/Counter objects) for comparison
tar : str
Target string (or QGrams/Counter objects) for comparison
Returns
-------
float
Normalized chord distance
Examples
--------
>>> cmp = Chord()
>>> cmp.dist('cat', 'hat')
0.707106781186547
>>> cmp.dist('Niall', 'Neil')
0.796775770420944
>>> cmp.dist('aluminum', 'Catalan')
0.94519820240106
>>> cmp.dist('ATCG', 'TAGC')
1.0
.. versionadded:: 0.4.0
"""
return round(self.dist_abs(src, tar) / (2 ** 0.5), 15)
if __name__ == '__main__':
import doctest
doctest.testmod()