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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.tests.test_distance. |
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This module contains unit tests for abydos.distance |
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""" |
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from __future__ import division, unicode_literals |
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import math |
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import os |
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import unittest |
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from difflib import SequenceMatcher |
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from abydos.compression import ac_train |
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from abydos.distance import bag, damerau_levenshtein, dist, dist_bag, \ |
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dist_baystat, dist_compression, dist_cosine, dist_damerau, dist_dice, \ |
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dist_editex, dist_hamming, dist_ident, dist_jaccard, dist_jaro_winkler, \ |
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dist_lcsseq, dist_lcsstr, dist_length, dist_levenshtein, dist_mlipns, \ |
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dist_monge_elkan, dist_mra, dist_overlap, dist_prefix, \ |
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dist_ratcliff_obershelp, dist_strcmp95, dist_suffix, dist_tversky, \ |
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editex, gotoh, hamming, lcsseq, lcsstr, levenshtein, mra_compare, \ |
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needleman_wunsch, sim, sim_bag, sim_baystat, sim_compression, sim_cosine, \ |
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sim_damerau, sim_dice, sim_editex, sim_hamming, sim_ident, sim_jaccard, \ |
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sim_jaro_winkler, sim_lcsseq, sim_lcsstr, sim_length, sim_levenshtein, \ |
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sim_matrix, sim_mlipns, sim_monge_elkan, sim_mra, sim_overlap, \ |
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sim_prefix, sim_ratcliff_obershelp, sim_strcmp95, sim_suffix, \ |
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sim_tanimoto, sim_tversky, smith_waterman, tanimoto |
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from abydos.qgram import QGrams |
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from six.moves import range |
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TESTDIR = os.path.dirname(__file__) |
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NIALL = ('Niall', 'Neal', 'Neil', 'Njall', 'Njáll', 'Nigel', 'Neel', 'Nele', |
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'Nigelli', 'Nel', 'Kneale', 'Uí Néill', 'O\'Neill', 'MacNeil', |
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'MacNele', 'Niall Noígíallach') |
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COLIN = ('Colin', 'Collin', 'Cullen', 'Cuilen', 'Cailean', 'MacCailean', |
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'Cuilén', 'Colle', 'Calum', 'Callum', 'Colinn', 'Colon', 'Colynn', |
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'Col', 'Cole', 'Nicolas', 'Nicholas', 'Cailean Mór Caimbeul') |
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class LevenshteinTestCases(unittest.TestCase): |
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"""Test Levenshtein functions. |
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abydos.distance.levenshtein, .dist_levenshtein, |
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.sim_levenshtein, .damerau, .dist_damerau, & .sim_damerau |
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""" |
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def test_levenshtein(self): |
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"""Test abydos.distance.levenshtein.""" |
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self.assertEqual(levenshtein('', ''), 0) |
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# http://oldfashionedsoftware.com/tag/levenshtein-distance/ |
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self.assertEqual(levenshtein('a', ''), 1) |
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self.assertEqual(levenshtein('', 'a'), 1) |
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self.assertEqual(levenshtein('abc', ''), 3) |
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self.assertEqual(levenshtein('', 'abc'), 3) |
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self.assertEqual(levenshtein('', ''), 0) |
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self.assertEqual(levenshtein('a', 'a'), 0) |
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self.assertEqual(levenshtein('abc', 'abc'), 0) |
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self.assertEqual(levenshtein('', 'a'), 1) |
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self.assertEqual(levenshtein('a', 'ab'), 1) |
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self.assertEqual(levenshtein('b', 'ab'), 1) |
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self.assertEqual(levenshtein('ac', 'abc'), 1) |
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self.assertEqual(levenshtein('abcdefg', 'xabxcdxxefxgx'), 6) |
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self.assertEqual(levenshtein('a', ''), 1) |
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self.assertEqual(levenshtein('ab', 'a'), 1) |
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self.assertEqual(levenshtein('ab', 'b'), 1) |
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self.assertEqual(levenshtein('abc', 'ac'), 1) |
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self.assertEqual(levenshtein('xabxcdxxefxgx', 'abcdefg'), 6) |
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self.assertEqual(levenshtein('a', 'b'), 1) |
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self.assertEqual(levenshtein('ab', 'ac'), 1) |
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self.assertEqual(levenshtein('ac', 'bc'), 1) |
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self.assertEqual(levenshtein('abc', 'axc'), 1) |
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self.assertEqual(levenshtein('xabxcdxxefxgx', '1ab2cd34ef5g6'), 6) |
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self.assertEqual(levenshtein('example', 'samples'), 3) |
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self.assertEqual(levenshtein('sturgeon', 'urgently'), 6) |
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self.assertEqual(levenshtein('levenshtein', 'frankenstein'), 6) |
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self.assertEqual(levenshtein('distance', 'difference'), 5) |
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self.assertEqual(levenshtein('java was neat', 'scala is great'), 7) |
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# https://en.wikipedia.org/wiki/Damerau%E2%80%93Levenshtein_distance |
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self.assertEqual(levenshtein('CA', 'ABC', 'dam'), 2) |
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self.assertEqual(levenshtein('CA', 'ABC', 'osa'), 3) |
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# test cost of insert |
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self.assertEqual(levenshtein('', 'b', 'lev', cost=(5, 7, 10, 10)), 5) |
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self.assertEqual(levenshtein('', 'b', 'osa', cost=(5, 7, 10, 10)), 5) |
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self.assertEqual(levenshtein('', 'b', 'dam', cost=(5, 7, 10, 10)), 5) |
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self.assertEqual(levenshtein('a', 'ab', 'lev', cost=(5, 7, 10, 10)), 5) |
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self.assertEqual(levenshtein('a', 'ab', 'osa', cost=(5, 7, 10, 10)), 5) |
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self.assertEqual(levenshtein('a', 'ab', 'dam', cost=(5, 7, 10, 10)), 5) |
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# test cost of delete |
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self.assertEqual(levenshtein('b', '', 'lev', cost=(5, 7, 10, 10)), 7) |
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self.assertEqual(levenshtein('b', '', 'osa', cost=(5, 7, 10, 10)), 7) |
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self.assertEqual(levenshtein('b', '', 'dam', cost=(5, 7, 10, 10)), 7) |
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self.assertEqual(levenshtein('ab', 'a', 'lev', cost=(5, 7, 10, 10)), 7) |
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self.assertEqual(levenshtein('ab', 'a', 'osa', cost=(5, 7, 10, 10)), 7) |
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self.assertEqual(levenshtein('ab', 'a', 'dam', cost=(5, 7, 10, 10)), 7) |
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# test cost of substitute |
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self.assertEqual(levenshtein('a', 'b', 'lev', cost=(10, 10, 5, 10)), 5) |
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self.assertEqual(levenshtein('a', 'b', 'osa', cost=(10, 10, 5, 10)), 5) |
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self.assertEqual(levenshtein('a', 'b', 'dam', cost=(10, 10, 5, 10)), 5) |
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self.assertEqual(levenshtein('ac', 'bc', 'lev', |
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cost=(10, 10, 5, 10)), 5) |
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self.assertEqual(levenshtein('ac', 'bc', 'osa', |
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cost=(10, 10, 5, 10)), 5) |
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self.assertEqual(levenshtein('ac', 'bc', 'dam', |
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cost=(10, 10, 5, 10)), 5) |
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# test cost of transpose |
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self.assertEqual(levenshtein('ab', 'ba', 'lev', |
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cost=(10, 10, 10, 5)), 20) |
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self.assertEqual(levenshtein('ab', 'ba', 'osa', |
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cost=(10, 10, 10, 5)), 5) |
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self.assertEqual(levenshtein('ab', 'ba', 'dam', |
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cost=(5, 5, 10, 5)), 5) |
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self.assertEqual(levenshtein('abc', 'bac', 'lev', |
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cost=(10, 10, 10, 5)), 20) |
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self.assertEqual(levenshtein('abc', 'bac', 'osa', |
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cost=(10, 10, 10, 5)), 5) |
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self.assertEqual(levenshtein('abc', 'bac', 'dam', |
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cost=(5, 5, 10, 5)), 5) |
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self.assertEqual(levenshtein('cab', 'cba', 'lev', |
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cost=(10, 10, 10, 5)), 20) |
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self.assertEqual(levenshtein('cab', 'cba', 'osa', |
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cost=(10, 10, 10, 5)), 5) |
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self.assertEqual(levenshtein('cab', 'cba', 'dam', |
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cost=(5, 5, 10, 5)), 5) |
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# test exception |
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self.assertRaises(ValueError, levenshtein, 'ab', 'ba', 'dam', |
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cost=(10, 10, 10, 5)) |
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def test_dist_levenshtein(self): |
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"""Test abydos.distance.dist_levenshtein.""" |
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self.assertEqual(dist_levenshtein('', ''), 0) |
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self.assertEqual(dist_levenshtein('a', 'a'), 0) |
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self.assertEqual(dist_levenshtein('ab', 'ab'), 0) |
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self.assertEqual(dist_levenshtein('', 'a'), 1) |
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self.assertEqual(dist_levenshtein('', 'ab'), 1) |
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self.assertEqual(dist_levenshtein('a', 'c'), 1) |
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self.assertAlmostEqual(dist_levenshtein('abc', 'ac'), 1/3) |
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self.assertAlmostEqual(dist_levenshtein('abbc', 'ac'), 1/2) |
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self.assertAlmostEqual(dist_levenshtein('abbc', 'abc'), 1/4) |
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def test_sim_levenshtein(self): |
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"""Test abydos.distance.sim_levenshtein.""" |
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self.assertEqual(sim_levenshtein('', ''), 1) |
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self.assertEqual(sim_levenshtein('a', 'a'), 1) |
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self.assertEqual(sim_levenshtein('ab', 'ab'), 1) |
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self.assertEqual(sim_levenshtein('', 'a'), 0) |
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self.assertEqual(sim_levenshtein('', 'ab'), 0) |
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self.assertEqual(sim_levenshtein('a', 'c'), 0) |
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self.assertAlmostEqual(sim_levenshtein('abc', 'ac'), 2/3) |
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self.assertAlmostEqual(sim_levenshtein('abbc', 'ac'), 1/2) |
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self.assertAlmostEqual(sim_levenshtein('abbc', 'abc'), 3/4) |
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def test_damerau_levenshtein(self): |
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"""Test abydos.distance.damerau_levenshtein.""" |
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self.assertEqual(damerau_levenshtein('', ''), 0) |
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self.assertEqual(damerau_levenshtein('CA', 'CA'), 0) |
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self.assertEqual(damerau_levenshtein('CA', 'ABC'), 2) |
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self.assertEqual(damerau_levenshtein('', 'b', cost=(5, 7, 10, 10)), 5) |
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self.assertEqual(damerau_levenshtein('a', 'ab', cost=(5, 7, 10, 10)), |
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5) |
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self.assertEqual(damerau_levenshtein('b', '', cost=(5, 7, 10, 10)), 7) |
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self.assertEqual(damerau_levenshtein('ab', 'a', cost=(5, 7, 10, 10)), |
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7) |
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self.assertEqual(damerau_levenshtein('a', 'b', cost=(10, 10, 5, 10)), |
