abydos.distance._lcsstr.LCSstr.sim() - Code Metrics - Inspection of "0.3.6" - chrislit/abydos - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — master (#149)

by Chris

created 2018-11-17 08:37 UTC

abydos.distance._lcsstr.LCSstr.sim() A

↳ Parent: abydos.distance._lcsstr

Complexity

Conditions

Size

Total Lines	37
Code Lines	6

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	6
CRAP Score	4

Importance

Changes

Metric	Value
cc	4
eloc	6
nop	3
dl	0
loc	37
ccs	6
cts	6
cp	1
crap	4
rs	10
c	0
b	0
f	0

# -*- coding: utf-8 -*-

# Copyright 2014-2018 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._lcsstr.

Longest common substring
"""

from __future__ import (
    absolute_import,
    division,
    print_function,
    unicode_literals,
)

from numpy import int as np_int
from numpy import zeros as np_zeros

from six.moves import range

from ._distance import _Distance

__all__ = ['LCSstr', 'dist_lcsstr', 'lcsstr', 'sim_lcsstr']


class LCSstr(_Distance):

    """Longest common substring."""

    def lcsstr(self, src, tar):
class Foo:
    def some_method(self, x, y):
        return x + y;
        """Return the longest common substring of two strings.

        Longest common substring (LCSstr).

        Based on the code from
        https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Longest_common_substring
        :cite:`Wikibooks:2018`.
        This is licensed Creative Commons: Attribution-ShareAlike 3.0.

        Modifications include:

            - conversion to a numpy array in place of a list of lists
            - conversion to Python 2/3-safe range from xrange via six

        Parameters
        ----------
        src : str
            Source string for comparison
        tar : str
            Target string for comparison

        Returns
        -------
        str
            The longest common substring

        Examples
        --------
        >>> sstr = LCSstr()
        >>> sstr.lcsstr('cat', 'hat')
        'at'
        >>> sstr.lcsstr('Niall', 'Neil')
        'N'
        >>> sstr.lcsstr('aluminum', 'Catalan')
        'al'
        >>> sstr.lcsstr('ATCG', 'TAGC')
        'A'

        """
        lengths = np_zeros((len(src) + 1, len(tar) + 1), dtype=np_int)
        longest, i_longest = 0, 0
        for i in range(1, len(src) + 1):
            for j in range(1, len(tar) + 1):
                if src[i - 1] == tar[j - 1]:
                    lengths[i, j] = lengths[i - 1, j - 1] + 1
                    if lengths[i, j] > longest:
                        longest = lengths[i, j]
                        i_longest = i
                else:
                    lengths[i, j] = 0
        return src[i_longest - longest : i_longest]

    def sim(self, src, tar):

        r"""Return the longest common substring similarity of two strings.

        Longest common substring similarity (:math:`sim_{LCSstr}`).

        This employs the LCS function to derive a similarity metric:
        :math:`sim_{LCSstr}(s,t) = \frac{|LCSstr(s,t)|}{max(|s|, |t|)}`

        Parameters
        ----------
        src : str
            Source string for comparison
        tar : str
            Target string for comparison

        Returns
        -------
        float
            LCSstr similarity

        Examples
        --------
        >>> sim_lcsstr('cat', 'hat')
        0.6666666666666666
        >>> sim_lcsstr('Niall', 'Neil')
        0.2
        >>> sim_lcsstr('aluminum', 'Catalan')
        0.25
        >>> sim_lcsstr('ATCG', 'TAGC')
        0.25

        """
        if src == tar:
            return 1.0
        elif not src or not tar:
            return 0.0
        return len(self.lcsstr(src, tar)) / max(len(src), len(tar))


def lcsstr(src, tar):
    """Return the longest common substring of two strings.

    This is a wrapper for :py:meth:`LCSstr.lcsstr`.

    Parameters
    ----------
    src : str
        Source string for comparison
    tar : str
        Target string for comparison

    Returns
    -------
    str
        The longest common substring

    Examples
    --------
    >>> lcsstr('cat', 'hat')
    'at'
    >>> lcsstr('Niall', 'Neil')
    'N'
    >>> lcsstr('aluminum', 'Catalan')
    'al'
    >>> lcsstr('ATCG', 'TAGC')
    'A'

    """
    return LCSstr().lcsstr(src, tar)


def sim_lcsstr(src, tar):
    """Return the longest common substring similarity of two strings.

