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# Copyright 2019-2020 by Christopher C. Little. |
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# This file is part of Abydos. |
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# |
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# Abydos is free software: you can redistribute it and/or modify |
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# it under the terms of the GNU General Public License as published by |
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# the Free Software Foundation, either version 3 of the License, or |
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# (at your option) any later version. |
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# |
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# Abydos is distributed in the hope that it will be useful, |
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# but WITHOUT ANY WARRANTY; without even the implied warranty of |
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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# GNU General Public License for more details. |
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# |
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# You should have received a copy of the GNU General Public License |
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# along with Abydos. If not, see <http://www.gnu.org/licenses/>. |
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"""abydos.distance._flexmetric. |
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FlexMetric distance |
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""" |
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from typing import ( |
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Any, |
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Callable, |
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FrozenSet, |
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List, |
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Optional, |
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Sequence, |
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Set, |
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Tuple, |
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Union, |
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cast, |
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) |
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from numpy import float_ as np_float |
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from numpy import zeros as np_zeros |
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from ._distance import _Distance |
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__all__ = ['FlexMetric'] |
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class FlexMetric(_Distance): |
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r"""FlexMetric distance. |
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FlexMetric distance :cite:`Kempken:2005` |
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1 |
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.. versionadded:: 0.4.0 |
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""" |
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def __init__( |
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self, |
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normalizer: Callable[[List[float]], float] = max, |
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indel_costs: Optional[ |
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List[Tuple[Union[Sequence[str], Set[str], FrozenSet[str]], float]] |
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] = None, |
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subst_costs: Optional[ |
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List[Tuple[Union[Sequence[str], Set[str], FrozenSet[str]], float]] |
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] = None, |
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**kwargs: Any |
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) -> None: |
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"""Initialize FlexMetric instance. |
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Parameters |
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---------- |
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normalizer : function |
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A function that takes an list and computes a normalization term |
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by which the edit distance is divided (max by default). Another |
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good option is the sum function. |
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indel_costs : list of tuples |
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A list of insertion and deletion costs. Each list element should |
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be a tuple consisting of an iterable (sets are best) and a float |
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value. The iterable consists of those letters whose insertion |
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or deletion has a cost equal to the float value. |
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subst_costs : list of tuples |
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A list of substitution costs. Each list element should |
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be a tuple consisting of an iterable (sets are best) and a float |
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value. The iterable consists of the letters in each letter class, |
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which may be substituted for each other at cost equal to the float |
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value. |
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**kwargs |
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Arbitrary keyword arguments |
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.. versionadded:: 0.4.0 |
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""" |
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super(FlexMetric, self).__init__(**kwargs) |
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self._normalizer = normalizer |
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def _get_second( |
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s: Tuple[Union[Sequence[str], Set[str], FrozenSet[str]], float] |
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) -> float: |
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return s[1] |
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if indel_costs is None: |
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self._indel_costs = [ |
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(frozenset('dtch'), 0.4), |
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(frozenset('e'), 0.5), |
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(frozenset('u'), 0.9), |
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(frozenset('rpn'), 0.95), |
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] # type: List[Tuple[Union[Sequence[str], Set[str], FrozenSet[str]], float]] # noqa: E501 |
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else: |
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self._indel_costs = sorted(indel_costs, key=_get_second) |
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if subst_costs is None: |
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self._subst_costs = [ |
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(frozenset('szß'), 0.1), |
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(frozenset('dt'), 0.1), |
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(frozenset('iy'), 0.1), |
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(frozenset('ckq'), 0.1), |
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(frozenset('eä'), 0.1), |
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(frozenset('uüv'), 0.1), |
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(frozenset('iü'), 0.1), |
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(frozenset('fv'), 0.1), |
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(frozenset('zc'), 0.1), |
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(frozenset('ij'), 0.1), |
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(frozenset('bp'), 0.1), |