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5) |
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self.assertEqual(damerau_levenshtein('ac', 'bc', |
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cost=(10, 10, 5, 10)), 5) |
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self.assertEqual(damerau_levenshtein('ab', 'ba', |
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cost=(5, 5, 10, 5)), 5) |
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self.assertEqual(damerau_levenshtein('abc', 'bac', |
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cost=(5, 5, 10, 5)), 5) |
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self.assertEqual(damerau_levenshtein('cab', 'cba', |
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cost=(5, 5, 10, 5)), 5) |
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self.assertRaises(ValueError, damerau_levenshtein, 'ab', 'ba', |
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cost=(10, 10, 10, 5)) |
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def test_dist_damerau(self): |
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"""Test abydos.distance.dist_damerau.""" |
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self.assertEqual(dist_damerau('', ''), 0) |
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self.assertEqual(dist_damerau('a', 'a'), 0) |
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self.assertEqual(dist_damerau('ab', 'ab'), 0) |
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self.assertEqual(dist_damerau('', 'a'), 1) |
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self.assertEqual(dist_damerau('', 'ab'), 1) |
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self.assertEqual(dist_damerau('a', 'c'), 1) |
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self.assertAlmostEqual(dist_damerau('abc', 'ac'), 1/3) |
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self.assertAlmostEqual(dist_damerau('abbc', 'ac'), 1/2) |
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self.assertAlmostEqual(dist_damerau('abbc', 'abc'), 1/4) |
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self.assertAlmostEqual(dist_damerau('CA', 'ABC'), 2/3) |
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self.assertAlmostEqual(dist_damerau('', 'b', cost=(5, 7, 10, 10)), 1) |
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self.assertAlmostEqual(dist_damerau('a', 'ab', |
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cost=(5, 7, 10, 10)), 1/2) |
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self.assertAlmostEqual(dist_damerau('b', '', cost=(5, 7, 10, 10)), 1) |
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self.assertAlmostEqual(dist_damerau('ab', 'a', |
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cost=(5, 7, 10, 10)), 1/2) |
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self.assertAlmostEqual(dist_damerau('a', 'b', |
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cost=(10, 10, 5, 10)), 1/2) |
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self.assertAlmostEqual(dist_damerau('ac', 'bc', |
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cost=(10, 10, 5, 10)), 1/4) |
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self.assertAlmostEqual(dist_damerau('ab', 'ba', |
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cost=(5, 5, 10, 5)), 1/2) |
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self.assertAlmostEqual(dist_damerau('abc', 'bac', |
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cost=(5, 5, 10, 5)), 1/3) |
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self.assertAlmostEqual(dist_damerau('cab', 'cba', |
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cost=(5, 5, 10, 5)), 1/3) |
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self.assertRaises(ValueError, dist_damerau, 'ab', 'ba', |
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cost=(10, 10, 10, 5)) |
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def test_sim_damerau(self): |
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"""Test abydos.distance.sim_damerau.""" |
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self.assertEqual(sim_damerau('', ''), 1) |
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self.assertEqual(sim_damerau('a', 'a'), 1) |
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self.assertEqual(sim_damerau('ab', 'ab'), 1) |
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self.assertEqual(sim_damerau('', 'a'), 0) |
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self.assertEqual(sim_damerau('', 'ab'), 0) |
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self.assertEqual(sim_damerau('a', 'c'), 0) |
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251
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self.assertAlmostEqual(sim_damerau('abc', 'ac'), 2/3) |
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self.assertAlmostEqual(sim_damerau('abbc', 'ac'), 1/2) |
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253
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self.assertAlmostEqual(sim_damerau('abbc', 'abc'), 3/4) |
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255
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self.assertAlmostEqual(sim_damerau('CA', 'ABC'), 1/3) |
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256
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self.assertAlmostEqual(sim_damerau('', 'b', cost=(5, 7, 10, 10)), 0) |
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257
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self.assertAlmostEqual(sim_damerau('a', 'ab', cost=(5, 7, 10, 10)), |
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258
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1/2) |
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259
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self.assertAlmostEqual(sim_damerau('b', '', cost=(5, 7, 10, 10)), 0) |
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260
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self.assertAlmostEqual(sim_damerau('ab', 'a', cost=(5, 7, 10, 10)), |
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261
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1/2) |
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262
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self.assertAlmostEqual(sim_damerau('a', 'b', cost=(10, 10, 5, 10)), |
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263
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1/2) |
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264
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self.assertAlmostEqual(sim_damerau('ac', 'bc', |
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265
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cost=(10, 10, 5, 10)), 3/4) |
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266
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self.assertAlmostEqual(sim_damerau('ab', 'ba', |
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267
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cost=(5, 5, 10, 5)), 1/2) |
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268
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self.assertAlmostEqual(sim_damerau('abc', 'bac', |
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269
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cost=(5, 5, 10, 5)), 2/3) |
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270
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self.assertAlmostEqual(sim_damerau('cab', 'cba', |
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271
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cost=(5, 5, 10, 5)), 2/3) |
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272
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self.assertRaises(ValueError, sim_damerau, 'ab', 'ba', |
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273
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cost=(10, 10, 10, 5)) |
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274
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275
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276
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class HammingTestCases(unittest.TestCase): |
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277
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"""Test Hamming functions. |
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278
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279
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abydos.distance.hamming, .dist_hamming, & .sim_hamming |
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280
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""" |
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281
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282
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def test_hamming(self): |
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283
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"""Test abydos.distance.hamming.""" |
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284
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self.assertEqual(hamming('', ''), 0) |
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285
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self.assertEqual(hamming('', '', False), 0) |
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286
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287
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self.assertEqual(hamming('a', ''), 1) |
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288
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self.assertEqual(hamming('a', 'a'), 0) |
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289
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self.assertEqual(hamming('a', 'a', False), 0) |
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290
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self.assertEqual(hamming('a', 'b'), 1) |
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291
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self.assertEqual(hamming('a', 'b', False), 1) |
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292
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self.assertEqual(hamming('abc', 'cba'), 2) |
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293
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self.assertEqual(hamming('abc', 'cba', False), 2) |
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294
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self.assertEqual(hamming('abc', ''), 3) |
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295
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self.assertEqual(hamming('bb', 'cbab'), 3) |
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296
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297
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# test exception |
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298
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self.assertRaises(ValueError, hamming, 'ab', 'a', False) |
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299
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300
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# https://en.wikipedia.org/wiki/Hamming_distance |
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301
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self.assertEqual(hamming('karolin', 'kathrin'), 3) |
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302
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self.assertEqual(hamming('karolin', 'kerstin'), 3) |
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303
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self.assertEqual(hamming('1011101', '1001001'), 2) |
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304
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self.assertEqual(hamming('2173896', '2233796'), 3) |
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305
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306
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def test_dist_hamming(self): |
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307
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"""Test abydos.distance.dist_hamming.""" |
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308
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self.assertEqual(dist_hamming('', ''), 0) |
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309
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self.assertEqual(dist_hamming('', '', False), 0) |
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310
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311
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self.assertEqual(dist_hamming('a', ''), 1) |
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312
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self.assertEqual(dist_hamming('a', 'a'), 0) |
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313
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self.assertEqual(dist_hamming('a', 'a', False), 0) |
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314
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self.assertEqual(dist_hamming('a', 'b'), 1) |
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315
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self.assertEqual(dist_hamming('a', 'b', False), 1) |
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316
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self.assertAlmostEqual(dist_hamming('abc', 'cba'), 2/3) |
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317
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self.assertAlmostEqual(dist_hamming('abc', 'cba', False), 2/3) |
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318
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self.assertEqual(dist_hamming('abc', ''), 1) |
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319
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self.assertAlmostEqual(dist_hamming('bb', 'cbab'), 3/4) |
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320
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321
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# test exception |
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322
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self.assertRaises(ValueError, dist_hamming, 'ab', 'a', False) |
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323
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324
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# https://en.wikipedia.org/wiki/Hamming_distance |
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325
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self.assertAlmostEqual(dist_hamming('karolin', 'kathrin'), 3/7) |
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326
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self.assertAlmostEqual(dist_hamming('karolin', 'kerstin'), 3/7) |
|
327
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self.assertAlmostEqual(dist_hamming('1011101', '1001001'), 2/7) |
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328
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self.assertAlmostEqual(dist_hamming('2173896', '2233796'), 3/7) |