    This is a wrapper for :py:meth:`LCSstr.sim`.

    Parameters
    ----------
    src : str
        Source string for comparison
    tar : str
        Target string for comparison

    Returns
    -------
    float
        LCSstr similarity

    Examples
    --------
    >>> sim_lcsstr('cat', 'hat')
    0.6666666666666666
    >>> sim_lcsstr('Niall', 'Neil')
    0.2
    >>> sim_lcsstr('aluminum', 'Catalan')
    0.25
    >>> sim_lcsstr('ATCG', 'TAGC')
    0.25

    """
    return LCSstr().sim(src, tar)


def dist_lcsstr(src, tar):
    """Return the longest common substring distance between two strings.

    This is a wrapper for :py:meth:`LCSstr.dist`.

    Parameters
    ----------
    src : str
        Source string for comparison
    tar : str
        Target string for comparison

    Returns
    -------
    float
        LCSstr distance

    Examples
    --------
    >>> dist_lcsstr('cat', 'hat')
    0.33333333333333337
    >>> dist_lcsstr('Niall', 'Neil')
    0.8
    >>> dist_lcsstr('aluminum', 'Catalan')
    0.75
    >>> dist_lcsstr('ATCG', 'TAGC')
    0.75

    """
    return LCSstr().dist(src, tar)


if __name__ == '__main__':
    import doctest

    doctest.testmod()