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(frozenset('eoö'), 0.2), |
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(frozenset('aä'), 0.2), |
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(frozenset('mbp'), 0.4), |
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(frozenset('uw'), 0.4), |
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(frozenset('uo'), 0.8), |
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(frozenset('aeiouy'), 0.9), |
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] # type: List[Tuple[Union[Sequence[str], Set[str], FrozenSet[str]], float]] # noqa: E501 |
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else: |
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self._subst_costs = sorted(subst_costs, key=_get_second) |
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def _cost(self, src: str, s_pos: int, tar: str, t_pos: int) -> float: |
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if s_pos == -1: |
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if t_pos > 0 and tar[t_pos - 1] == tar[t_pos]: |
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return 0.0 |
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for letter_set in self._indel_costs: |
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if tar[t_pos] in letter_set[0]: |
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return letter_set[1] |
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else: |
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return 1.0 |
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elif t_pos == -1: |
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if s_pos > 0 and src[s_pos - 1] == src[s_pos]: |
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return 0.0 |
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for letter_set in self._indel_costs: |
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if src[s_pos] in letter_set[0]: |
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return letter_set[1] |
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else: |
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return 1.0 |
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for letter_set in self._subst_costs: |
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if src[s_pos] in letter_set[0] and tar[t_pos] in letter_set[0]: |
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return letter_set[1] |
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else: |
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return 1.0 |
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def dist_abs(self, src: str, tar: str) -> float: |
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"""Return the FlexMetric distance of two strings. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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Returns |
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------- |
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float |
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FlexMetric distance |
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Examples |
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-------- |
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>>> cmp = FlexMetric() |
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>>> cmp.dist_abs('cat', 'hat') |
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0.8 |
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>>> cmp.dist_abs('Niall', 'Neil') |
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1.5 |
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>>> cmp.dist_abs('aluminum', 'Catalan') |
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6.7 |
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>>> cmp.dist_abs('ATCG', 'TAGC') |
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2.1999999999999997 |
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.. versionadded:: 0.4.0 |
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""" |
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src_len = len(src) |
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tar_len = len(tar) |
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if src == tar: |
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return 0 |
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if not src: |
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return sum(self._cost('', -1, tar, j) for j in range(len(tar))) |
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if not tar: |
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return sum(self._cost(src, i, '', -1) for i in range(len(src))) |
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d_mat = np_zeros((src_len + 1, tar_len + 1), dtype=np_float) |
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for i in range(1, src_len + 1): |
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d_mat[i, 0] = d_mat[i - 1, 0] + self._cost(src, i - 1, '', -1) |
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for j in range(1, tar_len + 1): |
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d_mat[0, j] = d_mat[0, j - 1] + self._cost('', -1, tar, j - 1) |
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src_lc = src.lower() |
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tar_lc = tar.lower() |
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for i in range(src_len): |
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for j in range(tar_len): |
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d_mat[i + 1, j + 1] = min( |
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d_mat[i + 1, j] + self._cost('', -1, tar_lc, j), # ins |
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d_mat[i, j + 1] + self._cost(src_lc, i, '', -1), # del |
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d_mat[i, j] |
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+ ( |
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self._cost(src_lc, i, tar_lc, j) |
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if src[i] != tar[j] |
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else 0 |
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), # sub/== |
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) |
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return cast(float, d_mat[src_len, tar_len]) |
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def dist(self, src: str, tar: str) -> float: |
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"""Return the normalized FlexMetric distance of two strings. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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Returns |
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------- |
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float |
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Normalized FlexMetric distance |
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Examples |
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-------- |
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>>> cmp = FlexMetric() |
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>>> cmp.dist('cat', 'hat') |
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0.26666666666666666 |
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>>> cmp.dist('Niall', 'Neil') |
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0.3 |
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>>> cmp.dist('aluminum', 'Catalan') |
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0.8375 |
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>>> cmp.dist('ATCG', 'TAGC') |
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0.5499999999999999 |
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.. versionadded:: 0.4.0 |
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""" |
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score = self.dist_abs(src, tar) |
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if score: |
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return score / self._normalizer([len(src), len(tar)]) |
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return 0.0 |
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if __name__ == '__main__': |
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import doctest |
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doctest.testmod() |
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chrislit /
abydos