|
329
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|
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|
330
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|
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def test_sim_hamming(self): |
|
331
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|
|
"""Test abydos.distance.sim_hamming.""" |
|
332
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self.assertEqual(sim_hamming('', ''), 1) |
|
333
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self.assertEqual(sim_hamming('', '', False), 1) |
|
334
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|
|
|
|
335
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|
self.assertEqual(sim_hamming('a', ''), 0) |
|
336
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|
|
self.assertEqual(sim_hamming('a', 'a'), 1) |
|
337
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|
|
self.assertEqual(sim_hamming('a', 'a', False), 1) |
|
338
|
|
|
self.assertEqual(sim_hamming('a', 'b'), 0) |
|
339
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|
|
self.assertEqual(sim_hamming('a', 'b', False), 0) |
|
340
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|
self.assertAlmostEqual(sim_hamming('abc', 'cba'), 1/3) |
|
341
|
|
|
self.assertAlmostEqual(sim_hamming('abc', 'cba', False), 1/3) |
|
342
|
|
|
self.assertEqual(sim_hamming('abc', ''), 0) |
|
343
|
|
|
self.assertAlmostEqual(sim_hamming('bb', 'cbab'), 1/4) |
|
344
|
|
|
|
|
345
|
|
|
# test exception |
|
346
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|
|
self.assertRaises(ValueError, sim_hamming, 'ab', 'a', False) |
|
347
|
|
|
|
|
348
|
|
|
# https://en.wikipedia.org/wiki/Hamming_distance |
|
349
|
|
|
self.assertAlmostEqual(sim_hamming('karolin', 'kathrin'), 4/7) |
|
350
|
|
|
self.assertAlmostEqual(sim_hamming('karolin', 'kerstin'), 4/7) |
|
351
|
|
|
self.assertAlmostEqual(sim_hamming('1011101', '1001001'), 5/7) |
|
352
|
|
|
self.assertAlmostEqual(sim_hamming('2173896', '2233796'), 4/7) |
|
353
|
|
|
|
|
354
|
|
|
|
|
355
|
|
|
NONQ_FROM = 'The quick brown fox jumped over the lazy dog.' |
|
356
|
|
|
NONQ_TO = 'That brown dog jumped over the fox.' |
|
357
|
|
|
|
|
358
|
|
|
|
|
359
|
|
|
class TverskyIndexTestCases(unittest.TestCase): |
|
360
|
|
|
"""Test Tversky functions. |
|
361
|
|
|
|
|
362
|
|
|
abydos.distance.sim_tversky & .dist_tversky |
|
363
|
|
|
""" |
|
364
|
|
|
|
|
365
|
|
|
def test_sim_tversky(self): |
|
366
|
|
|
"""Test abydos.distance.sim_tversky.""" |
|
367
|
|
|
self.assertEqual(sim_tversky('', ''), 1) |
|
368
|
|
|
self.assertEqual(sim_tversky('nelson', ''), 0) |
|
369
|
|
|
self.assertEqual(sim_tversky('', 'neilsen'), 0) |
|
370
|
|
|
self.assertAlmostEqual(sim_tversky('nelson', 'neilsen'), 4/11) |
|
371
|
|
|
|
|
372
|
|
|
self.assertEqual(sim_tversky('', '', 2), 1) |
|
373
|
|
|
self.assertEqual(sim_tversky('nelson', '', 2), 0) |
|
374
|
|
|
self.assertEqual(sim_tversky('', 'neilsen', 2), 0) |
|
375
|
|
|
self.assertAlmostEqual(sim_tversky('nelson', 'neilsen', 2), 4/11) |
|
376
|
|
|
|
|
377
|
|
|
# test valid alpha & beta |
|
378
|
|
|
self.assertRaises(ValueError, sim_tversky, 'abcd', 'dcba', 2, -1, -1) |
|
379
|
|
|
self.assertRaises(ValueError, sim_tversky, 'abcd', 'dcba', 2, -1, 0) |
|
380
|
|
|
self.assertRaises(ValueError, sim_tversky, 'abcd', 'dcba', 2, 0, -1) |
|
381
|
|
|
|
|
382
|
|
|
# test empty QGrams |
|
383
|
|
|
self.assertAlmostEqual(sim_tversky('nelson', 'neilsen', 7), 0.0) |
|
384
|
|
|
|
|
385
|
|
|
# test unequal alpha & beta |
|
386
|
|
|
self.assertAlmostEqual(sim_tversky('niall', 'neal', 2, 2, 1), 3/11) |
|
387
|
|
|
self.assertAlmostEqual(sim_tversky('niall', 'neal', 2, 1, 2), 3/10) |
|
388
|
|
|
self.assertAlmostEqual(sim_tversky('niall', 'neal', 2, 2, 2), 3/13) |
|
389
|
|
|
|
|
390
|
|
|
# test bias parameter |
|
391
|
|
|
self.assertAlmostEqual(sim_tversky('niall', 'neal', 2, 1, 1, 0.5), |
|
392
|
|
|
7/11) |
|
393
|
|
|
self.assertAlmostEqual(sim_tversky('niall', 'neal', 2, 2, 1, 0.5), 7/9) |
|
394
|
|
|
self.assertAlmostEqual(sim_tversky('niall', 'neal', 2, 1, 2, 0.5), |
|
395
|
|
|
7/15) |
|
396
|
|
|
self.assertAlmostEqual(sim_tversky('niall', 'neal', 2, 2, 2, 0.5), |
|
397
|
|
|
7/11) |
|
398
|
|
|
|
|
399
|
|
|
# supplied q-gram tests |
|
400
|
|
|
self.assertEqual(sim_tversky(QGrams(''), QGrams('')), 1) |
|
401
|
|
|
self.assertEqual(sim_tversky(QGrams('nelson'), QGrams('')), 0) |
|
402
|
|
|
self.assertEqual(sim_tversky(QGrams(''), QGrams('neilsen')), 0) |
|
403
|
|
|
self.assertAlmostEqual(sim_tversky(QGrams('nelson'), |
|
404
|
|
|
QGrams('neilsen')), 4/11) |
|
405
|
|
|
|
|
406
|
|
|
# non-q-gram tests |
|
407
|
|
|
self.assertEqual(sim_tversky('', '', None), 1) |
|
408
|
|
|
self.assertEqual(sim_tversky('the quick', '', None), 0) |
|
409
|
|
|
self.assertEqual(sim_tversky('', 'the quick', None), 0) |
|
410
|
|
|
self.assertAlmostEqual(sim_tversky(NONQ_FROM, NONQ_TO, None), 1/3) |
|
411
|
|
|
self.assertAlmostEqual(sim_tversky(NONQ_TO, NONQ_FROM, None), 1/3) |
|
412
|
|
|
|
|
413
|
|
|
def test_dist_tversky(self): |
|
414
|
|
|
"""Test abydos.distance.dist_tversky.""" |
|
415
|
|
|
self.assertEqual(dist_tversky('', ''), 0) |
|
416
|
|
|
self.assertEqual(dist_tversky('nelson', ''), 1) |
|
417
|
|
|
self.assertEqual(dist_tversky('', 'neilsen'), 1) |
|
418
|
|
|
self.assertAlmostEqual(dist_tversky('nelson', 'neilsen'), 7/11) |
|
419
|
|
|
|
|
420
|
|
|
self.assertEqual(dist_tversky('', '', 2), 0) |
|
421
|
|
|
self.assertEqual(dist_tversky('nelson', '', 2), 1) |
|
422
|
|
|
self.assertEqual(dist_tversky('', 'neilsen', 2), 1) |
|
423
|
|
|
self.assertAlmostEqual(dist_tversky('nelson', 'neilsen', 2), 7/11) |
|
424
|
|
|
|
|
425
|
|
|
# test valid alpha & beta |
|
426
|
|
|
self.assertRaises(ValueError, dist_tversky, 'abcd', 'dcba', 2, -1, -1) |
|
427
|
|
|
self.assertRaises(ValueError, dist_tversky, 'abcd', 'dcba', 2, -1, 0) |
|
428
|
|
|
self.assertRaises(ValueError, dist_tversky, 'abcd', 'dcba', 2, 0, -1) |
|
429
|
|
|
|
|
430
|
|
|
# test empty QGrams |
|
431
|
|
|
self.assertAlmostEqual(dist_tversky('nelson', 'neilsen', 7), 1.0) |
|
432
|
|
|
|
|
433
|
|
|
# test unequal alpha & beta |
|
434
|
|
|
self.assertAlmostEqual(dist_tversky('niall', 'neal', 2, 2, 1), 8/11) |
|
435
|
|
|
self.assertAlmostEqual(dist_tversky('niall', 'neal', 2, 1, 2), 7/10) |
|
436
|
|
|
self.assertAlmostEqual(dist_tversky('niall', 'neal', 2, 2, 2), 10/13) |
|
437
|
|
|
|
|
438
|
|
|
# test bias parameter |
|
439
|
|
|
self.assertAlmostEqual(dist_tversky('niall', 'neal', 2, 1, 1, 0.5), |
|
440
|
|
|
4/11) |
|
441
|
|
|
self.assertAlmostEqual(dist_tversky('niall', 'neal', 2, 2, 1, 0.5), |
|
442
|
|
|
2/9) |
|
443
|
|
|
self.assertAlmostEqual(dist_tversky('niall', 'neal', 2, 1, 2, 0.5), |
|
444
|
|
|
8/15) |
|
445
|
|
|
self.assertAlmostEqual(dist_tversky('niall', 'neal', 2, 2, 2, 0.5), |
|
446
|
|
|
4/11) |
|
447
|
|
|
|
|
448
|
|
|
# supplied q-gram tests |
|
449
|
|
|
self.assertEqual(dist_tversky(QGrams(''), QGrams('')), 0) |
|
450
|
|
|
self.assertEqual(dist_tversky(QGrams('nelson'), QGrams('')), 1) |
|
451
|
|
|
self.assertEqual(dist_tversky(QGrams(''), QGrams('neilsen')), 1) |
|
452
|
|
|
self.assertAlmostEqual(dist_tversky(QGrams('nelson'), |
|
453
|
|
|
QGrams('neilsen')), 7/11) |
|
454
|
|
|
|
|
455
|
|
|
# non-q-gram tests |
|
456
|
|
|
self.assertEqual(dist_tversky('', '', None), 0) |
|
457
|
|
|
self.assertEqual(dist_tversky('the quick', '', None), 1) |
|
458
|
|
|
self.assertEqual(dist_tversky('', 'the quick', None), 1) |
|
459
|
|
|
self.assertAlmostEqual(dist_tversky(NONQ_FROM, NONQ_TO, None), 2/3) |
|
460
|
|
|
self.assertAlmostEqual(dist_tversky(NONQ_TO, NONQ_FROM, None), 2/3) |
|
461
|
|
|
|
|
462
|
|
|
|
|
463
|
|
|
class DiceTestCases(unittest.TestCase): |
|
464
|
|
|
"""Test Dice functions. |
|
465
|
|
|
|
|
466
|
|
|
abydos.distance.sim_dice & .dist_dice |
|
467
|
|
|
""" |
|
468
|
|
|
|
|
469
|
|
|
def test_sim_dice(self): |
|
470
|
|
|
"""Test abydos.distance.sim_dice.""" |
|
471
|
|
|
self.assertEqual(sim_dice('', ''), 1) |
|
472
|
|
|
self.assertEqual(sim_dice('nelson', ''), 0) |
|
473
|
|
|
self.assertEqual(sim_dice('', 'neilsen'), 0) |
|
474
|
|
|
self.assertAlmostEqual(sim_dice('nelson', 'neilsen'), 8/15) |
|
475
|
|
|
|
|
476
|
|
|
self.assertEqual(sim_dice('', '', 2), 1) |
|
477
|
|
|
self.assertEqual(sim_dice('nelson', '', 2), 0) |
|
478
|
|
|
self.assertEqual(sim_dice('', 'neilsen', 2), 0) |
|
479
|
|
|
self.assertAlmostEqual(sim_dice('nelson', 'neilsen', 2), 8/15) |
|
480
|
|
|
|
|
481
|
|
|
# supplied q-gram tests |
|
482
|
|
|
self.assertEqual(sim_dice(QGrams(''), QGrams('')), 1) |
|
483
|
|
|
self.assertEqual(sim_dice(QGrams('nelson'), QGrams('')), 0) |
|
484
|
|
|
self.assertEqual(sim_dice(QGrams(''), QGrams('neilsen')), 0) |
|
485
|
|
|
self.assertAlmostEqual(sim_dice(QGrams('nelson'), QGrams('neilsen')), |
|
486
|
|
|
8/15) |
|
487
|
|
|
|
|
488
|
|
|
# non-q-gram tests |
|
489
|
|
|
self.assertEqual(sim_dice('', '', None), 1) |
|
490
|
|
|
self.assertEqual(sim_dice('the quick', '', None), 0) |
|
491
|
|
|
self.assertEqual(sim_dice('', 'the quick', None), 0) |
|
492
|
|
|
self.assertAlmostEqual(sim_dice(NONQ_FROM, NONQ_TO, None), 1/2) |
|
493
|
|
|
self.assertAlmostEqual(sim_dice(NONQ_TO, NONQ_FROM, None), 1/2) |
|
494
|
|
|
|
|
495
|
|
|
def test_dist_dice(self): |
|
496
|
|
|
"""Test abydos.distance.dist_dice.""" |
|
497
|
|
|
self.assertEqual(dist_dice('', ''), 0) |
|
498
|
|
|
self.assertEqual(dist_dice('nelson', ''), 1) |
|
499
|
|
|
self.assertEqual(dist_dice('', 'neilsen'), 1) |
|
500
|
|
|
self.assertAlmostEqual(dist_dice('nelson', 'neilsen'), 7/15) |
|
501
|
|
|
|
|
502
|
|
|
self.assertEqual(dist_dice('', '', 2), 0) |
|
503
|
|
|
self.assertEqual(dist_dice('nelson', '', 2), 1) |
|
504
|
|
|
self.assertEqual(dist_dice('', 'neilsen', 2), 1) |
|
505
|
|
|
self.assertAlmostEqual(dist_dice('nelson', 'neilsen', 2), 7/15) |
|
506
|
|
|
|
|
507
|
|
|
# supplied q-gram tests |
|
508
|
|
|
self.assertEqual(dist_dice(QGrams(''), QGrams('')), 0) |
|
509
|
|
|
self.assertEqual(dist_dice(QGrams('nelson'), QGrams('')), 1) |
|
510
|
|
|
self.assertEqual(dist_dice(QGrams(''), QGrams('neilsen')), 1) |
|
511
|
|
|
self.assertAlmostEqual(dist_dice(QGrams('nelson'), QGrams('neilsen')), |
|
512
|
|
|
7/15) |
|
513
|
|
|
|
|
514
|
|
|
# non-q-gram tests |
|
515
|
|
|
self.assertEqual(dist_dice('', '', None), 0) |
|
516
|
|
|
self.assertEqual(dist_dice('the quick', '', None), 1) |
|
517
|
|
|
self.assertEqual(dist_dice('', 'the quick', None), 1) |
|
518
|
|
|
self.assertAlmostEqual(dist_dice(NONQ_FROM, NONQ_TO, None), 1/2) |
|
519
|
|
|
self.assertAlmostEqual(dist_dice(NONQ_TO, NONQ_FROM, None), 1/2) |
|
520
|
|
|
|
|
521
|
|
|
|
|
522
|
|
|
class JaccardTestCases(unittest.TestCase): |
|
523
|
|
|
"""Test Jaccard functions. |
|
524
|
|
|
|
|
525
|
|
|
abydos.distance.sim_jaccard & .dist_jaccard |
|
526
|
|
|
""" |
|
527
|
|
|
|
|
528
|
|
|
def test_sim_jaccard(self): |
|
529
|
|
|
"""Test abydos.distance.sim_jaccard.""" |
|
530
|
|
|
self.assertEqual(sim_jaccard('', ''), 1) |
|
531
|
|
|
self.assertEqual(sim_jaccard('nelson', ''), 0) |
|
532
|
|
|
self.assertEqual(sim_jaccard('', 'neilsen'), 0) |
|
533
|
|
|
self.assertAlmostEqual(sim_jaccard('nelson', 'neilsen'), 4/11) |
|
534
|
|
|
|
|
535
|
|
|
self.assertEqual(sim_jaccard('', '', 2), 1) |
|
536
|
|
|
self.assertEqual(sim_jaccard('nelson', '', 2), 0) |
|
537
|
|
|
self.assertEqual(sim_jaccard('', 'neilsen', 2), 0) |
|
538
|
|
|
self.assertAlmostEqual(sim_jaccard('nelson', 'neilsen', 2), 4/11) |
|
539
|
|
|
|
|
540
|
|
|
# supplied q-gram tests |
|
541
|
|
|
self.assertEqual(sim_jaccard(QGrams(''), QGrams('')), 1) |
|
542
|
|
|
self.assertEqual(sim_jaccard(QGrams('nelson'), QGrams('')), 0) |
|
543
|
|
|
self.assertEqual(sim_jaccard(QGrams(''), QGrams('neilsen')), 0) |
|
544
|
|
|
self.assertAlmostEqual(sim_jaccard(QGrams('nelson'), |
|
545
|
|
|
QGrams('neilsen')), 4/11) |
|
546
|
|
|
|
|
547
|
|
|
# non-q-gram tests |
|
548
|
|
|
self.assertEqual(sim_jaccard('', '', None), 1) |
|
549
|
|
|
self.assertEqual(sim_jaccard('the quick', '', None), 0) |
|
550
|
|
|
self.assertEqual(sim_jaccard('', 'the quick', None), 0) |
|
551
|
|
|
self.assertAlmostEqual(sim_jaccard(NONQ_FROM, NONQ_TO, None), 1/3) |
|
552
|
|
|
self.assertAlmostEqual(sim_jaccard(NONQ_TO, NONQ_FROM, None), 1/3) |
|
553
|
|
|
|
|
554
|
|
|
def test_dist_jaccard(self): |
|
555
|
|
|
"""Test abydos.distance.dist_jaccard.""" |
|
556
|
|
|
self.assertEqual(dist_jaccard('', ''), 0) |
|
557
|
|
|
self.assertEqual(dist_jaccard('nelson', ''), 1) |
|
558
|
|
|
self.assertEqual(dist_jaccard('', 'neilsen'), 1) |
|
559
|
|
|
self.assertAlmostEqual(dist_jaccard('nelson', 'neilsen'), 7/11) |
|
560
|
|
|
|
|
561
|
|
|
self.assertEqual(dist_jaccard('', '', 2), 0) |
|
562
|
|
|
self.assertEqual(dist_jaccard('nelson', '', 2), 1) |
|
563
|
|
|
self.assertEqual(dist_jaccard('', 'neilsen', 2), 1) |
|
564
|
|
|
self.assertAlmostEqual(dist_jaccard('nelson', 'neilsen', 2), 7/11) |
|
565
|
|
|
|
|
566
|
|
|
# supplied q-gram tests |
|
567
|
|
|
self.assertEqual(dist_jaccard(QGrams(''), QGrams('')), 0) |
|
568
|
|
|
self.assertEqual(dist_jaccard(QGrams('nelson'), QGrams('')), 1) |
|
569
|
|
|
self.assertEqual(dist_jaccard(QGrams(''), QGrams('neilsen')), 1) |
|
570
|
|
|
self.assertAlmostEqual(dist_jaccard(QGrams('nelson'), |
|
571
|
|
|
QGrams('neilsen')), 7/11) |
|
572
|
|
|
|
|
573
|
|
|
# non-q-gram tests |
|
574
|
|
|
self.assertEqual(dist_jaccard('', '', None), 0) |
|
575
|
|
|
self.assertEqual(dist_jaccard('the quick', '', None), 1) |
|
576
|
|
|
self.assertEqual(dist_jaccard('', 'the quick', None), 1) |
|
577
|
|
|
self.assertAlmostEqual(dist_jaccard(NONQ_FROM, NONQ_TO, None), 2/3) |
|
578
|
|
|
self.assertAlmostEqual(dist_jaccard(NONQ_TO, NONQ_FROM, None), 2/3) |
|
579
|
|
|
|
|
580
|
|
|
|
|
581
|
|
|
class OverlapTestCases(unittest.TestCase): |
|
582
|
|
|
"""Test overlap functions. |
|
583
|
|
|
|
|
584
|
|
|
abydos.distance.sim_overlap & .dist_overlap |
|
585
|
|
|
""" |
|
586
|
|
|
|
|
587
|
|
|
def test_sim_overlap(self): |
|
588
|
|
|
"""Test abydos.distance.sim_overlap.""" |
|
589
|
|
|
self.assertEqual(sim_overlap('', ''), 1) |
|
590
|
|
|
self.assertEqual(sim_overlap('nelson', ''), 0) |
|
591
|
|
|
self.assertEqual(sim_overlap('', 'neilsen'), 0) |
|
592
|
|
|
self.assertAlmostEqual(sim_overlap('nelson', 'neilsen'), 4/7) |
|
593
|
|
|
|
|
594
|
|
|
self.assertEqual(sim_overlap('', '', 2), 1) |
|
595
|
|
|
self.assertEqual(sim_overlap('nelson', '', 2), 0) |
|
596
|
|
|
self.assertEqual(sim_overlap('', 'neilsen', 2), 0) |
|
597
|
|
|
self.assertAlmostEqual(sim_overlap('nelson', 'neilsen', 2), 4/7) |
|
598
|
|
|
|
|
599
|
|
|
# supplied q-gram tests |
|
600
|
|
|
self.assertEqual(sim_overlap(QGrams(''), QGrams('')), 1) |
|
601
|
|
|
self.assertEqual(sim_overlap(QGrams('nelson'), QGrams('')), 0) |
|
602
|
|
|
self.assertEqual(sim_overlap(QGrams(''), QGrams('neilsen')), 0) |
|
603
|
|
|
self.assertAlmostEqual(sim_overlap(QGrams('nelson'), |
|
604
|
|
|
QGrams('neilsen')), 4/7) |
|
605
|
|
|
|
|
606
|
|
|
# non-q-gram tests |
|
607
|
|
|
self.assertEqual(sim_overlap('', '', None), 1) |
|
608
|
|
|
self.assertEqual(sim_overlap('the quick', '', None), 0) |
|
609
|
|
|
self.assertEqual(sim_overlap('', 'the quick', None), 0) |
|
610
|
|
|
self.assertAlmostEqual(sim_overlap(NONQ_FROM, NONQ_TO, None), 4/7) |
|
611
|
|
|
self.assertAlmostEqual(sim_overlap(NONQ_TO, NONQ_FROM, None), 4/7) |
|
612
|
|
|
|
|
613
|
|
|
def test_dist_overlap(self): |
|
614
|
|
|
"""Test abydos.distance.dist_overlap.""" |
|
615
