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# -*- coding: utf-8 -*- |
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# Copyright 2014-2018 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._indel. |
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Indel distance |
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""" |
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from __future__ import ( |
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absolute_import, |
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division, |
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print_function, |
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unicode_literals, |
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) |
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from ._distance import _Distance |
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from ._levenshtein import Levenshtein |
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__all__ = ['Indel', 'dist_indel', 'indel', 'sim_indel'] |
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class Indel(_Distance): |
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"""Indel distance. |
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This is equivalent to Levenshtein distance, when only inserts and deletes |
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are possible. |
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""" |
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_lev = Levenshtein() |
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def dist_abs(self, src, tar): |
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"""Return the indel distance between 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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int |
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Indel distance |
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Examples |
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-------- |
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>>> cmp = Indel() |
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>>> cmp.dist_abs('cat', 'hat') |
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2 |
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>>> cmp.dist_abs('Niall', 'Neil') |
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3 |
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>>> cmp.dist_abs('Colin', 'Cuilen') |
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5 |
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>>> cmp.dist_abs('ATCG', 'TAGC') |
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4 |
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""" |
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return self._lev.dist_abs( |
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src, tar, mode='lev', cost=(1, 1, 9999, 9999) |
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) |
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def dist(self, src, tar): |
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"""Return the normalized indel distance between two strings. |
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This is equivalent to normalized Levenshtein distance, when only |
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inserts and deletes are possible. |
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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 indel distance |
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Examples |
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-------- |
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>>> cmp = Indel() |
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>>> round(cmp.dist('cat', 'hat'), 12) |
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0.333333333333 |
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>>> round(cmp.dist('Niall', 'Neil'), 12) |
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0.333333333333 |
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>>> round(cmp.dist('Colin', 'Cuilen'), 12) |
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0.454545454545 |
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>>> cmp.dist('ATCG', 'TAGC') |
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0.5 |
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""" |
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if src == tar: |
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return 0.0 |
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return self.dist_abs(src, tar) / (len(src) + len(tar)) |
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def indel(src, tar): |
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"""Return the indel distance between 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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int |
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Indel distance |
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Examples |
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-------- |
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>>> indel('cat', 'hat') |
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2 |
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>>> indel('Niall', 'Neil') |
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3 |
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>>> indel('Colin', 'Cuilen') |
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>>> indel('ATCG', 'TAGC') |
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4 |
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""" |
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return Indel().dist_abs(src, tar) |
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def dist_indel(src, tar): |
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"""Return the normalized indel distance between two strings. |
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This is equivalent to normalized Levenshtein distance, when only inserts |
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and deletes are possible. |
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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 indel distance |
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Examples |
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-------- |
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>>> round(dist_indel('cat', 'hat'), 12) |
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0.333333333333 |
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>>> round(dist_indel('Niall', 'Neil'), 12) |
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0.333333333333 |
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>>> round(dist_indel('Colin', 'Cuilen'), 12) |
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0.454545454545 |
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>>> dist_indel('ATCG', 'TAGC') |
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0.5 |
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""" |
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return Indel().dist(src, tar) |
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def sim_indel(src, tar): |
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"""Return the normalized indel similarity of two strings. |
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This is equivalent to normalized Levenshtein similarity, when only inserts |
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and deletes are possible. |
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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 indel similarity |
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Examples |
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-------- |
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>>> round(sim_indel('cat', 'hat'), 12) |
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0.666666666667 |
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>>> round(sim_indel('Niall', 'Neil'), 12) |
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0.666666666667 |
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>>> round(sim_indel('Colin', 'Cuilen'), 12) |
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0.545454545455 |
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>>> sim_indel('ATCG', 'TAGC') |
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0.5 |
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""" |
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return Indel().sim(src, tar) |
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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