1		# -- coding: utf-8 --
2
3		# Copyright 2014-2018 by Christopher C. Little.
4		# This file is part of Abydos.
5		#
6		# Abydos is free software: you can redistribute it and/or modify
7		# it under the terms of the GNU General Public License as published by
8		# the Free Software Foundation, either version 3 of the License, or
9		# (at your option) any later version.
10		#
11		# Abydos is distributed in the hope that it will be useful,
12		# but WITHOUT ANY WARRANTY; without even the implied warranty of
13		# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14		# GNU General Public License for more details.
15		#
16		# You should have received a copy of the GNU General Public License
17		# along with Abydos. If not, see <http://www.gnu.org/licenses/>.
18
19	1	"""abydos.distance._lcsstr.
20
21		Longest common substring
22		"""
23
24	1	from __future__ import (
25		absolute_import,
26		division,
27		print_function,
28		unicode_literals,
29		)
30
31	1	from numpy import int as np_int
32	1	from numpy import zeros as np_zeros
33
34	1	from six.moves import range
35
36	1	from ._distance import _Distance
37
38	1	__all__ = ['LCSstr', 'dist_lcsstr', 'lcsstr', 'sim_lcsstr']
39
40
41	1	class LCSstr(_Distance):
		0 ignored issues – show Unused Code introduced 2018-11-10 01:42 UTC by Report Bug Copy Issue Report The variable `__class__` seems to be unused. Loading history...
42		"""Longest common substring."""
43
44	1	def lcsstr(self, src, tar):
		0 ignored issues – show Coding Style introduced 2018-11-04 08:02 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
45		"""Return the longest common substring of two strings.
46
47		Longest common substring (LCSstr).
48
49		Based on the code from
50		https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Longest_common_substring
51		:cite:`Wikibooks:2018`.
52		This is licensed Creative Commons: Attribution-ShareAlike 3.0.
53
54		Modifications include:
55
56		- conversion to a numpy array in place of a list of lists
57		- conversion to Python 2/3-safe range from xrange via six
58
59		Parameters
60		----------
61		src : str
62		Source string for comparison
63		tar : str
64		Target string for comparison
65
66		Returns
67		-------
68		str
69		The longest common substring
70
71		Examples
72		--------
73		>>> sstr = LCSstr()
74		>>> sstr.lcsstr('cat', 'hat')
75		'at'
76		>>> sstr.lcsstr('Niall', 'Neil')
77		'N'
78		>>> sstr.lcsstr('aluminum', 'Catalan')
79		'al'
80		>>> sstr.lcsstr('ATCG', 'TAGC')
81		'A'
82
83		"""
84	1	lengths = np_zeros((len(src) + 1, len(tar) + 1), dtype=np_int)
85	1	longest, i_longest = 0, 0
86	1	for i in range(1, len(src) + 1):
87	1	for j in range(1, len(tar) + 1):
88	1	if src[i - 1] == tar[j - 1]:
89	1	lengths[i, j] = lengths[i - 1, j - 1] + 1
90	1	if lengths[i, j] > longest:
91	1	longest = lengths[i, j]
92	1	i_longest = i
93		else:
94	1	lengths[i, j] = 0
95	1	return src[i_longest - longest : i_longest]
96
97	1	def sim(self, src, tar):
		0 ignored issues – show Bug introduced 2018-11-04 08:02 UTC by Report Bug Copy Issue Report Parameters differ from overridden 'sim' method Loading history...
98		r"""Return the longest common substring similarity of two strings.
99
100		Longest common substring similarity (:math:`sim_{LCSstr}`).
101
102		This employs the LCS function to derive a similarity metric:
103		:math:`sim_{LCSstr}(s,t) = \frac{\|LCSstr(s,t)\|}{max(\|s\|, \|t\|)}`
104
105		Parameters
106		----------
107		src : str
108		Source string for comparison
109		tar : str
110		Target string for comparison
111
112		Returns
113		-------
114		float
115		LCSstr similarity
116
117		Examples
118		--------
119		>>> sim_lcsstr('cat', 'hat')
120		0.6666666666666666
121		>>> sim_lcsstr('Niall', 'Neil')
122		0.2
123		>>> sim_lcsstr('aluminum', 'Catalan')
124		0.25
125		>>> sim_lcsstr('ATCG', 'TAGC')
126		0.25
127
128		"""
129	1	if src == tar:
130	1	return 1.0
131	1	elif not src or not tar:
132	1	return 0.0
133	1	return len(self.lcsstr(src, tar)) / max(len(src), len(tar))
134
135
136	1	def lcsstr(src, tar):
137		"""Return the longest common substring of two strings.
138
139		This is a wrapper for :py:meth:`LCSstr.lcsstr`.
140
141		Parameters
142		----------
143		src : str
144		Source string for comparison
145		tar : str
146		Target string for comparison
147
148		Returns
149		-------
150		str
151		The longest common substring
152
153		Examples
154		--------
155		>>> lcsstr('cat', 'hat')
156		'at'
157		>>> lcsstr('Niall', 'Neil')
158		'N'
159		>>> lcsstr('aluminum', 'Catalan')
160		'al'
161		>>> lcsstr('ATCG', 'TAGC')
162		'A'
163
164		"""
165	1	return LCSstr().lcsstr(src, tar)
166
167
168	1	def sim_lcsstr(src, tar):
169		"""Return the longest common substring similarity of two strings.
170
171		This is a wrapper for :py:meth:`LCSstr.sim`.
172
173		Parameters
174		----------
175		src : str
176		Source string for comparison
177		tar : str
178		Target string for comparison
179
180		Returns
181		-------
182		float
183		LCSstr similarity
184
185		Examples
186		--------
187		>>> sim_lcsstr('cat', 'hat')
188		0.6666666666666666
189		>>> sim_lcsstr('Niall', 'Neil')
190		0.2
191		>>> sim_lcsstr('aluminum', 'Catalan')
192		0.25
193		>>> sim_lcsstr('ATCG', 'TAGC')
194		0.25
195
196		"""
197	1	return LCSstr().sim(src, tar)
198
199
200	1	def dist_lcsstr(src, tar):
201		"""Return the longest common substring distance between two strings.
202
203		This is a wrapper for :py:meth:`LCSstr.dist`.
204
205		Parameters
206		----------
207		src : str
208		Source string for comparison
209		tar : str
210		Target string for comparison
211
212		Returns
213		-------
214		float
215		LCSstr distance
216
217		Examples
218		--------
219		>>> dist_lcsstr('cat', 'hat')
220		0.33333333333333337
221		>>> dist_lcsstr('Niall', 'Neil')
222		0.8
223		>>> dist_lcsstr('aluminum', 'Catalan')
224		0.75
225		>>> dist_lcsstr('ATCG', 'TAGC')
226		0.75
227
228		"""
229	1	return LCSstr().dist(src, tar)
230
231
232		if __name__ == '__main__':
233		import doctest
234
235		doctest.testmod()
236

chrislit / abydos

Pull Request — master (#149)

abydos.distance._lcsstr.LCSstr.sim() A

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