|
|
|
self.assertEqual(dist_overlap('', ''), 0) |
|
616
|
|
|
self.assertEqual(dist_overlap('nelson', ''), 1) |
|
617
|
|
|
self.assertEqual(dist_overlap('', 'neilsen'), 1) |
|
618
|
|
|
self.assertAlmostEqual(dist_overlap('nelson', 'neilsen'), 3/7) |
|
619
|
|
|
|
|
620
|
|
|
self.assertEqual(dist_overlap('', '', 2), 0) |
|
621
|
|
|
self.assertEqual(dist_overlap('nelson', '', 2), 1) |
|
622
|
|
|
self.assertEqual(dist_overlap('', 'neilsen', 2), 1) |
|
623
|
|
|
self.assertAlmostEqual(dist_overlap('nelson', 'neilsen', 2), 3/7) |
|
624
|
|
|
|
|
625
|
|
|
# supplied q-gram tests |
|
626
|
|
|
self.assertEqual(dist_overlap(QGrams(''), QGrams('')), 0) |
|
627
|
|
|
self.assertEqual(dist_overlap(QGrams('nelson'), QGrams('')), 1) |
|
628
|
|
|
self.assertEqual(dist_overlap(QGrams(''), QGrams('neilsen')), 1) |
|
629
|
|
|
self.assertAlmostEqual(dist_overlap(QGrams('nelson'), |
|
630
|
|
|
QGrams('neilsen')), 3/7) |
|
631
|
|
|
|
|
632
|
|
|
# non-q-gram tests |
|
633
|
|
|
self.assertEqual(dist_overlap('', '', None), 0) |
|
634
|
|
|
self.assertEqual(dist_overlap('the quick', '', None), 1) |
|
635
|
|
|
self.assertEqual(dist_overlap('', 'the quick', None), 1) |
|
636
|
|
|
self.assertAlmostEqual(dist_overlap(NONQ_FROM, NONQ_TO, None), 3/7) |
|
637
|
|
|
self.assertAlmostEqual(dist_overlap(NONQ_TO, NONQ_FROM, None), 3/7) |
|
638
|
|
|
|
|
639
|
|
|
|
|
640
|
|
|
class TanimotoTestCases(unittest.TestCase): |
|
641
|
|
|
"""Test Tanimoto functions. |
|
642
|
|
|
|
|
643
|
|
|
abydos.distance.sim_tanimoto & .tanimoto |
|
644
|
|
|
""" |
|
645
|
|
|
|
|
646
|
|
|
def test_tanimoto_coeff(self): |
|
647
|
|
|
"""Test abydos.distance.sim_tanimoto.""" |
|
648
|
|
|
self.assertEqual(sim_tanimoto('', ''), 1) |
|
649
|
|
|
self.assertEqual(sim_tanimoto('nelson', ''), 0) |
|
650
|
|
|
self.assertEqual(sim_tanimoto('', 'neilsen'), 0) |
|
651
|
|
|
self.assertAlmostEqual(sim_tanimoto('nelson', 'neilsen'), 4/11) |
|
652
|
|
|
|
|
653
|
|
|
self.assertEqual(sim_tanimoto('', '', 2), 1) |
|
654
|
|
|
self.assertEqual(sim_tanimoto('nelson', '', 2), 0) |
|
655
|
|
|
self.assertEqual(sim_tanimoto('', 'neilsen', 2), 0) |
|
656
|
|
|
self.assertAlmostEqual(sim_tanimoto('nelson', 'neilsen', 2), 4/11) |
|
657
|
|
|
|
|
658
|
|
|
# supplied q-gram tests |
|
659
|
|
|
self.assertEqual(sim_tanimoto(QGrams(''), QGrams('')), 1) |
|
660
|
|
|
self.assertEqual(sim_tanimoto(QGrams('nelson'), QGrams('')), 0) |
|
661
|
|
|
self.assertEqual(sim_tanimoto(QGrams(''), QGrams('neilsen')), 0) |
|
662
|
|
|
self.assertAlmostEqual(sim_tanimoto(QGrams('nelson'), |
|
663
|
|
|
QGrams('neilsen')), 4/11) |
|
664
|
|
|
|
|
665
|
|
|
# non-q-gram tests |
|
666
|
|
|
self.assertEqual(sim_tanimoto('', '', None), 1) |
|
667
|
|
|
self.assertEqual(sim_tanimoto('the quick', '', None), 0) |
|
668
|
|
|
self.assertEqual(sim_tanimoto('', 'the quick', None), 0) |
|
669
|
|
|
self.assertAlmostEqual(sim_tanimoto(NONQ_FROM, NONQ_TO, None), 1/3) |
|
670
|
|
|
self.assertAlmostEqual(sim_tanimoto(NONQ_TO, NONQ_FROM, None), 1/3) |
|
671
|
|
|
|
|
672
|
|
|
def test_tanimoto(self): |
|
673
|
|
|
"""Test abydos.distance.tanimoto.""" |
|
674
|
|
|
self.assertEqual(tanimoto('', ''), 0) |
|
675
|
|
|
self.assertEqual(tanimoto('nelson', ''), float('-inf')) |
|
676
|
|
|
self.assertEqual(tanimoto('', 'neilsen'), float('-inf')) |
|
677
|
|
|
self.assertAlmostEqual(tanimoto('nelson', 'neilsen'), |
|
678
|
|
|
math.log(4/11, 2)) |
|
679
|
|
|
|
|
680
|
|
|
self.assertEqual(tanimoto('', '', 2), 0) |
|
681
|
|
|
self.assertEqual(tanimoto('nelson', '', 2), float('-inf')) |
|
682
|
|
|
self.assertEqual(tanimoto('', 'neilsen', 2), float('-inf')) |
|
683
|
|
|
self.assertAlmostEqual(tanimoto('nelson', 'neilsen', 2), |
|
684
|
|
|
math.log(4/11, 2)) |
|
685
|
|
|
|
|
686
|
|
|
# supplied q-gram tests |
|
687
|
|
|
self.assertEqual(tanimoto(QGrams(''), QGrams('')), 0) |
|
688
|
|
|
self.assertEqual(tanimoto(QGrams('nelson'), QGrams('')), float('-inf')) |
|
689
|
|
|
self.assertEqual(tanimoto(QGrams(''), QGrams('neilsen')), |
|
690
|
|
|
float('-inf')) |
|
691
|
|
|
self.assertAlmostEqual(tanimoto(QGrams('nelson'), QGrams('neilsen')), |
|
692
|
|
|
math.log(4/11, 2)) |
|
693
|
|
|
|
|
694
|
|
|
# non-q-gram tests |
|
695
|
|
|
self.assertEqual(tanimoto('', '', None), 0) |
|
696
|
|
|
self.assertEqual(tanimoto('the quick', '', None), float('-inf')) |
|
697
|
|
|
self.assertEqual(tanimoto('', 'the quick', None), float('-inf')) |
|
698
|
|
|
self.assertAlmostEqual(tanimoto(NONQ_FROM, NONQ_TO, None), |
|
699
|
|
|
math.log(1/3, 2)) |
|
700
|
|
|
self.assertAlmostEqual(tanimoto(NONQ_TO, NONQ_FROM, None), |
|
701
|
|
|
math.log(1/3, 2)) |
|
702
|
|
|
|
|
703
|
|
|
|
|
704
|
|
|
class CosineSimilarityTestCases(unittest.TestCase): |
|
705
|
|
|
"""Test cosine similarity functions. |
|
706
|
|
|
|
|
707
|
|
|
abydos.distance.sim_cosine & .dist_cosine |
|
708
|
|
|
""" |
|
709
|
|
|
|
|
710
|
|
|
def test_sim_cosine(self): |
|
711
|
|
|
"""Test abydos.distance.sim_cosine.""" |
|
712
|
|
|
self.assertEqual(sim_cosine('', ''), 1) |
|
713
|
|
|
self.assertEqual(sim_cosine('nelson', ''), 0) |
|
714
|
|
|
self.assertEqual(sim_cosine('', 'neilsen'), 0) |
|
715
|
|
|
self.assertAlmostEqual(sim_cosine('nelson', 'neilsen'), |
|
716
|
|
|
4/math.sqrt(7*8)) |
|
717
|
|
|
|
|
718
|
|
|
self.assertEqual(sim_cosine('', '', 2), 1) |
|
719
|
|
|
self.assertEqual(sim_cosine('nelson', '', 2), 0) |
|
720
|
|
|
self.assertEqual(sim_cosine('', 'neilsen', 2), 0) |
|
721
|
|
|
self.assertAlmostEqual(sim_cosine('nelson', 'neilsen', 2), |
|
722
|
|
|
4/math.sqrt(7*8)) |
|
723
|
|
|
|
|
724
|
|
|
# supplied q-gram tests |
|
725
|
|
|
self.assertEqual(sim_cosine(QGrams(''), QGrams('')), 1) |
|
726
|
|
|
self.assertEqual(sim_cosine(QGrams('nelson'), QGrams('')), 0) |
|
727
|
|
|
self.assertEqual(sim_cosine(QGrams(''), QGrams('neilsen')), 0) |
|
728
|
|
|
self.assertAlmostEqual(sim_cosine(QGrams('nelson'), QGrams('neilsen')), |
|
729
|
|
|
4/math.sqrt(7*8)) |
|
730
|
|
|
|
|
731
|
|
|
# non-q-gram tests |
|
732
|
|
|
self.assertEqual(sim_cosine('', '', None), 1) |
|
733
|
|
|
self.assertEqual(sim_cosine('the quick', '', None), 0) |
|
734
|
|
|
self.assertEqual(sim_cosine('', 'the quick', None), 0) |
|
735
|
|
|
self.assertAlmostEqual(sim_cosine(NONQ_FROM, NONQ_TO, None), |
|
736
|
|
|
4/math.sqrt(9*7)) |
|
737
|
|
|
self.assertAlmostEqual(sim_cosine(NONQ_TO, NONQ_FROM, None), |
|
738
|
|
|
4/math.sqrt(9*7)) |
|
739
|
|
|
|
|
740
|
|
|
def test_dist_cosine(self): |
|
741
|
|
|
"""Test abydos.distance.dist_cosine.""" |
|
742
|
|
|
self.assertEqual(dist_cosine('', ''), 0) |
|
743
|
|
|
self.assertEqual(dist_cosine('nelson', ''), 1) |
|
744
|
|
|
self.assertEqual(dist_cosine('', 'neilsen'), 1) |
|
745
|
|
|
self.assertAlmostEqual(dist_cosine('nelson', 'neilsen'), |
|
746
|
|
|
1-(4/math.sqrt(7*8))) |
|
747
|
|
|
|
|
748
|
|
|
self.assertEqual(dist_cosine('', '', 2), 0) |
|
749
|
|
|
self.assertEqual(dist_cosine('nelson', '', 2), 1) |
|
750
|
|
|
self.assertEqual(dist_cosine('', 'neilsen', 2), 1) |
|
751
|
|
|
self.assertAlmostEqual(dist_cosine('nelson', 'neilsen', 2), |
|
752
|
|
|
1-(4/math.sqrt(7*8))) |
|
753
|
|
|
|
|
754
|
|
|
# supplied q-gram tests |
|
755
|
|
|
self.assertEqual(dist_cosine(QGrams(''), QGrams('')), 0) |
|
756
|
|
|
self.assertEqual(dist_cosine(QGrams('nelson'), QGrams('')), 1) |
|
757
|
|
|
self.assertEqual(dist_cosine(QGrams(''), QGrams('neilsen')), 1) |
|
758
|
|
|
self.assertAlmostEqual(dist_cosine(QGrams('nelson'), |
|
759
|
|
|
QGrams('neilsen')), |
|
760
|
|
|
1-(4/math.sqrt(7*8))) |
|
761
|
|
|
|
|
762
|
|
|
# non-q-gram tests |
|
763
|
|
|
self.assertEqual(dist_cosine('', '', None), 0) |
|
764
|
|
|
self.assertEqual(dist_cosine('the quick', '', None), 1) |
|
765
|
|
|
self.assertEqual(dist_cosine('', 'the quick', None), 1) |
|
766
|
|
|
self.assertAlmostEqual(dist_cosine(NONQ_FROM, NONQ_TO, None), |
|
767
|
|
|
1-4/math.sqrt(9*7)) |
|
768
|
|
|
self.assertAlmostEqual(dist_cosine(NONQ_TO, NONQ_FROM, None), |
|
769
|
|
|
1-4/math.sqrt(9*7)) |
|
770
|
|
|
|
|
771
|
|
|
|
|
772
|
|
|
class JaroWinklerTestCases(unittest.TestCase): |
|
773
|
|
|
"""Test Jaro(-Winkler) functions. |
|
774
|
|
|
|
|
775
|
|
|
abydos.distance.sim_strcmp95, .dist_strcmp95, .sim_jaro_winkler, & |
|
776
|
|
|
.dist_jaro_winkler |
|
777
|
|
|
""" |
|
778
|
|
|
|
|
779
|
|
|
def test_sim_strcmp95(self): |
|
780
|
|
|
"""Test abydos.distance.sim_strcmp95.""" |
|
781
|
|
|
self.assertEqual(sim_strcmp95('', ''), 1) |
|
782
|
|
|
self.assertEqual(sim_strcmp95('MARTHA', ''), 0) |
|
783
|
|
|
self.assertEqual(sim_strcmp95('', 'MARTHA'), 0) |
|
784
|
|
|
self.assertEqual(sim_strcmp95('MARTHA', 'MARTHA'), 1) |
|
785
|
|
|
|
|
786
|
|
|
self.assertAlmostEqual(sim_strcmp95('MARTHA', 'MARHTA'), 0.96111111) |
|
787
|
|
|
self.assertAlmostEqual(sim_strcmp95('DWAYNE', 'DUANE'), 0.873) |
|
788
|
|
|
self.assertAlmostEqual(sim_strcmp95('DIXON', 'DICKSONX'), 0.839333333) |
|
789
|
|
|
|
|
790
|
|
|
self.assertAlmostEqual(sim_strcmp95('ABCD', 'EFGH'), 0.0) |
|
791
|
|
|
|
|
792
|
|
|
# long_strings = True |
|
793
|
|
|
self.assertAlmostEqual(sim_strcmp95('DIXON', 'DICKSONX', True), |
|
794
|
|
|
0.85393939) |
|
795
|
|
|
self.assertAlmostEqual(sim_strcmp95('DWAYNE', 'DUANE', True), |
|
796
|
|
|
0.89609090) |
|
797
|
|
|
self.assertAlmostEqual(sim_strcmp95('MARTHA', 'MARHTA', True), |
|
798
|
|
|
0.97083333) |
|
799
|
|
|
|
|
800
|
|
|
def test_dist_strcmp95(self): |
|
801
|
|
|
"""Test abydos.distance.dist_strcmp95.""" |
|
802
|
|
|
self.assertEqual(dist_strcmp95('', ''), 0) |
|
803
|
|
|
self.assertEqual(dist_strcmp95('MARTHA', ''), 1) |
|
804
|
|
|
self.assertEqual(dist_strcmp95('', 'MARTHA'), 1) |
|
805
|
|
|
self.assertEqual(dist_strcmp95('MARTHA', 'MARTHA'), 0) |
|
806
|
|
|
|
|
807
|
|
|
self.assertAlmostEqual(dist_strcmp95('MARTHA', 'MARHTA'), 0.03888888) |
|
808
|
|
|
self.assertAlmostEqual(dist_strcmp95('DWAYNE', 'DUANE'), 0.127) |
|
809
|
|
|
self.assertAlmostEqual(dist_strcmp95('DIXON', 'DICKSONX'), 0.160666666) |
|
810
|
|
|
|
|
811
|
|
|
self.assertAlmostEqual(dist_strcmp95('ABCD', 'EFGH'), 1.0) |
|
812
|
|
|
|
|
813
|
|
|
def test_sim_jaro_winkler(self): |
|
814
|
|
|
"""Test abydos.distance.sim_jaro_winkler.""" |
|
815
|
|
|
self.assertEqual(sim_jaro_winkler('', '', mode='jaro'), 1) |
|
816
|
|
|
self.assertEqual(sim_jaro_winkler('', '', mode='winkler'), 1) |
|
817
|
|
|
self.assertEqual(sim_jaro_winkler('MARTHA', '', mode='jaro'), 0) |
|
818
|
|
|
self.assertEqual(sim_jaro_winkler('MARTHA', '', mode='winkler'), 0) |
|
819
|
|
|
self.assertEqual(sim_jaro_winkler('', 'MARHTA', mode='jaro'), 0) |
|
820
|
|
|
self.assertEqual(sim_jaro_winkler('', 'MARHTA', mode='winkler'), 0) |
|
821
|
|
|
self.assertEqual(sim_jaro_winkler('MARTHA', 'MARTHA', mode='jaro'), 1) |
|
822
|
|
|
self.assertEqual(sim_jaro_winkler('MARTHA', 'MARTHA', mode='winkler'), |
|
823
|
|
|
1) |
|
824
|
|
|
|
|
825
|
|
|
# https://en.wikipedia.org/wiki/Jaro-Winkler_distance |
|
826
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('MARTHA', 'MARHTA', |
|
827
|
|
|
mode='jaro'), 0.94444444) |
|
828
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('MARTHA', 'MARHTA', |
|
829
|
|
|
mode='winkler'), 0.96111111) |
|
830
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('DWAYNE', 'DUANE', |
|
831
|
|
|
mode='jaro'), 0.82222222) |
|
832
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('DWAYNE', 'DUANE', |
|
833
|
|
|
mode='winkler'), 0.84) |
|
834
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('DIXON', 'DICKSONX', |
|
835
|
|
|
mode='jaro'), 0.76666666) |
|
836
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('DIXON', 'DICKSONX', |
|
837
|
|
|
mode='winkler'), 0.81333333) |
|
838
|
|
|
|
|
839
|
|
|
self.assertRaises(ValueError, sim_jaro_winkler, 'abcd', 'dcba', |
|
840
|
|
|
boost_threshold=2) |
|
841
|
|
|
self.assertRaises(ValueError, sim_jaro_winkler, 'abcd', 'dcba', |
|
842
|
|
|
boost_threshold=-1) |
|
843
|
|
|
self.assertRaises(ValueError, sim_jaro_winkler, 'abcd', 'dcba', |
|
844
|
|
|
scaling_factor=0.3) |
|
845
|
|
|
self.assertRaises(ValueError, sim_jaro_winkler, 'abcd', 'dcba', |
|
846
|
|
|
scaling_factor=-1) |
|
847
|
|
|
|
|
848
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('ABCD', 'EFGH'), 0.0) |
|
849
|
|
|
|
|
850
|
|
|
# long_strings = True (applies only to Jaro-Winkler, not Jaro) |
|
851
|
|
|
self.assertEqual(sim_jaro_winkler('ABCD', 'EFGH', long_strings=True), |
|
852
|
|
|
sim_jaro_winkler('ABCD', 'EFGH')) |
|
853
|
|
|
self.assertEqual(sim_jaro_winkler('DIXON', 'DICKSONX', mode='jaro', |
|
854
|
|
|
long_strings=True), |
|
855
|
|
|
sim_jaro_winkler('DIXON', 'DICKSONX', |
|
856
|
|
|
mode='jaro')) |
|
857
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('DIXON', 'DICKSONX', |
|
858
|
|
|
mode='winkler', |
|
859
|
|
|
long_strings=True), 0.83030303) |
|
860
|
|
|
self.assertAlmostEqual(sim_jaro_winkler('MARTHA', 'MARHTA', |
|
861
|
|
|
mode='winkler', |
|
862
|
|
|
long_strings=True), 0.97083333) |
|
863
|
|
|
|
|
864
|
|
|
def test_dist_jaro_winkler(self): |
|
865
|
|
|
"""Test abydos.distance.dist_jaro_winkler.""" |
|
866
|
|
|
self.assertEqual(dist_jaro_winkler('', '', mode='jaro'), 0) |
|
867
|
|
|
self.assertEqual(dist_jaro_winkler('', '', mode='winkler'), 0) |
|
868
|
|
|
self.assertEqual(dist_jaro_winkler('MARTHA', '', mode='jaro'), 1) |
|
869
|
|
|
self.assertEqual(dist_jaro_winkler('MARTHA', '', mode='winkler'), 1) |
|
870
|
|
|
self.assertEqual(dist_jaro_winkler('', 'MARHTA', mode='jaro'), 1) |
|
871
|
|
|
self.assertEqual(dist_jaro_winkler('', 'MARHTA', mode='winkler'), 1) |
|
872
|
|
|
self.assertEqual(dist_jaro_winkler('MARTHA', 'MARTHA', mode='jaro'), 0) |
|
873
|
|
|
self.assertEqual(dist_jaro_winkler('MARTHA', 'MARTHA', mode='winkler'), |
|
874
|
|
|
0) |
|
875
|
|
|
|
|
876
|
|
|
# https://en.wikipedia.org/wiki/Jaro-Winkler_distance |
|
877
|
|
|
self.assertAlmostEqual(dist_jaro_winkler('MARTHA', 'MARHTA', |
|
878
|
|
|
mode='jaro'), 0.05555555) |
|
879
|
|
|
self.assertAlmostEqual(dist_jaro_winkler('MARTHA', 'MARHTA', |
|
880
|
|
|
mode='winkler'), 0.03888888) |
|
881
|
|
|
self.assertAlmostEqual(dist_jaro_winkler('DWAYNE', 'DUANE', |
|
882
|
|
|
mode='jaro'), 0.17777777) |
|
883
|
|
|
self.assertAlmostEqual(dist_jaro_winkler('DWAYNE', 'DUANE', |
|
884
|
|
|
mode='winkler'), 0.16) |
|
885
|
|
|
self.assertAlmostEqual(dist_jaro_winkler('DIXON', 'DICKSONX', |
|
886
|
|
|
mode='jaro'), 0.23333333) |
|
887
|
|
|
self.assertAlmostEqual(dist_jaro_winkler('DIXON', 'DICKSONX', |
|
888
|
|
|
mode='winkler'), 0.18666666) |
|
889
|
|
|
|
|
890
|
|
|
self.assertRaises(ValueError, dist_jaro_winkler, 'abcd', 'dcba', |
|
891
|
|
|
boost_threshold=2) |
|
892
|
|
|
self.assertRaises(ValueError, dist_jaro_winkler, 'abcd', 'dcba', |
|
893
|
|
|
boost_threshold=-1) |
|
894
|
|
|
self.assertRaises(ValueError, dist_jaro_winkler, 'abcd', 'dcba', |
|
895
|
|
|
scaling_factor=0.3) |
|
896
|
|
|
self.assertRaises(ValueError, dist_jaro_winkler, 'abcd', 'dcba', |
|
897
|
|
|
scaling_factor=-1) |
|
898
|
|
|
|
|
899
|
|
|
self.assertAlmostEqual(dist_jaro_winkler('ABCD', 'EFGH'), 1.0) |
|
900
|
|
|
|
|
901
|
|
|
|
|
902
|
|
|
class LcsseqTestCases(unittest.TestCase): |
|
903
|
|
|
"""Test LCSseq functions. |
|
904
|
|
|
|
|
905
|
|
|
abydos.distance.lcsseq, .sim_lcsseq, & .dist_lcsseq |
|
906
|
|
|
""" |
|
907
|
|
|
|
|
908
|
|
|
def test_lcsseq(self): |
|
909
|
|
|
"""Test abydos.distance.lcsseq.""" |
|
910
|
|
|
self.assertEqual(lcsseq('', ''), '') |
|
911
|
|
|
self.assertEqual(lcsseq('A', ''), '') |
|
912
|
|
|
self.assertEqual(lcsseq('', 'A'), '') |
|
913
|
|
|
self.assertEqual(lcsseq('A', 'A'), 'A') |
|
914
|
|
|
self.assertEqual(lcsseq('ABCD', ''), '') |
|
915
|
|
|
self.assertEqual(lcsseq('', 'ABCD'), '') |
|
916
|
|
|
self.assertEqual(lcsseq('ABCD', 'ABCD'), 'ABCD') |
|
917
|
|
|
self.assertEqual(lcsseq('ABCD', 'BC'), 'BC') |
|
918
|
|
|
self.assertEqual(lcsseq('ABCD', 'AD'), 'AD') |
|
919
|
|
|
self.assertEqual(lcsseq('ABCD', 'AC'), 'AC') |
|
920
|
|
|
self.assertEqual(lcsseq('AB', 'CD'), '') |
|
921
|
|
|
self.assertEqual(lcsseq('ABC', 'BCD'), 'BC') |
|
922
|
|
|
|
|
923
|
|
|
self.assertEqual(lcsseq('DIXON', 'DICKSONX'), 'DION') |
|
924
|
|
|
|
|
925
|
|
|
# https://en.wikipedia.org/wiki/Longest_common_subsequence_problem |
|
926
|
|
|
self.assertEqual(lcsseq('AGCAT', 'GAC'), 'AC') |
|
927
|
|
|
self.assertEqual(lcsseq('XMJYAUZ', 'MZJAWXU'), 'MJAU') |
|
928
|
|
|
|
|
929
|
|
|
# https://github.com/jwmerrill/factor/blob/master/basis/lcs/lcs-tests.factor |
|
930
|
|
|
self.assertEqual(lcsseq('hell', 'hello'), 'hell') |
|
931
|
|
|
self.assertEqual(lcsseq('hello', 'hell'), 'hell') |
|
932
|
|
|
self.assertEqual(lcsseq('ell', 'hell'), 'ell') |
|
933
|
|
|
self.assertEqual(lcsseq('hell', 'ell'), 'ell') |
|
934
|
|
|
self.assertEqual(lcsseq('faxbcd', 'abdef'), 'abd') |
|
935
|
|
|
|
|
936
|
|
|
# http://www.unesco.org/culture/languages-atlas/assets/_core/php/qcubed_unit_tests.php |
|
937
|
|
|
self.assertEqual(lcsseq('hello world', 'world war 2'), 'world') |
|
938
|
|
|
self.assertEqual(lcsseq('foo bar', 'bar foo'), 'foo') |
|
939
|
|
|
self.assertEqual(lcsseq('aaa', 'aa'), 'aa') |
|
940
|
|
|
self.assertEqual(lcsseq('cc', 'bbbbcccccc'), 'cc') |
|
941
|
|
|
self.assertEqual(lcsseq('ccc', 'bcbb'), 'c') |
|
942
|
|
|
|
|
943
|
|
|
def test_sim_lcsseq(self): |
|
944
|
|
|
"""Test abydos.distance.sim_lcsseq.""" |
|
945
|
|
|
self.assertEqual(sim_lcsseq('', ''), 1) |
|
946
|
|
|
self.assertEqual(sim_lcsseq('A', ''), 0) |
|
947
|
|
|
self.assertEqual(sim_lcsseq('', 'A'), 0) |
|
948
|
|
|
self.assertEqual(sim_lcsseq('A', 'A'), 1) |
|
949
|
|
|
self.assertEqual(sim_lcsseq('ABCD', ''), 0) |
|
950
|
|
|
self.assertEqual(sim_lcsseq('', 'ABCD'), 0) |
|
951
|
|
|
self.assertEqual(sim_lcsseq('ABCD', 'ABCD'), 1) |
|
952
|
|
|
self.assertAlmostEqual(sim_lcsseq('ABCD', 'BC'), 2/4) |
|
953
|
|
|
self.assertAlmostEqual(sim_lcsseq('ABCD', 'AD'), 2/4) |
|
954
|
|
|
self.assertAlmostEqual(sim_lcsseq('ABCD', 'AC'), 2/4) |
|
955
|
|
|
self.assertAlmostEqual(sim_lcsseq('AB', 'CD'), 0) |
|
956
|
|
|
self.assertAlmostEqual(sim_lcsseq('ABC', 'BCD'), 2/3) |
|
957
|
|
|
|
|
958
|
|
|
self.assertAlmostEqual(sim_lcsseq('DIXON', 'DICKSONX'), 4/8) |
|
959
|
|
|
|
|
960
|
|
|
# https://en.wikipedia.org/wiki/Longest_common_subsequence_problem |
|
961
|
|
|
self.assertAlmostEqual(sim_lcsseq('AGCAT', 'GAC'), 2/5) |
|
962
|
|
|
self.assertAlmostEqual(sim_lcsseq('XMJYAUZ', 'MZJAWXU'), 4/7) |
|
963
|
|
|
|
|
964
|
|
|
# https://github.com/jwmerrill/factor/blob/master/basis/lcs/lcs-tests.factor |
|
965
|
|
|
self.assertAlmostEqual(sim_lcsseq('hell', 'hello'), 4/5) |
|
966
|
|
|
self.assertAlmostEqual(sim_lcsseq('hello', 'hell'), 4/5) |
|
967
|
|
|
self.assertAlmostEqual(sim_lcsseq('ell', 'hell'), 3/4) |
|
968
|
|
|
self.assertAlmostEqual(sim_lcsseq('hell', 'ell'), 3/4) |
|
969
|
|
|
self.assertAlmostEqual(sim_lcsseq('faxbcd', 'abdef'), 3/6) |
|
970
|
|
|
|
|
971
|
|
|
# http://www.unesco.org/culture/languages-atlas/assets/_core/php/qcubed_unit_tests.php |
|
972
|
|
|
self.assertAlmostEqual(sim_lcsseq('hello world', 'world war 2'), 5/11) |
|
973
|
|
|
self.assertAlmostEqual(sim_lcsseq('foo bar', 'bar foo'), 3/7) |
|
974
|
|
|
self.assertAlmostEqual(sim_lcsseq('aaa', 'aa'), 2/3) |
|
975
|
|
|
self.assertAlmostEqual(sim_lcsseq('cc', 'bbbbcccccc'), 2/10) |
|
976
|
|
|
self.assertAlmostEqual(sim_lcsseq('ccc', 'bcbb'), 1/4) |
|
977
|
|
|
|
|
978
|
|
|
def test_dist_lcsseq(self): |
|
979
|
|
|
"""Test abydos.distance.dist_lcsseq.""" |
|
980
|
|
|
self.assertEqual(dist_lcsseq('', ''), 0) |
|
981
|
|
|
self.assertEqual(dist_lcsseq('A', ''), 1) |
|
982
|
|
|
self.assertEqual(dist_lcsseq('', 'A'), 1) |
|
983
|
|
|
self.assertEqual(dist_lcsseq('A', 'A'), 0) |
|
984
|
|
|
self.assertEqual(dist_lcsseq('ABCD', ''), 1) |
|
985
|
|
|
self.assertEqual(dist_lcsseq('', 'ABCD'), 1) |
|
986
|
|
|
self.assertEqual(dist_lcsseq('ABCD', 'ABCD'), 0) |
|
987
|
|
|
self.assertAlmostEqual(dist_lcsseq('ABCD', 'BC'), 2/4) |
|
988
|
|
|
self.assertAlmostEqual(dist_lcsseq('ABCD', 'AD'), 2/4) |
|
989
|
|
|
self.assertAlmostEqual(dist_lcsseq('ABCD', 'AC'), 2/4) |
|
990
|
|
|
self.assertAlmostEqual(dist_lcsseq('AB', 'CD'), 1) |
|
991
|
|
|
self.assertAlmostEqual(dist_lcsseq('ABC', 'BCD'), 1/3) |
|
992
|
|
|
|
|
993
|
|
|
self.assertAlmostEqual(dist_lcsseq('DIXON', 'DICKSONX'), 4/8) |
|
994
|
|
|
|
|
995
|
|
|
# https://en.wikipedia.org/wiki/Longest_common_subsequence_problem |
|
996
|
|
|
self.assertAlmostEqual(dist_lcsseq('AGCAT', 'GAC'), 3/5) |
|
997
|
|
|
self.assertAlmostEqual(dist_lcsseq('XMJYAUZ', 'MZJAWXU'), 3/7) |
|
998
|
|
|
|
|
999
|
|
|
# https://github.com/jwmerrill/factor/blob/master/basis/lcs/lcs-tests.factor |
|
1000
|
|
|
self.assertAlmostEqual(dist_lcsseq('hell', 'hello'), 1/5) |
|
1001
|
|
|
self.assertAlmostEqual(dist_lcsseq('hello', 'hell'), 1/5) |
|
1002
|
|
|
self.assertAlmostEqual(dist_lcsseq('ell', 'hell'), 1/4) |
|
1003
|
|
|
self.assertAlmostEqual(dist_lcsseq('hell', 'ell'), 1/4) |
|
1004
|
|
|
self.assertAlmostEqual(dist_lcsseq('faxbcd', 'abdef'), 3/6) |
|
1005
|
|
|
|
|
1006
|
|
|
# http://www.unesco.org/culture/languages-atlas/assets/_core/php/qcubed_unit_tests.php |
|
1007
|
|
|
self.assertAlmostEqual(dist_lcsseq('hello world', 'world war 2'), 6/11) |
|
1008
|
|
|
self.assertAlmostEqual(dist_lcsseq('foo bar', 'bar foo'), 4/7) |
|
1009
|
|
|
self.assertAlmostEqual(dist_lcsseq('aaa', 'aa'), 1/3) |
|
1010
|
|
|
self.assertAlmostEqual(dist_lcsseq('cc', 'bbbbcccccc'), 8/10) |
|
1011
|
|
|
self.assertAlmostEqual(dist_lcsseq('ccc', 'bcbb'), 3/4) |
|
1012
|
|
|
|
|
1013
|
|
|
|
|
1014
|
|
|
class LcsstrTestCases(unittest.TestCase): |
|
1015
|
|
|
"""Test LCSstr functions. |
|
1016
|
|
|
|
|
1017
|
|
|
abydos.distance.lcsstr, .sim_lcsstr, & .dist_lcsstr |
|
1018
|
|
|
""" |
|
1019
|
|
|
|
|
1020
|
|
|
def test_lcsstr(self): |
|
1021
|
|
|
"""Test abydos.distance.lcsstr.""" |
|
1022
|
|
|
self.assertEqual(lcsstr('', ''), '') |
|
1023
|
|
|
self.assertEqual(lcsstr('A', ''), '') |
|
1024
|
|
|
self.assertEqual(lcsstr('', 'A'), '') |
|
1025
|
|
|
self.assertEqual(lcsstr('A', 'A'), 'A') |
|
1026
|
|
|
self.assertEqual(lcsstr('ABCD', ''), '') |
|
1027
|
|
|
self.assertEqual(lcsstr('', 'ABCD'), '') |
|
1028
|
|
|
self.assertEqual(lcsstr('ABCD', 'ABCD'), 'ABCD') |
|
1029
|
|
|
self.assertEqual(lcsstr('ABCD', 'BC'), 'BC') |
|
1030
|
|
|
self.assertEqual(lcsstr('ABCD', 'AD'), 'A') |
|
1031
|
|
|
self.assertEqual(lcsstr('ABCD', 'AC'), 'A') |
|
1032
|
|
|
self.assertEqual(lcsstr('AB', 'CD'), '') |
|
1033
|
|
|
self.assertEqual(lcsstr('ABC', 'BCD'), 'BC') |
|
1034
|
|
|
|
|
1035
|
|
|
self.assertEqual(lcsstr('DIXON', 'DICKSONX'), 'DI') |
|
1036
|
|
|
|
|
1037
|
|
|
# https://en.wikipedia.org/wiki/Longest_common_subsequence_problem |
|
1038
|
|
|
self.assertEqual(lcsstr('AGCAT', 'GAC'), 'A') |
|
1039
|
|
|
self.assertEqual(lcsstr('XMJYAUZ', 'MZJAWXU'), 'X') |
|
1040
|
|
|
|
|
1041
|
|
|
# https://github.com/jwmerrill/factor/blob/master/basis/lcs/lcs-tests.factor |
|
1042
|
|
|
self.assertEqual(lcsstr('hell', 'hello'), 'hell') |
|
1043
|
|
|
self.assertEqual(lcsstr('hello', 'hell'), 'hell') |
|
1044
|
|
|
self.assertEqual(lcsstr('ell', 'hell'), 'ell') |
|
1045
|
|
|
self.assertEqual(lcsstr('hell', 'ell'), 'ell') |
|
1046
|
|
|
self.assertEqual(lcsstr('faxbcd', 'abdef'), 'f') |
|
1047
|
|
|
|
|
1048
|
|
|
# http://www.unesco.org/culture/languages-atlas/assets/_core/php/qcubed_unit_tests.php |
|
1049
|
|
|
self.assertEqual(lcsstr('hello world', 'world war 2'), 'world') |
|
1050
|
|
|
self.assertEqual(lcsstr('foo bar', 'bar foo'), 'foo') |
|
1051
|
|
|
self.assertEqual(lcsstr('aaa', 'aa'), 'aa') |
|
1052
|
|
|
self.assertEqual(lcsstr('cc', 'bbbbcccccc'), 'cc') |
|
1053
|
|
|
self.assertEqual(lcsstr('ccc', 'bcbb'), 'c') |
|
1054
|
|
|
|
|
1055
|
|
|
# http://www.maplesoft.com/support/help/Maple/view.aspx?path=StringTools/LongestCommonSubString |
|
1056
|
|
|
self.assertEqual(lcsstr('abax', 'bax'), 'bax') |
|
1057
|
|
|
self.assertEqual(lcsstr('tsaxbaxyz', 'axcaxy'), 'axy') |
|
1058
|
|
|
self.assertEqual(lcsstr('abcde', 'uvabxycde'), 'cde') |
|
1059
|
|
|
self.assertEqual(lcsstr('abc', 'xyz'), '') |
|
1060
|
|
|
self.assertEqual(lcsstr('TAAGGTCGGCGCGCACGCTGGCGAGTATGGTGCGGAGGCCCTGGAG\ |
|
1061
|
|
|
AGGTGAGGCTCCCTCCCCTGCTCCGACCCGGGCTCCTCGCCCGCCCGGACCCAC', 'AAGCGCCGCGCAGTCTGGGCT\ |
|
1062
|
|
|
CCGCACACTTCTGGTCCAGTCCGACTGAGAAGGAACCACCATGGTGCTGTCTCCCGCTGACAAGACCAACATCAAGACT\ |
|
1063
|
|
|
GCCTGGGAAAAGATCGGCAGCCACGGTGGCGAGTATGGCGCCGAGGCCGT'), 'TGGCGAGTATGG') |
|
1064
|
|
|
|
|
1065
|
|
|
def test_sim_lcsstr(self): |
|
1066
|
|
|
"""Test abydos.distance.sim_lcsstr.""" |
|
1067
|
|
|
self.assertEqual(sim_lcsstr('', ''), 1) |
|
1068
|
|
|
self.assertEqual(sim_lcsstr('A', ''), 0) |
|
1069
|
|
|
self.assertEqual(sim_lcsstr('', 'A'), 0) |
|
1070
|
|
|
self.assertEqual(sim_lcsstr('A', 'A'), 1) |
|
1071
|
|
|
self.assertEqual(sim_lcsstr('ABCD', ''), 0) |
|
1072
|
|
|
self.assertEqual(sim_lcsstr('', 'ABCD'), 0) |
|
1073
|
|
|
self.assertEqual(sim_lcsstr('ABCD', 'ABCD'), 1) |
|
1074
|
|
|
self.assertAlmostEqual(sim_lcsstr('ABCD', 'BC'), 2/4) |
|
1075
|
|
|
self.assertAlmostEqual(sim_lcsstr('ABCD', 'AD'), 1/4) |
|
1076
|
|
|
self.assertAlmostEqual(sim_lcsstr('ABCD', 'AC'), 1/4) |
|
1077
|
|
|
self.assertAlmostEqual(sim_lcsstr('AB', 'CD'), 0) |
|
1078
|
|
|
self.assertAlmostEqual(sim_lcsstr('ABC', 'BCD'), 2/3) |
|
1079
|
|
|
|
|
1080
|
|
|
self.assertAlmostEqual(sim_lcsstr('DIXON', 'DICKSONX'), 2/8) |
|
1081
|
|
|
|
|
1082
|
|
|
# https://en.wikipedia.org/wiki/Longest_common_subsequence_problem |
|
1083
|
|
|
self.assertAlmostEqual(sim_lcsstr('AGCAT', 'GAC'), 1/5) |
|
1084
|
|
|
self.assertAlmostEqual(sim_lcsstr('XMJYAUZ', 'MZJAWXU'), 1/7) |
|
1085
|
|
|
|
|
1086
|
|
|
# https://github.com/jwmerrill/factor/blob/master/basis/lcs/lcs-tests.factor |
|
1087
|
|
|
self.assertAlmostEqual(sim_lcsstr('hell', 'hello'), 4/5) |
|
1088
|
|
|
self.assertAlmostEqual(sim_lcsstr('hello', 'hell'), 4/5) |
|
1089
|
|
|
self.assertAlmostEqual(sim_lcsstr('ell', 'hell'), 3/4) |
|
1090
|
|
|
self.assertAlmostEqual(sim_lcsstr('hell', 'ell'), 3/4) |
|
1091
|
|
|
self.assertAlmostEqual(sim_lcsstr('faxbcd', 'abdef'), 1/6) |
|
1092
|
|
|
|
|
1093
|
|
|
# http://www.unesco.org/culture/languages-atlas/assets/_core/php/qcubed_unit_tests.php |
|
1094
|
|
|
self.assertAlmostEqual(sim_lcsstr('hello world', 'world war 2'), 5/11) |
|
1095
|
|
|
self.assertAlmostEqual(sim_lcsstr('foo bar', 'bar foo'), 3/7) |
|
1096
|
|
|
self.assertAlmostEqual(sim_lcsstr('aaa', 'aa'), 2/3) |
|
1097
|
|
|
self.assertAlmostEqual(sim_lcsstr('cc', 'bbbbcccccc'), 2/10) |
|
1098
|
|
|
self.assertAlmostEqual(sim_lcsstr('ccc', 'bcbb'), 1/4) |
|
1099
|
|
|
|
|
1100
|
|
|
def test_dist_lcsstr(self): |
|
1101
|
|
|
"""Test abydos.distance.dist_lcsstr.""" |
|
1102
|
|
|
self.assertEqual(dist_lcsstr('', ''), 0) |
|
1103
|
|
|
self.assertEqual(dist_lcsstr('A', ''), 1) |
|
1104
|
|
|
self.assertEqual(dist_lcsstr('', 'A'), 1) |
|
1105
|
|
|
self.assertEqual(dist_lcsstr('A', 'A'), 0) |
|
1106
|
|
|
self.assertEqual(dist_lcsstr('ABCD', ''), 1) |
|
1107
|
|
|
self.assertEqual(dist_lcsstr('', 'ABCD'), 1) |
|
1108
|
|
|
self.assertEqual(dist_lcsstr('ABCD', 'ABCD'), 0) |
|
1109
|
|
|
self.assertAlmostEqual(dist_lcsstr('ABCD', 'BC'), 2/4) |
|
1110
|
|
|
self.assertAlmostEqual(dist_lcsstr('ABCD', 'AD'), 3/4) |
|
1111
|
|
|
self.assertAlmostEqual(dist_lcsstr('ABCD', 'AC'), 3/4) |
|
1112
|
|
|
self.assertAlmostEqual(dist_lcsstr('AB', 'CD'), 1) |
|
1113
|
|
|
self.assertAlmostEqual(dist_lcsstr('ABC', 'BCD'), 1/3) |
|
1114
|
|
|
|
|
1115
|
|
|
self.assertAlmostEqual(dist_lcsstr('DIXON', 'DICKSONX'), 6/8) |
|
1116
|
|
|
|
|
1117
|
|
|
# https://en.wikipedia.org/wiki/Longest_common_subsequence_problem |
|
1118
|
|
|
self.assertAlmostEqual(dist_lcsstr('AGCAT', 'GAC'), 4/5) |
|
1119
|
|
|
self.assertAlmostEqual(dist_lcsstr('XMJYAUZ', 'MZJAWXU'), 6/7) |
|
1120
|
|
|
|
|
1121
|
|
|
# https://github.com/jwmerrill/factor/blob/master/basis/lcs/lcs-tests.factor |
|
1122
|
|
|
self.assertAlmostEqual(dist_lcsstr('hell', 'hello'), 1/5) |
|
1123
|
|
|
self.assertAlmostEqual(dist_lcsstr('hello', 'hell'), 1/5) |
|
1124
|
|
|
self.assertAlmostEqual(dist_lcsstr('ell', 'hell'), 1/4) |
|
1125
|
|
|
self.assertAlmostEqual(dist_lcsstr('hell', 'ell'), 1/4) |
|
1126
|
|
|
self.assertAlmostEqual(dist_lcsstr('faxbcd', 'abdef'), 5/6) |
|
1127
|
|
|
|
|
1128
|
|
|
# http://www.unesco.org/culture/languages-atlas/assets/_core/php/qcubed_unit_tests.php |
|
1129
|
|
|
self.assertAlmostEqual(dist_lcsstr('hello world', 'world war 2'), 6/11) |
|
1130
|
|
|
self.assertAlmostEqual(dist_lcsstr('foo bar', 'bar foo'), 4/7) |
|
1131
|
|
|
self.assertAlmostEqual(dist_lcsstr('aaa', 'aa'), 1/3) |
|
1132
|
|
|
self.assertAlmostEqual(dist_lcsstr('cc', 'bbbbcccccc'), 8/10) |
|
1133
|
|
|
self.assertAlmostEqual(dist_lcsstr('ccc', 'bcbb'), 3/4) |
|
1134
|
|
|
|
|
1135
|
|
|
|
|
1136
|
|
|
class RatcliffObershelpTestCases(unittest.TestCase): |
|
1137
|
|
|
"""Test Ratcliff-Obserhelp functions. |
|
1138
|
|
|
|
|
1139
|
|
|
abydos.distance.sim_ratcliff_obershelp, & |
|
1140
|
|
|
abydos.distance.dist_ratcliff_obershelp |
|
1141
|
|
|
""" |
|
1142
|
|
|
|
|
1143
|
|
|
def test_sim_ratcliff_obershelp(self): |
|
1144
|
|
|
"""Test abydos.distance.sim_ratcliff_obershelp.""" |
|
1145
|
|
|
# https://github.com/rockymadden/stringmetric/blob/master/core/src/test/scala/com/rockymadden/stringmetric/similarity/RatcliffObershelpMetricSpec.scala |
|
1146
|
|
|
self.assertEqual(sim_ratcliff_obershelp('', ''), 1) |
|
1147
|
|
|
self.assertEqual(sim_ratcliff_obershelp('abc', ''), 0) |
|
1148
|
|
|
self.assertEqual(sim_ratcliff_obershelp('', 'xyz'), 0) |
|
1149
|
|
|
self.assertEqual(sim_ratcliff_obershelp('abc', 'abc'), 1) |
|
1150
|
|
|
self.assertEqual(sim_ratcliff_obershelp('123', '123'), 1) |
|
1151
|
|
|
self.assertEqual(sim_ratcliff_obershelp('abc', 'xyz'), 0) |
|
1152
|
|
|
self.assertEqual(sim_ratcliff_obershelp('123', '456'), 0) |
|
1153
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp('aleksander', |
|
1154
|
|
|
'alexandre'), |
|
1155
|
|
|
0.7368421052631579) |
|
1156
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp('alexandre', |
|
1157
|
|
|
'aleksander'), |
|
1158
|
|
|
0.7368421052631579) |
|
1159
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp('pennsylvania', |
|
1160
|
|
|
'pencilvaneya'), |
|
1161
|
|
|
0.6666666666666666) |
|
1162
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp('pencilvaneya', |
|
1163
|
|
|
'pennsylvania'), |
|
1164
|
|
|
0.6666666666666666) |
|
1165
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp('abcefglmn', 'abefglmo'), |
|
1166
|
|
|
0.8235294117647058) |
|
1167
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp('abefglmo', 'abcefglmn'), |
|
1168
|
|
|
0.8235294117647058) |
|
1169
|
|
|
|
|
1170
|
|
|
with open(TESTDIR+'/corpora/variantNames.csv') as cav_testset: |
|
1171
|
|
|
next(cav_testset) |
|
1172
|
|
|
for line in cav_testset: |
|
1173
|
|
|
line = line.strip().split(',') |
|
1174
|
|
|
word1, word2 = line[0], line[4] |
|
1175
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp(word1, word2), |
|
1176
|
|
|
SequenceMatcher(None, word1, |
|
1177
|
|
|
word2).ratio()) |
|
1178
|
|
|
|
|
1179
|
|
|
with open(TESTDIR+'/corpora/wikipediaCommonMisspellings.csv') as missp: |
|
1180
|
|
|
next(missp) |
|
1181
|
|
|
for line in missp: |
|
1182
|
|
|
line = line.strip().upper() |
|
1183
|
|
|
line = ''.join([_ for _ in line.strip() if _ in |
|
1184
|
|
|
tuple('ABCDEFGHIJKLMNOPQRSTUVWXYZ,')]) |
|
1185
|
|
|
word1, word2 = line.split(',') |
|
1186
|
|
|
# print(word1, word2e) |
|
1187
|
|
|
self.assertAlmostEqual(sim_ratcliff_obershelp(word1, word2), |
|
1188
|
|
|
SequenceMatcher(None, word1, |
|
1189
|
|
|
word2).ratio()) |
|
1190
|
|
|
|
|
1191
|
|
|
def test_dist_ratcliff_obershelp(self): |
|
1192
|
|
|
"""Test abydos.distance.dist_ratcliff_obershelp.""" |
|
1193
|
|
|
# https://github.com/rockymadden/stringmetric/blob/master/core/src/test/scala/com/rockymadden/stringmetric/similarity/RatcliffObershelpMetricSpec.scala |
|
1194
|
|
|
self.assertEqual(dist_ratcliff_obershelp('', ''), 0) |
|
1195
|
|
|
self.assertEqual(dist_ratcliff_obershelp('abc', ''), 1) |
|
1196
|
|
|
self.assertEqual(dist_ratcliff_obershelp('', 'xyz'), 1) |
|
1197
|
|
|
self.assertEqual(dist_ratcliff_obershelp('abc', 'abc'), 0) |
|
1198
|
|
|
self.assertEqual(dist_ratcliff_obershelp('123', '123'), 0) |
|
1199
|
|
|
self.assertEqual(dist_ratcliff_obershelp('abc', 'xyz'), 1) |
|
1200
|
|
|
self.assertEqual(dist_ratcliff_obershelp('123', '456'), 1) |
|
1201
|
|
|
self.assertAlmostEqual(dist_ratcliff_obershelp('aleksander', |
|
1202
|
|
|
'alexandre'), |
|
1203
|
|
|
0.2631578947368421) |
|
1204
|
|
|
self.assertAlmostEqual(dist_ratcliff_obershelp('alexandre', |
|
1205
|
|
|
'aleksander'), |
|
1206
|
|
|
0.2631578947368421) |
|
1207
|
|
|
self.assertAlmostEqual(dist_ratcliff_obershelp('pennsylvania', |
|
1208
|
|
|
'pencilvaneya'), |
|
1209
|
|
|
0.3333333333333333) |
|
1210
|
|
|
self.assertAlmostEqual(dist_ratcliff_obershelp('pencilvaneya', |
|
1211
|
|
|
'pennsylvania'), |
|
1212
|
|
|
0.3333333333333333) |
|
1213
|
|
|
self.assertAlmostEqual(dist_ratcliff_obershelp('abcefglmn', |
|
1214
|
|
|
'abefglmo'), |
|
1215
|
|
|
0.1764705882352941) |
|
1216
|
|
|
self.assertAlmostEqual(dist_ratcliff_obershelp('abefglmo', |
|
1217
|
|
|
'abcefglmn'), |
|
1218
|
|
|
0.1764705882352941) |
|
1219
|
|
|
|
|
1220
|
|
|
|
|
1221
|
|
|
class MraTestCases(unittest.TestCase): |
|
1222
|
|
|
"""Test MRA functions. |
|
1223
|
|
|
|
|
1224
|
|
|
abydos.distance.mra_compare, .sim_mra & .dist_mra |
|
1225
|
|
|
""" |
|
1226
|
|
|
|
|
1227
|
|
|
def test_mra_compare(self): |
|
1228
|
|
|
"""Test abydos.distance.mra_compare.""" |
|
1229
|
|
|
self.assertEqual(mra_compare('', ''), 6) |
|
1230
|
|
|
self.assertEqual(mra_compare('a', 'a'), 6) |
|
1231
|
|
|
self.assertEqual(mra_compare('abcdefg', 'abcdefg'), 6) |
|
1232
|
|
|
self.assertEqual(mra_compare('abcdefg', ''), 0) |
|
1233
|
|
|
self.assertEqual(mra_compare('', 'abcdefg'), 0) |
|
1234
|
|
|
|
|
1235
|
|
|
# https://en.wikipedia.org/wiki/Match_rating_approach |
|
1236
|
|
|
self.assertEqual(mra_compare('Byrne', 'Boern'), 5) |
|
1237
|
|
|
self.assertEqual(mra_compare('Smith', 'Smyth'), 5) |
|
1238
|
|
|
self.assertEqual(mra_compare('Catherine', 'Kathryn'), 4) |
|
1239
|
|
|
|
|
1240
|
|
|
self.assertEqual(mra_compare('ab', 'abcdefgh'), 0) |
|
1241
|
|
|
self.assertEqual(mra_compare('ab', 'ac'), 5) |
|
1242
|
|
|
self.assertEqual(mra_compare('abcdefik', 'abcdefgh'), 3) |
|
1243
|
|
|
self.assertEqual(mra_compare('xyz', 'abc'), 0) |
|
1244
|
|
|
|
|
1245
|
|
|
def test_sim_mra(self): |
|
1246
|
|
|
"""Test abydos.distance.sim_mra.""" |
|
1247
|
|
|
self.assertEqual(sim_mra('', ''), 1) |
|
1248
|
|
|
self.assertEqual(sim_mra('a', 'a'), 1) |
|
1249
|
|
|
self.assertEqual(sim_mra('abcdefg', 'abcdefg'), 1) |
|
1250
|
|
|
self.assertEqual(sim_mra('abcdefg', ''), 0) |
|
1251
|
|
|
self.assertEqual(sim_mra('', 'abcdefg'), 0) |
|
1252
|
|
|
|
|
1253
|
|
|
# https://en.wikipedia.org/wiki/Match_rating_approach |
|
1254
|
|
|
self.assertEqual(sim_mra('Byrne', 'Boern'), 5/6) |
|
1255
|
|
|
self.assertEqual(sim_mra('Smith', 'Smyth'), 5/6) |
|
1256
|
|
|
self.assertEqual(sim_mra('Catherine', 'Kathryn'), 4/6) |
|
1257
|
|
|
|
|
1258
|
|
|
self.assertEqual(sim_mra('ab', 'abcdefgh'), 0) |
|
1259
|
|
|
self.assertEqual(sim_mra('ab', 'ac'), 5/6) |
|
1260
|
|
|
self.assertEqual(sim_mra('abcdefik', 'abcdefgh'), 3/6) |
|
1261
|
|
|
self.assertEqual(sim_mra('xyz', 'abc'), 0) |
|
1262
|
|
|
|
|
1263
|
|
|
def test_dist_mra(self): |
|
1264
|
|
|
"""Test abydos.distance.dist_mra.""" |
|
1265
|
|
|
self.assertEqual(dist_mra('', ''), 0) |
|
1266
|
|
|
self.assertEqual(dist_mra('a', 'a'), 0) |
|
1267
|
|
|
self.assertEqual(dist_mra('abcdefg', 'abcdefg'), 0) |
|
1268
|
|
|
self.assertEqual(dist_mra('abcdefg', ''), 1) |
|
1269
|
|
|
self.assertEqual(dist_mra('', 'abcdefg'), 1) |
|
1270
|
|
|
|
|
1271
|
|
|
# https://en.wikipedia.org/wiki/Match_rating_approach |
|
1272
|
|
|
self.assertAlmostEqual(dist_mra('Byrne', 'Boern'), 1/6) |
|
1273
|
|
|
self.assertAlmostEqual(dist_mra('Smith', 'Smyth'), 1/6) |
|
1274
|
|
|
self.assertAlmostEqual(dist_mra('Catherine', 'Kathryn'), 2/6) |
|
1275
|
|
|
|
|
1276
|
|
|
self.assertEqual(dist_mra('ab', 'abcdefgh'), 1) |
|
1277
|
|
|
self.assertAlmostEqual(dist_mra('ab', 'ac'), 1/6) |
|
1278
|
|
|
self.assertAlmostEqual(dist_mra('abcdefik', 'abcdefgh'), 3/6) |
|
1279
|
|
|
self.assertEqual(dist_mra('xyz', 'abc'), 1) |
|
1280
|
|
|
|
|
1281
|
|
|
|
|
1282
|
|
|
class CompressionTestCases(unittest.TestCase): |
|
1283
|
|
|
"""Test compression distance functions. |
|
1284
|
|
|
|
|
1285
|
|
|
abydos.distance.dist_compression & .sim_compression |
|
1286
|
|
|
""" |
|
1287
|
|
|
|
|
1288
|
|
|
arith_dict = ac_train(' '.join(NIALL)) |
|
1289
|
|
|
|
|
1290
|
|
|
def test_dist_compression(self): |
|
1291
|
|
|
"""Test abydos.distance.dist_compression.""" |
|
1292
|
|
|
self.assertEqual(dist_compression('', ''), 0) |
|
1293
|
|
|
self.assertEqual(dist_compression('', '', 'bzip2'), 0) |
|
1294
|
|
|
self.assertEqual(dist_compression('', '', 'lzma'), 0) |
|
1295
|
|
|
self.assertEqual(dist_compression('', '', 'zlib'), 0) |
|
1296
|
|
|
self.assertEqual(dist_compression('', '', 'arith'), 0) |
|
1297
|
|
|
self.assertEqual(dist_compression('', '', 'arith', self.arith_dict), 0) |
|
1298
|
|
|
self.assertEqual(dist_compression('', '', 'rle'), 0) |
|
1299
|
|
|
self.assertEqual(dist_compression('', '', 'bwtrle'), 0) |
|
1300
|
|
|
|
|
1301
|
|
|
self.assertGreater(dist_compression('a', ''), 0) |
|
1302
|
|
|
self.assertGreater(dist_compression('a', '', 'bzip2'), 0) |
|
1303
|
|
|
self.assertGreater(dist_compression('a', '', 'lzma'), 0) |
|
1304
|
|
|
self.assertGreater(dist_compression('a', '', 'zlib'), 0) |
|
1305
|
|
|
self.assertGreater(dist_compression('a', '', 'arith'), 0) |
|
1306
|
|
|
self.assertGreater(dist_compression('a', '', 'arith', self.arith_dict), |
|
1307
|
|
|
0) |
|
1308
|
|
|
self.assertGreater(dist_compression('a', '', 'rle'), 0) |
|
1309
|
|
|
self.assertGreater(dist_compression('a', '', 'bwtrle'), 0) |
|
1310
|
|
|
|
|
1311
|
|
|
self.assertGreater(dist_compression('abcdefg', 'fg'), 0) |
|
1312
|
|
|
self.assertGreater(dist_compression('abcdefg', 'fg', 'bzip2'), 0) |
|
1313
|
|
|
self.assertGreater(dist_compression('abcdefg', 'fg', 'lzma'), 0) |
|
1314
|
|
|
self.assertGreater(dist_compression('abcdefg', 'fg', 'zlib'), 0) |
|
1315
|
|
|
self.assertGreater(dist_compression('abcdefg', 'fg', 'arith'), 0) |
|
1316
|
|
|
self.assertGreater(dist_compression('abcdefg', 'fg', 'rle'), 0) |
|
1317
|
|
|
self.assertGreater(dist_compression('abcdefg', 'fg', 'bwtrle'), 0) |
|
1318
|
|
|
|
|
1319
|
|
|
def test_dist_compression_arith(self): |
|
1320
|
|
|
"""Test abydos.distance.dist_compression (arithmetric compression).""" |
|
1321
|
|
|
self.assertAlmostEqual(dist_compression('Niall', 'Neil', 'arith', |
|
1322
|
|
|
self.arith_dict), |
|
1323
|
|
|
0.608695652173913) |
|
1324
|
|
|
self.assertAlmostEqual(dist_compression('Neil', 'Niall', 'arith', |
|
1325
|
|
|
self.arith_dict), |
|
1326
|
|
|
0.608695652173913) |
|
1327
|
|
|
self.assertAlmostEqual(dist_compression('Niall', 'Neil', 'arith'), |
|
1328
|
|
|
0.6875) |
|
1329
|
|
|
self.assertAlmostEqual(dist_compression('Neil', 'Niall', 'arith'), |
|
1330
|
|
|
0.6875) |
|
1331
|
|
|
self.assertAlmostEqual(dist_compression('Njáll', 'Njall', 'arith', |
|
1332
|
|
|
self.arith_dict), |
|
1333
|
|
|
0.714285714285714) |
|
1334
|
|
|
self.assertAlmostEqual(dist_compression('Njall', 'Njáll', 'arith', |
|
1335
|
|
|
self.arith_dict), |
|
1336
|
|
|
0.714285714285714) |
|
1337
|
|
|
self.assertAlmostEqual(dist_compression('Njáll', 'Njall', 'arith'), |
|
1338
|
|
|
0.75) |
|
1339
|
|
|
self.assertAlmostEqual(dist_compression('Njall', 'Njáll', 'arith'), |
|
1340
|
|
|
0.75) |
|
1341
|
|
|
|
|
1342
|
|
|
def test_dist_compression_rle(self): |
|
1343
|
|
|
"""Test abydos.distance.dist_compression (RLE & BWT+RLE).""" |
|
1344
|
|
|
self.assertAlmostEqual(dist_compression('abc', 'abc', 'rle'), 0) |
|
1345
|
|
|
self.assertAlmostEqual(dist_compression('abc', 'def', 'rle'), 1) |
|
1346
|
|
|
|
|
1347
|
|
|
self.assertAlmostEqual(dist_compression('abc', 'abc', 'bwtrle'), 0) |
|
1348
|
|
|
self.assertAlmostEqual(dist_compression('abc', 'def', 'bwtrle'), 0.75) |
|
1349
|
|
|
|
|
1350
|
|
|
self.assertAlmostEqual(dist_compression('aaa', 'bbaaa', 'rle'), 0.5) |
|
1351
|
|
|
self.assertAlmostEqual(dist_compression('abb', 'bbba', 'rle'), 1/3) |
|
1352
|
|
|
self.assertAlmostEqual(dist_compression('banana', 'banane', 'bwtrle'), |
|
1353
|
|
|
0.57142857142) |
|
1354
|
|
|
self.assertAlmostEqual(dist_compression('bananas', 'bananen', |
|
1355
|
|
|
'bwtrle'), |
|
1356
|
|
|
0.5) |
|
1357
|
|
|
|
|
1358
|
|
|
def test_sim_compression(self): |
|
1359
|
|
|
"""Test abydos.distance.sim_compression.""" |
|
1360
|
|
|
self.assertEqual(sim_compression('', ''), 1) |
|
1361
|
|
|
self.assertEqual(sim_compression('', '', 'bzip2'), 1) |
|
1362
|
|
|
self.assertEqual(sim_compression('', '', 'lzma'), 1) |
|
1363
|
|
|
self.assertEqual(sim_compression('', '', 'zlib'), 1) |
|
1364
|
|
|
self.assertEqual(sim_compression('', '', 'arith'), 1) |
|
1365
|
|
|
self.assertEqual(sim_compression('', '', 'arith', self.arith_dict), 1) |
|
1366
|
|
|
self.assertEqual(sim_compression('', '', 'rle'), 1) |
|
1367
|
|
|
self.assertEqual(sim_compression('', '', 'bwtrle'), 1) |
|
1368
|
|
|
|
|
1369
|
|
|
self.assertLess(sim_compression('a', ''), 1) |
|
1370
|
|
|
self.assertLess(sim_compression('a', '', 'bzip2'), 1) |
|
1371
|
|
|
self.assertLess(sim_compression('a', '', 'lzma'), 1) |
|
1372
|
|
|
self.assertLess(sim_compression('a', '', 'zlib'), 1) |
|
1373
|
|
|
self.assertLess(sim_compression('a', '', 'arith'), 1) |
|
1374
|
|
|
self.assertLess(sim_compression('a', '', 'arith', self.arith_dict), 1) |
|
1375
|
|
|
self.assertLess(sim_compression('a', '', 'rle'), 1) |
|
1376
|
|
|
self.assertLess(sim_compression('a', '', 'bwtrle'), 1) |
|
1377
|
|
|
|
|
1378
|
|
|
self.assertLess(sim_compression('abcdefg', 'fg'), 1) |
|
1379
|
|
|
self.assertLess(sim_compression('abcdefg', 'fg', 'bzip2'), 1) |
|
1380
|
|
|
self.assertLess(sim_compression('abcdefg', 'fg', 'lzma'), 1) |
|
1381
|
|
|
self.assertLess(sim_compression('abcdefg', 'fg', 'zlib'), 1) |
|
1382
|
|
|
self.assertLess(sim_compression('abcdefg', 'fg', 'arith'), 1) |
|
1383
|
|
|
self.assertLess(sim_compression('abcdefg', 'fg', 'rle'), 1) |
|
1384
|
|
|
self.assertLess(sim_compression('abcdefg', 'fg', 'bwtrle'), 1) |
|
1385
|
|
|
|
|
1386
|
|
|
def test_sim_compression_arith(self): |
|
1387
|
|
|
"""Test abydos.distance.sim_compression (arithmetric compression).""" |
|
1388
|
|
|
self.assertAlmostEqual(sim_compression('Niall', 'Neil', 'arith', |
|
1389
|
|
|
self.arith_dict), |
|
1390
|
|
|
0.3913043478260869) |
|
1391
|
|
|
self.assertAlmostEqual(sim_compression('Neil', 'Niall', 'arith', |
|
1392
|
|
|
self.arith_dict), |
|
1393
|
|
|
0.3913043478260869) |
|
1394
|
|
|
self.assertAlmostEqual(sim_compression('Niall', 'Neil', 'arith'), |
|
1395
|
|
|
0.3125) |
|
1396
|
|
|
self.assertAlmostEqual(sim_compression('Neil', 'Niall', 'arith'), |
|
1397
|
|
|
0.3125) |
|
1398
|
|
|
self.assertAlmostEqual(sim_compression('Njáll', 'Njall', 'arith', |
|
1399
|
|
|
self.arith_dict), |
|
1400
|
|
|
0.285714285714285) |
|
1401
|
|
|
self.assertAlmostEqual(sim_compression('Njall', 'Njáll', 'arith', |
|
1402
|
|
|
self.arith_dict), |
|
1403
|
|
|
0.285714285714285) |
|
1404
|
|
|
self.assertAlmostEqual(sim_compression('Njáll', 'Njall', 'arith'), |
|
1405
|
|
|
0.25) |
|
1406
|
|
|
self.assertAlmostEqual(sim_compression('Njall', 'Njáll', 'arith'), |
|
1407
|
|
|
0.25) |
|
1408
|
|
|
|
|
1409
|
|
|
def test_sim_compression_rle(self): |
|
1410
|
|
|
"""Test abydos.distance.sim_compression (RLE & BWT+RLE).""" |
|
1411
|
|
|
self.assertAlmostEqual(sim_compression('abc', 'abc', 'rle'), 1) |
|
1412
|
|
|
self.assertAlmostEqual(sim_compression('abc', 'def', 'rle'), 0) |
|
1413
|
|
|
|
|
1414
|
|
|
self.assertAlmostEqual(sim_compression('abc', 'abc', 'bwtrle'), 1) |
|
1415
|
|
|
self.assertAlmostEqual(sim_compression('abc', 'def', 'bwtrle'), 0.25) |
|
1416
|
|
|
|
|
1417
|
|
|
self.assertAlmostEqual(sim_compression('aaa', 'bbaaa', 'rle'), 0.5) |
|
1418
|
|
|
self.assertAlmostEqual(sim_compression('abb', 'bbba', 'rle'), 2/3) |
|
1419
|
|
|
self.assertAlmostEqual(sim_compression('banana', 'banane', 'bwtrle'), |
|
1420
|
|
|
0.42857142857) |
|
1421
|
|
|
self.assertAlmostEqual(sim_compression('bananas', 'bananen', 'bwtrle'), |
|
1422
|
|
|
0.5) |
|
1423
|
|
|
|
|
1424
|
|
|
|
|
1425
|
|
|
class MongeElkanTestCases(unittest.TestCase): |
|
1426
|
|
|
"""Test Monge-Elkan functions. |
|
1427
|
|
|
|
|
1428
|
|
|
abydos.distance.sim_monge_elkan & .dist_monge_elkan |
|
1429
|
|
|
""" |
|
1430
|
|
|
|
|
1431
|
|
|
def test_sim_monge_elkan(self): |
|
1432
|
|
|
"""Test abydos.distance.sim_monge_elkan.""" |
|
1433
|
|
|
self.assertEqual(sim_monge_elkan('', ''), 1) |
|
1434
|
|
|
self.assertEqual(sim_monge_elkan('', 'a'), 0) |
|
1435
|
|
|
self.assertEqual(sim_monge_elkan('a', 'a'), 1) |
|
1436
|
|
|
|
|
1437
|
|
|
self.assertEqual(sim_monge_elkan('Niall', 'Neal'), 3/4) |
|
1438
|
|
|
self.assertEqual(sim_monge_elkan('Niall', 'Njall'), 5/6) |
|
1439
|
|
|
self.assertEqual(sim_monge_elkan('Niall', 'Niel'), 3/4) |
|
1440
|
|
|
self.assertEqual(sim_monge_elkan('Niall', 'Nigel'), 3/4) |
|
1441
|
|
|
|
|
1442
|
|
|
self.assertEqual(sim_monge_elkan('Niall', 'Neal', symmetric=True), |
|
1443
|
|
|
31/40) |
|
1444
|
|
|
self.assertEqual(sim_monge_elkan('Niall', 'Njall', symmetric=True), |
|
1445
|
|
|
5/6) |
|
1446
|
|
|
self.assertEqual(sim_monge_elkan('Niall', 'Niel', symmetric=True), |
|
1447
|
|
|
31/40) |
|
1448
|
|
|
self.assertAlmostEqual(sim_monge_elkan('Niall', 'Nigel', |
|
1449
|
|
|
symmetric=True), 17/24) |
|
1450
|
|
|
|
|
1451
|
|
|
def test_dist_monge_elkan(self): |
|
1452
|
|
|
"""Test abydos.distance.dist_monge_elkan.""" |
|
1453
|
|
|
self.assertEqual(dist_monge_elkan('', ''), 0) |
|
1454
|
|
|
self.assertEqual(dist_monge_elkan('', 'a'), 1) |
|
1455
|
|
|
|
|
1456
|
|
|
self.assertEqual(dist_monge_elkan('Niall', 'Neal'), 1/4) |
|
1457
|
|
|
self.assertAlmostEqual(dist_monge_elkan('Niall', 'Njall'), 1/6) |
|
1458
|
|
|
self.assertEqual(dist_monge_elkan('Niall', 'Niel'), 1/4) |
|
1459
|
|
|
self.assertEqual(dist_monge_elkan('Niall', 'Nigel'), 1/4) |
|
1460
|
|
|
|
|
1461
|
|
|
self.assertAlmostEqual(dist_monge_elkan('Niall', 'Neal', |
|
1462
|
|
|
symmetric=True), 9/40) |
|
1463
|
|
|
self.assertAlmostEqual(dist_monge_elkan('Niall', 'Njall', |
|
1464
|
|
|
symmetric=True), 1/6) |
|
1465
|
|
|
self.assertAlmostEqual(dist_monge_elkan('Niall', 'Niel', |
|
1466
|
|
|
symmetric=True), 9/40) |
|
1467
|
|
|
self.assertAlmostEqual(dist_monge_elkan('Niall', 'Nigel', |
|
1468
|
|
|
symmetric=True), 7/24) |
|
1469
|
|
|
|
|
1470
|
|
|
|
|
1471
|
|
|
class IdentityTestCases(unittest.TestCase): |
|
1472
|
|
|
"""Test identity similarity functions. |
|
1473
|
|
|
|
|
1474
|
|
|
abydos.distance.sim_ident & .dist_ident |
|
1475
|
|
|
""" |
|
1476
|
|
|
|
|
1477
|
|
|
def test_sim_ident(self): |
|
1478
|
|
|
"""Test abydos.distance.sim_ident.""" |
|
1479
|
|
|
self.assertEqual(sim_ident('', ''), 1) |
|
1480
|
|
|
self.assertEqual(sim_ident('', 'a'), 0) |
|
1481
|
|
|
self.assertEqual(sim_ident('a', ''), 0) |
|
1482
|
|
|
self.assertEqual(sim_ident('a', 'a'), 1) |
|
1483
|
|
|
self.assertEqual(sim_ident('abcd', 'abcd'), 1) |
|
1484
|
|
|
self.assertEqual(sim_ident('abcd', 'dcba'), 0) |
|
1485
|
|
|
self.assertEqual(sim_ident('abc', 'cba'), 0) |
|
1486
|
|
|
|
|
1487
|
|
|
def test_dist_ident(self): |
|
1488
|
|
|
"""Test abydos.distance.dist_ident.""" |
|
1489
|
|
|
self.assertEqual(dist_ident('', ''), 0) |
|
1490
|
|
|
self.assertEqual(dist_ident('', 'a'), 1) |
|
1491
|
|
|
self.assertEqual(dist_ident('a', ''), 1) |
|
1492
|
|
|
self.assertEqual(dist_ident('a', 'a'), 0) |
|
1493
|
|
|
self.assertEqual(dist_ident('abcd', 'abcd'), 0) |
|
1494
|
|
|
self.assertEqual(dist_ident('abcd', 'dcba'), 1) |
|
1495
|
|
|
self.assertEqual(dist_ident('abc', 'cba'), 1) |
|
1496
|
|
|
|
|
1497
|
|
|
|
|
1498
|
|
|
def _sim_wikipedia(src, tar): |
|
1499
|
|
|
"""Return a similarity score for two DNA base pairs. |
|
1500
|
|
|
|
|
1501
|
|
|
Values copied from: |
|
1502
|
|
|
https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm |
|
1503
|
|
|
""" |
|
1504
|
|
|
nw_matrix = {('A', 'A'): 10, ('G', 'G'): 7, ('C', 'C'): 9, ('T', 'T'): 8, |
|
1505
|
|
|
('A', 'G'): -1, ('A', 'C'): -3, ('A', 'T'): -4, |
|
1506
|
|
|
('G', 'C'): -5, ('G', 'T'): -3, ('C', 'T'): 0} |
|
1507
|
|
|
return sim_matrix(src, tar, nw_matrix, symmetric=True, alphabet='CGAT') |
|
1508
|
|
|
|
|
1509
|
|
|
|
|
1510
|
|
|
def _sim_nw(src, tar): |
|
1511
|
|
|
"""Return 1 if src is tar, otherwise -1.""" |
|
1512
|
|
|
return 2*float(src is tar)-1 |
|
1513
|
|
|
|
|
1514
|
|
|
|
|
1515
|
|
|
class MatrixSimTestCases(unittest.TestCase): |
|
1516
|
|
|
"""Test matrix similarity functions. |
|
1517
|
|
|
|
|
1518
|
|
|
abydos.distance.sim_matrix |
|
1519
|
|
|
""" |
|
1520
|
|
|
|
|
1521
|
|
|
def test_sim_matrix(self): |
|
1522
|
|
|
"""Test abydos.distance.sim_matrix.""" |
|
1523
|
|
|
self.assertEqual(sim_matrix('', ''), 1) |
|
1524
|
|
|
self.assertEqual(sim_matrix('', 'a'), 0) |
|
1525
|
|
|
self.assertEqual(sim_matrix('a', ''), 0) |
|
1526
|
|
|
self.assertEqual(sim_matrix('a', 'a'), 1) |
|
1527
|
|
|
self.assertEqual(sim_matrix('abcd', 'abcd'), 1) |
|
1528
|
|
|
self.assertEqual(sim_matrix('abcd', 'dcba'), 0) |
|
1529
|
|
|
self.assertEqual(sim_matrix('abc', 'cba'), 0) |
|
1530
|
|
|
|
|
1531
|
|
|
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm |
|
1532
|
|
|
self.assertEqual(_sim_wikipedia('A', 'C'), -3) |
|
1533
|
|
|
self.assertEqual(_sim_wikipedia('G', 'G'), 7) |
|
1534
|
|
|
self.assertEqual(_sim_wikipedia('A', 'A'), 10) |
|
1535
|
|
|
self.assertEqual(_sim_wikipedia('T', 'A'), -4) |
|
1536
|
|
|
self.assertEqual(_sim_wikipedia('T', 'C'), 0) |
|
1537
|
|
|
self.assertEqual(_sim_wikipedia('A', 'G'), -1) |
|
1538
|
|
|
self.assertEqual(_sim_wikipedia('C', 'T'), 0) |
|
1539
|
|
|
|
|
1540
|
|
|
self.assertRaises(ValueError, sim_matrix, 'abc', 'cba', alphabet='ab') |
|
1541
|
|
|
self.assertRaises(ValueError, sim_matrix, 'abc', 'ba', alphabet='ab') |
|
1542
|
|
|
self.assertRaises(ValueError, sim_matrix, 'ab', 'cba', alphabet='ab') |
|
1543
|
|
|
|
|
1544
|
|
|
|
|
1545
|
|
|
class NeedlemanWunschTestCases(unittest.TestCase): |
|
1546
|
|
|
"""Test Needleman-Wunsch functions. |
|
1547
|
|
|
|
|
1548
|
|
|
abydos.distance.needleman_wunsch |
|
1549
|
|
|
""" |
|
1550
|
|
|
|
|
1551
|
|
|
def test_needleman_wunsch(self): |
|
1552
|
|
|
"""Test abydos.distance.needleman_wunsch.""" |
|
1553
|
|
|
self.assertEqual(needleman_wunsch('', ''), 0) |
|
1554
|
|
|
|
|
1555
|
|
|
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm |
|
1556
|
|
|
self.assertEqual(needleman_wunsch('GATTACA', 'GCATGCU', |
|
1557
|
|
|
1, _sim_nw), 0) |
|
1558
|
|
|
self.assertEqual(needleman_wunsch('AGACTAGTTAC', 'CGAGACGT', |
|
1559
|
|
|
5, _sim_wikipedia), 16) |
|
1560
|
|
|
|
|
1561
|
|
|
# checked against http://ds9a.nl/nwunsch/ (mismatch=1, gap=5, skew=5) |
|
1562
|
|
|
self.assertEqual(needleman_wunsch('CGATATCAG', 'TGACGSTGC', |
|
1563
|
|
|
5, _sim_nw), -5) |
|
1564
|
|
|
self.assertEqual(needleman_wunsch('AGACTAGTTAC', 'TGACGSTGC', |
|
1565
|
|
|
5, _sim_nw), -7) |
|
1566
|
|
|
self.assertEqual(needleman_wunsch('AGACTAGTTAC', 'CGAGACGT', |
|
1567
|
|
|
5, _sim_nw), -15) |
|
1568
|
|
|
|
|
1569
|
|
|
def test_needleman_wunsch_nialls(self): |
|
1570
|
|
|
"""Test abydos.distance.needleman_wunsch (Nialls set).""" |
|
1571
|
|
|
# checked against http://ds9a.nl/nwunsch/ (mismatch=1, gap=2, skew=2) |
|
1572
|
|
|
nw_vals = (5, 0, -2, 3, 1, 1, -2, -2, -1, -3, -3, -5, -3, -7, -7, -19) |
|
1573
|
|
|
for i in range(len(NIALL)): |
|
1574
|
|
|
self.assertEqual(needleman_wunsch(NIALL[0], NIALL[i], 2, |
|
1575
|
|
|
_sim_nw), nw_vals[i]) |
|
1576
|
|
|
|
|
1577
|
|
|
|
|
1578
|
|
|
class SmithWatermanTestCases(unittest.TestCase): |
|
1579
|
|
|
"""Test Smith-Waterman functions. |
|
1580
|
|
|
|
|
1581
|
|
|
abydos.distance.smith_waterman |
|
1582
|
|
|
""" |
|
1583
|
|
|
|
|
1584
|
|
|
def test_smith_waterman(self): |
|
1585
|
|
|
"""Test abydos.distance.smith_waterman.""" |
|
1586
|
|
|
self.assertEqual(smith_waterman('', ''), 0) |
|
1587
|
|
|
|
|
1588
|
|
|
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm |
|
1589
|
|
|
self.assertEqual(smith_waterman('GATTACA', 'GCATGCU', |
|
1590
|
|
|
1, _sim_nw), 0) |
|
1591
|
|
|
self.assertEqual(smith_waterman('AGACTAGTTAC', 'CGAGACGT', |
|
1592
|
|
|
5, _sim_wikipedia), 26) |
|
1593
|
|
|
|
|
1594
|
|
|
self.assertEqual(smith_waterman('CGATATCAG', 'TGACGSTGC', |
|
1595
|
|
|
5, _sim_nw), 0) |
|
1596
|
|
|
self.assertEqual(smith_waterman('AGACTAGTTAC', 'TGACGSTGC', |
|
1597
|
|
|
5, _sim_nw), 1) |
|
1598
|
|
|
self.assertEqual(smith_waterman('AGACTAGTTAC', 'CGAGACGT', |
|
1599
|
|
|
5, _sim_nw), 0) |
|
1600
|
|
|
|
|
1601
|
|
|
def test_smith_waterman_nialls(self): |
|
1602
|
|
|
"""Test abydos.distance.smith_waterman (Nialls set).""" |
|
1603
|
|
|
sw_vals = (5, 1, 1, 3, 2, 1, 1, 0, 0, 1, 1, 2, 2, 1, 0, 0) |
|
1604
|
|
|
for i in range(len(NIALL)): |
|
1605
|
|
|
self.assertEqual(smith_waterman(NIALL[0], NIALL[i], 2, |
|
1606
|
|
|
_sim_nw), sw_vals[i]) |
|
1607
|
|
|
|
|
1608
|
|
|
|
|
1609
|
|
|
class GotohTestCases(unittest.TestCase): |
|
1610
|
|
|
"""Test Gotoh functions. |
|
1611
|
|
|
|
|
1612
|
|
|
abydos.distance.gotoh |
|
1613
|
|
|
""" |
|
1614
|
|
|
|
|
1615
|
|
|
def test_gotoh(self): |
|
1616
|
|
|
"""Test abydos.distance.needleman_wunsch_affine.""" |
|
1617
|
|
|
self.assertEqual(gotoh('', ''), 0) |
|
1618
|
|
|
|
|
1619
|
|
|
# https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm |
|
1620
|
|
|
self.assertEqual(gotoh('GATTACA', 'GCATGCU', 1, 1, _sim_nw), 0) |
|
1621
|
|
|
self.assertGreaterEqual(gotoh('GATTACA', 'GCATGCU', 1, 0.5, _sim_nw), |
|
1622
|
|
|
needleman_wunsch('GATTACA', 'GCATGCU', 1, |
|
1623
|
|
|
_sim_nw)) |
|
1624
|
|
|
self.assertEqual(gotoh('AGACTAGTTAC', 'CGAGACGT', 5, 5, |
|
1625
|
|
|
_sim_wikipedia), 16) |
|
1626
|
|
|
self.assertGreaterEqual(gotoh('AGACTAGTTAC', 'CGAGACGT', 5, 2, |
|
1627
|
|
|
_sim_wikipedia), |
|
1628
|
|
|
needleman_wunsch('AGACTAGTTAC', 'CGAGACGT', 5, |
|
1629
|
|
|
_sim_wikipedia)) |
|
1630
|
|
|
|
|
1631
|
|
|
# checked against http://ds9a.nl/nwunsch/ (mismatch=1, gap=5, skew=5) |
|
1632
|
|
|
self.assertEqual(gotoh('CGATATCAG', 'TGACGSTGC', 5, 5, _sim_nw), -5) |
|
1633
|
|
|
self.assertGreaterEqual(gotoh('CGATATCAG', 'TGACGSTGC', 5, 2, _sim_nw), |
|
1634
|
|
|
needleman_wunsch('CGATATCAG', 'TGACGSTGC', 5, |
|
1635
|
|
|
_sim_nw)) |
|
1636
|
|
|
self.assertEqual(gotoh('AGACTAGTTAC', 'TGACGSTGC', 5, 5, _sim_nw), -7) |
|
1637
|
|
|
self.assertGreaterEqual(gotoh('AGACTAGTTAC', 'TGACGSTGC', 5, 2, |
|
1638
|
|
|
_sim_nw), |
|
1639
|
|
|
needleman_wunsch('AGACTAGTTAC', 'TGACGSTGC', 5, |
|
1640
|
|
|
_sim_nw)) |
|
1641
|
|
|
self.assertEqual(gotoh('AGACTAGTTAC', 'CGAGACGT', 5, 5, _sim_nw), -15) |
|
1642
|
|
|
self.assertGreaterEqual(gotoh('AGACTAGTTAC', 'CGAGACGT', 5, 2, |
|
1643
|
|
|
_sim_nw), |
|
1644
|
|
|
needleman_wunsch('AGACTAGTTAC', 'CGAGACGT', 5, |
|
1645
|
|
|
_sim_nw)) |
|
1646
|
|
|
|
|
1647
|
|
|
def test_gotoh_nialls(self): |
|
1648
|
|
|
"""Test abydos.distance.gotoh (Nialls set).""" |
|
1649
|
|
|
# checked against http://ds9a.nl/nwunsch/ (mismatch=1, gap=2, skew=2) |
|
1650
|
|
|
nw_vals = (5, 0, -2, 3, 1, 1, -2, -2, -1, -3, -3, -5, -3, -7, -7, -19) |
|
1651
|
|
|
for i in range(len(NIALL)): |
|
1652
|
|
|
self.assertEqual(gotoh(NIALL[0], NIALL[i], 2, 2, _sim_nw), |
|
1653
|
|
|
nw_vals[i]) |
|
1654
|
|
|
nw_vals2 = (5, 0, -2, 3, 1, 1, -2, -2, -1, -2, -3, -3, -2, -6, -6, -8) |
|
1655
|
|
|
for i in range(len(NIALL)): |
|
1656
|
|
|
self.assertEqual(gotoh(NIALL[0], NIALL[i], 2, 1, _sim_nw), |
|
1657
|
|
|
nw_vals2[i]) |
|
1658
|
|
|
self.assertGreaterEqual(gotoh(NIALL[0], NIALL[i], 2, 0.5, _sim_nw), |
|
1659
|
|
|
needleman_wunsch(NIALL[0], NIALL[i], 2, |
|
1660
|
|
|
_sim_nw)) |
|
1661
|
|
|
|
|
1662
|
|
|
|
|
1663
|
|
|
class LengthTestCases(unittest.TestCase): |
|
1664
|
|
|
"""Test length similarity functions. |
|
1665
|
|
|
|
|
1666
|
|
|
abydos.distance.sim_length & .dist_length |
|
1667
|
|
|
""" |
|
1668
|
|
|
|
|
1669
|
|
|
def test_sim_ident(self): |
|
1670
|
|
|
"""Test abydos.distance.sim_length.""" |
|
1671
|
|
|
self.assertEqual(sim_length('', ''), 1) |
|
1672
|
|
|
self.assertEqual(sim_length('', 'a'), 0) |
|
1673
|
|
|
self.assertEqual(sim_length('a', ''), 0) |
|
1674
|
|
|
self.assertEqual(sim_length('a', 'a'), 1) |
|
1675
|
|
|
self.assertEqual(sim_length('abcd', 'abcd'), 1) |
|
1676
|
|
|
self.assertEqual(sim_length('abcd', 'dcba'), 1) |
|
1677
|
|
|
self.assertEqual(sim_length('abc', 'cba'), 1) |
|
1678
|
|
|
self.assertEqual(sim_length('abc', 'dcba'), 0.75) |
|
1679
|
|
|
self.assertEqual(sim_length('abcd', 'cba'), 0.75) |
|
1680
|
|
|
self.assertEqual(sim_length('ab', 'dcba'), 0.5) |
|
1681
|
|
|
self.assertEqual(sim_length('abcd', 'ba'), 0.5) |
|
1682
|
|
|
|
|
1683
|
|
|
def test_dist_ident(self): |
|
1684
|
|
|
"""Test abydos.distance.dist_length.""" |
|
1685
|
|
|
self.assertEqual(dist_length('', ''), 0) |
|
1686
|
|
|
self.assertEqual(dist_length('', 'a'), 1) |
|
1687
|
|
|
self.assertEqual(dist_length('a', ''), 1) |
|
1688
|
|
|
self.assertEqual(dist_length('a', 'a'), 0) |
|
1689
|
|
|
self.assertEqual(dist_length('abcd', 'abcd'), 0) |
|
1690
|
|
|
self.assertEqual(dist_length('abcd', 'dcba'), 0) |
|
1691
|
|
|
self.assertEqual(dist_length('abc', 'cba'), 0) |
|
1692
|
|
|
self.assertEqual(dist_length('abc', 'dcba'), 0.25) |
|
1693
|
|
|
self.assertEqual(dist_length('abcd', 'cba'), 0.25) |
|
1694
|
|
|
self.assertEqual(dist_length('ab', 'dcba'), 0.5) |
|
1695
|
|
|
self.assertEqual(dist_length('abcd', 'ba'), 0.5) |
|
1696
|
|
|
|
|
1697
|
|
|
|
|
1698
|
|
|
class PrefixTestCases(unittest.TestCase): |
|
1699
|
|
|
"""Test prefix similarity functions. |
|
1700
|
|
|
|
|
1701
|
|
|
abydos.distance.sim_prefix & .dist_prefix |
|
1702
|
|
|
""" |
|
1703
|
|
|
|
|
1704
|
|
|
def test_sim_prefix(self): |
|
1705
|
|
|
"""Test abydos.distance.sim_prefix.""" |
|
1706
|
|
|
self.assertEqual(sim_prefix('', ''), 1) |
|
1707
|
|
|
self.assertEqual(sim_prefix('a', ''), 0) |
|
1708
|
|
|
self.assertEqual(sim_prefix('', 'a'), 0) |
|
1709
|
|
|
self.assertEqual(sim_prefix('a', 'a'), 1) |
|
1710
|
|
|
self.assertEqual(sim_prefix('ax', 'a'), 1) |
|
1711
|
|
|
self.assertEqual(sim_prefix('axx', 'a'), 1) |
|
1712
|
|
|
self.assertEqual(sim_prefix('ax', 'ay'), 1/2) |
|
1713
|
|
|
self.assertEqual(sim_prefix('a', 'ay'), 1) |
|
1714
|
|
|
self.assertEqual(sim_prefix('a', 'ayy'), 1) |
|
1715
|
|
|
self.assertEqual(sim_prefix('ax', 'ay'), 1/2) |
|
1716
|
|
|
self.assertEqual(sim_prefix('a', 'y'), 0) |
|
1717
|
|
|
self.assertEqual(sim_prefix('y', 'a'), 0) |
|
1718
|
|
|
self.assertEqual(sim_prefix('aaax', 'aaa'), 1) |
|
1719
|
|
|
self.assertAlmostEqual(sim_prefix('axxx', 'aaa'), 1/3) |
|
1720
|
|
|
self.assertEqual(sim_prefix('aaxx', 'aayy'), 1/2) |
|
1721
|
|
|
self.assertEqual(sim_prefix('xxaa', 'yyaa'), 0) |
|
1722
|
|
|
self.assertAlmostEqual(sim_prefix('aaxxx', 'aay'), 2/3) |
|
1723
|
|
|
self.assertEqual(sim_prefix('aaxxxx', 'aayyy'), 2/5) |
|
1724
|
|
|
self.assertEqual(sim_prefix('xa', 'a'), 0) |
|
1725
|
|
|
self.assertEqual(sim_prefix('xxa', 'a'), 0) |
|
1726
|
|
|
self.assertEqual(sim_prefix('xa', 'ya'), 0) |
|
1727
|
|
|
self.assertEqual(sim_prefix('a', 'ya'), 0) |
|
1728
|
|
|
self.assertEqual(sim_prefix('a', 'yya'), 0) |
|
1729
|
|
|
self.assertEqual(sim_prefix('xa', 'ya'), 0) |
|
1730
|
|
|
self.assertEqual(sim_prefix('xaaa', 'aaa'), 0) |
|
1731
|
|
|
self.assertEqual(sim_prefix('xxxa', 'aaa'), 0) |
|
1732
|
|
|
self.assertEqual(sim_prefix('xxxaa', 'yaa'), 0) |
|
1733
|
|
|
self.assertEqual(sim_prefix('xxxxaa', 'yyyaa'), 0) |
|
1734
|
|
|
|
|
1735
|
|
|
def test_dist_prefix(self): |
|
1736
|
|
|
"""Test abydos.distance.dist_prefix.""" |
|
1737
|
|
|
self.assertEqual(dist_prefix('', ''), 0) |
|
1738
|
|
|
self.assertEqual(dist_prefix('a', ''), 1) |
|
1739
|
|
|
self.assertEqual(dist_prefix('', 'a'), 1) |
|
1740
|
|
|
self.assertEqual(dist_prefix('a', 'a'), 0) |
|
1741
|
|
|
self.assertEqual(dist_prefix('ax', 'a'), 0) |
|
1742
|
|
|
self.assertEqual(dist_prefix('axx', 'a'), 0) |
|
1743
|
|
|
self.assertEqual(dist_prefix('ax', 'ay'), 1/2) |
|
1744
|
|
|
self.assertEqual(dist_prefix('a', 'ay'), 0) |
|
1745
|
|
|
self.assertEqual(dist_prefix('a', 'ayy'), 0) |
|
1746
|
|
|
self.assertEqual(dist_prefix('ax', 'ay'), 1/2) |
|
1747
|
|
|
self.assertEqual(dist_prefix('a', 'y'), 1) |
|
1748
|
|
|
self.assertEqual(dist_prefix('y', 'a'), 1) |
|
1749
|
|
|
self.assertEqual(dist_prefix('aaax', 'aaa'), 0) |
|
1750
|
|
|
self.assertAlmostEqual(dist_prefix('axxx', 'aaa'), 2/3) |
|
1751
|
|
|
self.assertEqual(dist_prefix('aaxx', 'aayy'), 1/2) |
|
1752
|
|
|
self.assertEqual(dist_prefix('xxaa', 'yyaa'), 1) |
|
1753
|
|
|
self.assertAlmostEqual(dist_prefix('aaxxx', 'aay'), 1/3) |
|
1754
|
|
|
self.assertEqual(dist_prefix('aaxxxx', 'aayyy'), 3/5) |
|
1755
|
|
|
self.assertEqual(dist_prefix('xa', 'a'), 1) |
|
1756
|
|
|
self.assertEqual(dist_prefix('xxa', 'a'), 1) |
|
1757
|
|
|
self.assertEqual(dist_prefix('xa', 'ya'), 1) |
|
1758
|
|
|
self.assertEqual(dist_prefix('a', 'ya'), 1) |
|
1759
|
|
|
self.assertEqual(dist_prefix('a', 'yya'), 1) |
|
1760
|
|
|
self.assertEqual(dist_prefix('xa', 'ya'), 1) |
|
1761
|
|
|
self.assertEqual(dist_prefix('xaaa', 'aaa'), 1) |
|
1762
|
|
|
self.assertEqual(dist_prefix('xxxa', 'aaa'), 1) |
|
1763
|
|
|
self.assertEqual(dist_prefix('xxxaa', 'yaa'), 1) |
|
1764
|
|
|
self.assertEqual(dist_prefix('xxxxaa', 'yyyaa'), 1) |
|
1765
|
|
|
|
|
1766
|
|
|
|
|
1767
|
|
|
class SuffixTestCases(unittest.TestCase): |
|
1768
|
|
|
"""Test suffix similarity functions. |
|
1769
|
|
|
|
|
1770
|
|
|
abydos.distance.sim_suffix & .dist_suffix |
|
1771
|
|
|
""" |
|
1772
|
|
|
|
|
1773
|
|
|
def test_sim_suffix(self): |
|
1774
|
|
|
"""Test abydos.distance.sim_suffix.""" |
|
1775
|
|
|
self.assertEqual(sim_suffix('', ''), 1) |
|
1776
|
|
|
self.assertEqual(sim_suffix('a', ''), 0) |
|
1777
|
|
|
self.assertEqual(sim_suffix('', 'a'), 0) |
|
1778
|
|
|
self.assertEqual(sim_suffix('a', 'a'), 1) |
|
1779
|
|
|
self.assertEqual(sim_suffix('ax', 'a'), 0) |
|
1780
|
|
|
self.assertEqual(sim_suffix('axx', 'a'), 0) |
|
1781
|
|
|
self.assertEqual(sim_suffix('ax', 'ay'), 0) |
|
1782
|
|
|
self.assertEqual(sim_suffix('a', 'ay'), 0) |
|
1783
|
|
|
self.assertEqual(sim_suffix('a', 'ayy'), 0) |
|
1784
|
|
|
self.assertEqual(sim_suffix('ax', 'ay'), 0) |
|
1785
|
|
|
self.assertEqual(sim_suffix('a', 'y'), 0) |
|
1786
|
|
|
self.assertEqual(sim_suffix('y', 'a'), 0) |
|
1787
|
|
|
self.assertEqual(sim_suffix('aaax', 'aaa'), 0) |
|
1788
|
|
|
self.assertEqual(sim_suffix('axxx', 'aaa'), 0) |
|
1789
|
|
|
self.assertEqual(sim_suffix('aaxx', 'aayy'), 0) |
|
1790
|
|
|
self.assertEqual(sim_suffix('xxaa', 'yyaa'), 1/2) |
|
1791
|
|
|
self.assertEqual(sim_suffix('aaxxx', 'aay'), 0) |
|
1792
|
|
|
self.assertEqual(sim_suffix('aaxxxx', 'aayyy'), 0) |
|
1793
|
|
|
self.assertEqual(sim_suffix('xa', 'a'), 1) |
|
1794
|
|
|
self.assertEqual(sim_suffix('xxa', 'a'), 1) |
|
1795
|
|
|
self.assertEqual(sim_suffix('xa', 'ya'), 1/2) |
|
1796
|
|
|
self.assertEqual(sim_suffix('a', 'ya'), 1) |
|
1797
|
|
|
self.assertEqual(sim_suffix('a', 'yya'), 1) |
|
1798
|
|
|
self.assertEqual(sim_suffix('xa', 'ya'), 1/2) |
|
1799
|
|
|
self.assertEqual(sim_suffix('xaaa', 'aaa'), 1) |
|
1800
|
|
|
self.assertAlmostEqual(sim_suffix('xxxa', 'aaa'), 1/3) |
|
1801
|
|
|
self.assertAlmostEqual(sim_suffix('xxxaa', 'yaa'), 2/3) |
|
1802
|
|
|
self.assertEqual(sim_suffix('xxxxaa', 'yyyaa'), 2/5) |
|
1803
|
|
|
|
|
1804
|
|
|
def test_dist_suffix(self): |
|
1805
|
|
|
"""Test abydos.distance.dist_suffix.""" |
|
1806
|
|
|
self.assertEqual(dist_suffix('', ''), 0) |
|
1807
|
|
|
self.assertEqual(dist_suffix('a', ''), 1) |
|
1808
|
|
|
self.assertEqual(dist_suffix('', 'a'), 1) |
|
1809
|
|
|
self.assertEqual(dist_suffix('a', 'a'), 0) |
|
1810
|
|
|
self.assertEqual(dist_suffix('ax', 'a'), 1) |
|
1811
|
|
|
self.assertEqual(dist_suffix('axx', 'a'), 1) |
|
1812
|
|
|
self.assertEqual(dist_suffix('ax', 'ay'), 1) |
|
1813
|
|
|
self.assertEqual(dist_suffix('a', 'ay'), 1) |
|
1814
|
|
|
self.assertEqual(dist_suffix('a', 'ayy'), 1) |
|
1815
|
|
|
self.assertEqual(dist_suffix('ax', 'ay'), 1) |
|
1816
|
|
|
self.assertEqual(dist_suffix('a', 'y'), 1) |
|
1817
|
|
|
self.assertEqual(dist_suffix('y', 'a'), 1) |
|
1818
|
|
|
self.assertEqual(dist_suffix('aaax', 'aaa'), 1) |
|
1819
|
|
|
self.assertEqual(dist_suffix('axxx', 'aaa'), 1) |
|
1820
|
|
|
self.assertEqual(dist_suffix('aaxx', 'aayy'), 1) |
|
1821
|
|
|
self.assertEqual(dist_suffix('xxaa', 'yyaa'), 1/2) |
|
1822
|
|
|
self.assertEqual(dist_suffix('aaxxx', 'aay'), 1) |
|
1823
|
|
|
self.assertEqual(dist_suffix('aaxxxx', 'aayyy'), 1) |
|
1824
|
|
|
self.assertEqual(dist_suffix('xa', 'a'), 0) |
|
1825
|
|
|
self.assertEqual(dist_suffix('xxa', 'a'), 0) |
|
1826
|
|
|
self.assertEqual(dist_suffix('xa', 'ya'), 1/2) |
|
1827
|
|
|
self.assertEqual(dist_suffix('a', 'ya'), 0) |
|
1828
|
|
|
self.assertEqual(dist_suffix('a', 'yya'), 0) |
|
1829
|
|
|
self.assertEqual(dist_suffix('xa', 'ya'), 1/2) |
|
1830
|
|
|
self.assertEqual(dist_suffix('xaaa', 'aaa'), 0) |
|
1831
|
|
|
self.assertAlmostEqual(dist_suffix('xxxa', 'aaa'), 2/3) |
|
1832
|
|
|
self.assertAlmostEqual(dist_suffix('xxxaa', 'yaa'), 1/3) |
|
1833
|
|
|
self.assertEqual(dist_suffix('xxxxaa', 'yyyaa'), 3/5) |
|
1834
|
|
|
|
|
1835
|
|
|
|
|
1836
|
|
|
class MLIPNSTestCases(unittest.TestCase): |
|
1837
|
|
|
"""Test MLIPNS functions. |
|
1838
|
|
|
|
|
1839
|
|
|
abydos.distance.sim_mlipns & .dist_mlipns |
|
1840
|
|
|
""" |
|
1841
|
|
|
|
|
1842
|
|
|
def test_sim_mlipns(self): |
|
1843
|
|
|
"""Test abydos.distance.sim_mlipns.""" |
|
1844
|
|
|
self.assertEqual(sim_mlipns('', ''), 1) |
|
1845
|
|
|
self.assertEqual(sim_mlipns('a', ''), 0) |
|
1846
|
|
|
self.assertEqual(sim_mlipns('', 'a'), 0) |
|
1847
|
|
|
self.assertEqual(sim_mlipns('a', 'a'), 1) |
|
1848
|
|
|
self.assertEqual(sim_mlipns('ab', 'a'), 1) |
|
1849
|
|
|
self.assertEqual(sim_mlipns('abc', 'abc'), 1) |
|
1850
|
|
|
self.assertEqual(sim_mlipns('abc', 'abcde'), 1) |
|
1851
|
|
|
self.assertEqual(sim_mlipns('abcg', 'abcdeg'), 1) |
|
1852
|
|
|
self.assertEqual(sim_mlipns('abcg', 'abcdefg'), 0) |
|
1853
|
|
|
self.assertEqual(sim_mlipns('Tomato', 'Tamato'), 1) |
|
1854
|
|
|
self.assertEqual(sim_mlipns('ato', 'Tam'), 1) |
|
1855
|
|
|
|
|
1856
|
|
|
def test_dist_mlipns(self): |
|
1857
|
|
|
"""Test abydos.distance.dist_mlipns.""" |
|
1858
|
|
|
self.assertEqual(dist_mlipns('', ''), 0) |
|
1859
|
|
|
self.assertEqual(dist_mlipns('a', ''), 1) |
|
1860
|
|
|
self.assertEqual(dist_mlipns('', 'a'), 1) |
|
1861
|
|
|
self.assertEqual(dist_mlipns('a', 'a'), 0) |
|
1862
|
|
|
self.assertEqual(dist_mlipns('ab', 'a'), 0) |
|
1863
|
|
|
self.assertEqual(dist_mlipns('abc', 'abc'), 0) |
|
1864
|
|
|
self.assertEqual(dist_mlipns('abc', 'abcde'), 0) |
|
1865
|
|
|
self.assertEqual(dist_mlipns('abcg', 'abcdeg'), 0) |
|
1866
|
|
|
self.assertEqual(dist_mlipns('abcg', 'abcdefg'), 1) |
|
1867
|
|
|
self.assertEqual(dist_mlipns('Tomato', 'Tamato'), 0) |
|
1868
|
|
|
self.assertEqual(dist_mlipns('ato', 'Tam'), 0) |
|
1869
|
|
|
|
|
1870
|
|
|
|
|
1871
|
|
|
class BagTestCases(unittest.TestCase): |
|
1872
|
|
|
"""Test bag similarity functions. |
|
1873
|
|
|
|
|
1874
|
|
|
abydos.distance.bag, .sim_bag & .dist_bag |
|
1875
|
|
|
""" |
|
1876
|
|
|
|
|
1877
|
|
|
def test_bag(self): |
|
1878
|
|
|
"""Test abydos.distance.bag.""" |
|
1879
|
|
|
self.assertEqual(bag('', ''), 0) |
|
1880
|
|
|
self.assertEqual(bag('nelson', ''), 6) |
|
1881
|
|
|
self.assertEqual(bag('', 'neilsen'), 7) |
|
1882
|
|
|
self.assertEqual(bag('ab', 'a'), 1) |
|
1883
|
|
|
self.assertEqual(bag('ab', 'c'), 2) |
|
1884
|
|
|
self.assertEqual(bag('nelson', 'neilsen'), 2) |
|
1885
|
|
|
self.assertEqual(bag('neilsen', 'nelson'), 2) |
|
1886
|
|
|
self.assertEqual(bag('niall', 'neal'), 2) |
|
1887
|
|
|
self.assertEqual(bag('aluminum', 'Catalan'), 5) |
|
1888
|
|
|
self.assertEqual(bag('abcdefg', 'hijklm'), 7) |
|
1889
|
|
|
self.assertEqual(bag('abcdefg', 'hijklmno'), 8) |
|
1890
|
|
|
|
|
1891
|
|
|
def test_sim_bag(self): |
|
1892
|
|
|
"""Test abydos.distance.sim_bag.""" |
|
1893
|
|
|
self.assertEqual(sim_bag('', ''), 1) |
|
1894
|
|
|
self.assertEqual(sim_bag('nelson', ''), 0) |
|
1895
|
|
|
self.assertEqual(sim_bag('', 'neilsen'), 0) |
|
1896
|
|
|
self.assertEqual(sim_bag('ab', 'a'), 0.5) |
|
1897
|
|
|
self.assertEqual(sim_bag('ab', 'c'), 0) |
|
1898
|
|
|
self.assertAlmostEqual(sim_bag('nelson', 'neilsen'), 5/7) |
|
1899
|
|
|
self.assertAlmostEqual(sim_bag('neilsen', 'nelson'), 5/7) |
|
1900
|
|
|
self.assertAlmostEqual(sim_bag('niall', 'neal'), 3/5) |
|
1901
|
|
|
self.assertAlmostEqual(sim_bag('aluminum', 'Catalan'), 3/8) |
|
1902
|
|
|
self.assertEqual(sim_bag('abcdefg', 'hijklm'), 0) |
|
1903
|
|
|
self.assertEqual(sim_bag('abcdefg', 'hijklmno'), 0) |
|
1904
|
|
|
|
|
1905
|
|
|
def test_dist_bag(self): |
|
1906
|
|
|
"""Test abydos.distance.dist_bag.""" |
|
1907
|
|
|
self.assertEqual(dist_bag('', ''), 0) |
|
1908
|
|
|
self.assertEqual(dist_bag('nelson', ''), 1) |
|
1909
|
|
|
self.assertEqual(dist_bag('', 'neilsen'), 1) |
|
1910
|
|
|
self.assertEqual(dist_bag('ab', 'a'), 0.5) |
|
1911
|
|
|
self.assertEqual(dist_bag('ab', 'c'), 1) |
|
1912
|
|
|
self.assertAlmostEqual(dist_bag('nelson', 'neilsen'), 2/7) |
|
1913
|
|
|
self.assertAlmostEqual(dist_bag('neilsen', 'nelson'), 2/7) |
|
1914
|
|
|
self.assertAlmostEqual(dist_bag('niall', 'neal'), 2/5) |
|
1915
|
|
|
self.assertAlmostEqual(dist_bag('aluminum', 'Catalan'), 5/8) |
|
1916
|
|
|
self.assertEqual(dist_bag('abcdefg', 'hijklm'), 1) |
|
1917
|
|
|
self.assertEqual(dist_bag('abcdefg', 'hijklmno'), 1) |
|
1918
|
|
|
|
|
1919
|
|
|
|
|
1920
|
|
|
class EditexTestCases(unittest.TestCase): |
|
1921
|
|
|
"""Test Editex functions. |
|
1922
|
|
|
|
|
1923
|
|
|
abydos.distance.editex, .sim_editex & .dist_editex |
|
1924
|
|
|
""" |
|
1925
|
|
|
|
|
1926
|
|
|
def test_editex(self): |
|
1927
|
|
|
"""Test abydos.distance.editex.""" |
|
1928
|
|
|
self.assertEqual(editex('', ''), 0) |
|
1929
|
|
|
self.assertEqual(editex('nelson', ''), 12) |
|
1930
|
|
|
self.assertEqual(editex('', 'neilsen'), 14) |
|
1931
|
|
|
self.assertEqual(editex('ab', 'a'), 2) |
|
1932
|
|
|
self.assertEqual(editex('ab', 'c'), 4) |
|
1933
|
|
|
self.assertEqual(editex('nelson', 'neilsen'), 2) |
|
1934
|
|
|
self.assertEqual(editex('neilsen', 'nelson'), 2) |
|
1935
|
|
|
self.assertEqual(editex('niall', 'neal'), 1) |
|
1936
|
|
|
self.assertEqual(editex('neal', 'niall'), 1) |
|
1937
|
|
|
self.assertEqual(editex('niall', 'nihal'), 2) |
|
1938
|
|
|
self.assertEqual(editex('nihal', 'niall'), 2) |
|
1939
|
|
|
self.assertEqual(editex('neal', 'nihl'), 3) |
|
1940
|
|
|
self.assertEqual(editex('nihl', 'neal'), 3) |
|
1941
|
|
|
|
|
1942
|
|
|
def test_editex_local(self): |
|
1943
|
|
|
"""Test abydos.distance.editex (local variant).""" |
|
1944
|
|
|
self.assertEqual(editex('', '', local=True), 0) |
|
1945
|
|
|
self.assertEqual(editex('nelson', '', local=True), 12) |
|
1946
|
|
|
self.assertEqual(editex('', 'neilsen', local=True), 14) |
|
1947
|
|
|
self.assertEqual(editex('ab', 'a', local=True), 2) |
|
1948
|
|
|
self.assertEqual(editex('ab', 'c', local=True), 2) |
|
1949
|
|
|
self.assertEqual(editex('nelson', 'neilsen', local=True), 2) |
|
1950
|
|
|
self.assertEqual(editex('neilsen', 'nelson', local=True), 2) |
|
1951
|
|
|
self.assertEqual(editex('niall', 'neal', local=True), 1) |
|
1952
|
|
|
self.assertEqual(editex('neal', 'niall', local=True), 1) |
|
1953
|
|
|
self.assertEqual(editex('niall', 'nihal', local=True), 2) |
|
1954
|
|
|
self.assertEqual(editex('nihal', 'niall', local=True), 2) |
|
1955
|
|
|
self.assertEqual(editex('neal', 'nihl', local=True), 3) |
|
1956
|
|
|
self.assertEqual(editex('nihl', 'neal', local=True), 3) |
|
1957
|
|
|
|
|
1958
|
|
|
def test_sim_editex(self): |
|
1959
|
|
|
"""Test abydos.distance.sim_editex.""" |
|
1960
|
|
|
self.assertEqual(sim_editex('', ''), 1) |
|
1961
|
|
|
self.assertEqual(sim_editex('nelson', ''), 0) |
|
1962
|
|
|
self.assertEqual(sim_editex('', 'neilsen'), 0) |
|
1963
|
|
|
self.assertEqual(sim_editex('ab', 'a'), 0.5) |
|
1964
|
|
|
self.assertEqual(sim_editex('ab', 'c'), 0) |
|
1965
|
|
|
self.assertAlmostEqual(sim_editex('nelson', 'neilsen'), 12/14) |
|
1966
|
|
|
self.assertAlmostEqual(sim_editex('neilsen', 'nelson'), 12/14) |
|
1967
|
|
|
self.assertEqual(sim_editex('niall', 'neal'), 0.9) |
|
1968
|
|
|
|
|
1969
|
|
|
def test_dist_editex(self): |
|
1970
|
|
|
"""Test abydos.distance.dist_editex.""" |
|
1971
|
|
|
self.assertEqual(dist_editex('', ''), 0) |
|
1972
|
|
|
self.assertEqual(dist_editex('nelson', ''), 1) |
|
1973
|
|
|
self.assertEqual(dist_editex('', 'neilsen'), 1) |
|
1974
|
|
|
self.assertEqual(dist_editex('ab', 'a'), 0.5) |
|
1975
|
|
|
self.assertEqual(dist_editex('ab', 'c'), 1) |
|
1976
|
|
|
self.assertAlmostEqual(dist_editex('nelson', 'neilsen'), 2/14) |
|
1977
|
|
|
self.assertAlmostEqual(dist_editex('neilsen', 'nelson'), 2/14) |
|
1978
|
|
|
self.assertEqual(dist_editex('niall', 'neal'), 0.1) |
|
1979
|
|
|
|
|
1980
|
|
|
|
|
1981
|
|
|
class BaystatTestCases(unittest.TestCase): |
|
1982
|
|
|
"""Test Editex functions. |
|
1983
|
|
|
|
|
1984
|
|
|
abydos.distance.sim_baystat & .dist_baystat |
|
1985
|
|
|
""" |
|
1986
|
|
|
|
|
1987
|
|
|
def test_sim_baystat(self): |
|
1988
|
|
|
"""Test abydos.distance.sim_editex.""" |
|
1989
|
|
|
# Base cases |
|
1990
|
|
|
self.assertEqual(sim_baystat('', ''), 1) |
|
1991
|
|
|
self.assertEqual(sim_baystat('Colin', ''), 0) |
|
1992
|
|
|
self.assertEqual(sim_baystat('Colin', 'Colin'), 1) |
|
1993
|
|
|
|
|
1994
|
|
|
# Examples given in the paper |
|
1995
|
|
|
# https://www.statistik.bayern.de/medien/statistik/zensus/zusammenf__hrung_von_datenbest__nden_ohne_numerische_identifikatoren.pdf |
|
1996
|
|
|
self.assertAlmostEqual(sim_baystat('DRAKOMENA', 'DRAOMINA'), 7/9) |
|
1997
|
|
|
self.assertAlmostEqual(sim_baystat('RIEKI', 'RILKI'), 4/5) |
|
1998
|
|
|
self.assertAlmostEqual(sim_baystat('ATANASSIONI', 'ATANASIOU'), 8/11) |
|
1999
|
|
|
self.assertAlmostEqual(sim_baystat('LIESKOVSKY', 'LIESZKOVSZKY'), |
|
2000
|
|
|
10/12) |
|
2001
|
|
|
self.assertAlmostEqual(sim_baystat('JEANETTE', 'JEANNETTE'), 8/9) |
|
2002
|
|
|
self.assertAlmostEqual(sim_baystat('JOHANNES', 'JOHAN'), 0.625) |
|
2003
|
|
|
self.assertAlmostEqual(sim_baystat('JOHANNES', 'HANS'), 0.375) |
|
2004
|
|
|
self.assertAlmostEqual(sim_baystat('JOHANNES', 'HANNES'), 0.75) |
|
2005
|
|
|
self.assertAlmostEqual(sim_baystat('ZIMMERMANN', 'SEMMERMANN'), 0.8) |
|
2006
|
|
|
self.assertAlmostEqual(sim_baystat('ZIMMERMANN', 'ZIMMERER'), 0.6) |
|
2007
|
|
|
self.assertAlmostEqual(sim_baystat('ZIMMERMANN', 'ZIMMER'), 0.6) |
|
2008
|
|
|
|
|
2009
|
|
|
def test_dist_baystat(self): |
|
2010
|
|
|
"""Test abydos.distance.dist_editex.""" |
|
2011
|
|
|
# Base cases |
|
2012
|
|
|
self.assertEqual(dist_baystat('', ''), 0) |
|
2013
|
|
|
self.assertEqual(dist_baystat('Colin', ''), 1) |
|
2014
|
|
|
self.assertEqual(dist_baystat('Colin', 'Colin'), 0) |
|
2015
|
|
|
|
|
2016
|
|
|
# Examples given in the paper |
|
2017
|
|
|
# https://www.statistik.bayern.de/medien/statistik/zensus/zusammenf__hrung_von_datenbest__nden_ohne_numerische_identifikatoren.pdf |
|
2018
|
|
|
self.assertAlmostEqual(dist_baystat('DRAKOMENA', 'DRAOMINA'), 2/9) |
|
2019
|
|
|
self.assertAlmostEqual(dist_baystat('RIEKI', 'RILKI'), 1/5) |
|
2020
|
|
|
self.assertAlmostEqual(dist_baystat('ATANASSIONI', 'ATANASIOU'), 3/11) |
|
2021
|
|
|
self.assertAlmostEqual(dist_baystat('LIESKOVSKY', 'LIESZKOVSZKY'), |
|
2022
|
|
|
2/12) |
|
2023
|
|
|
self.assertAlmostEqual(dist_baystat('JEANETTE', 'JEANNETTE'), 1/9) |
|
2024
|
|
|
self.assertAlmostEqual(dist_baystat('JOHANNES', 'JOHAN'), 0.375) |
|
2025
|
|
|
self.assertAlmostEqual(dist_baystat('JOHANNES', 'HANS'), 0.625) |
|
2026
|
|
|
self.assertAlmostEqual(dist_baystat('JOHANNES', 'HANNES'), 0.25) |
|
2027
|
|
|
self.assertAlmostEqual(dist_baystat('ZIMMERMANN', 'SEMMERMANN'), 0.2) |
|
2028
|
|
|
self.assertAlmostEqual(dist_baystat('ZIMMERMANN', 'ZIMMERER'), 0.4) |
|
2029
|
|
|
self.assertAlmostEqual(dist_baystat('ZIMMERMANN', 'ZIMMER'), 0.4) |
|
2030
|
|
|
|
|
2031
|
|
|
|
|
2032
|
|
|
class SimTFIDFTestCases(unittest.TestCase): |
|
2033
|
|
|
"""Test TF-IDF similarity functions. |
|
2034
|
|
|
|
|
2035
|
|
|
abydos.distance.sim_tfidf |
|
2036
|
|
|
""" |
|
2037
|
|
|
|
|
2038
|
|
|
def test_sim(self): |
|
2039
|
|
|
"""Test abydos.distance.sim_tfidf.""" |
|
2040
|
|
|
pass |
|
2041
|
|
|
|
|
2042
|
|
|
|
|
2043
|
|
|
class SimDistTestCases(unittest.TestCase): |
|
2044
|
|
|
"""Test generic sim & dist functions. |
|
2045
|
|
|
|
|
2046
|
|
|
abydos.distance.sim & .dist |
|
2047
|
|
|
""" |
|
2048
|
|
|
|
|
2049
|
|
|
def test_sim(self): |
|
2050
|
|
|
"""Test abydos.distance.sim.""" |
|
2051
|
|
|
self.assertEqual(sim('Niall', 'Nigel'), |
|
2052
|
|
|
sim_levenshtein('Niall', 'Nigel')) |
|
2053
|
|
|
self.assertRaises(AttributeError, sim, 'abc', 'abc', 0) |
|
2054
|
|
|
|
|
2055
|
|
|
def test_dist(self): |
|
2056
|
|
|
"""Test abydos.distance.dist.""" |
|
2057
|
|
|
self.assertEqual(dist('Niall', 'Nigel'), |
|
2058
|
|
|
dist_levenshtein('Niall', 'Nigel')) |
|
2059
|
|
|
self.assertRaises(AttributeError, dist, 'abc', 'abc', 0) |
|
2060
|
|
|
|
|
2061
|
|
|
|
|
2062
|
|
|
if __name__ == '__main__': |
|
2063
|
|
|
unittest.main() |
|
2064
|
|
|
|
chrislit /
abydos
