def test_smith_waterman_dist_abs(self): """Test abydos.distance.SmithWaterman.dist_abs.""" self.assertEqual(SmithWaterman().dist_abs('', ''), 0) # https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm self.assertEqual( SmithWaterman(1, _sim_nw).dist_abs('GATTACA', 'GCATGCU'), 0 ) self.assertEqual( SmithWaterman(5, _sim_wikipedia).dist_abs( 'AGACTAGTTAC', 'CGAGACGT' ), 26, ) sw5 = SmithWaterman(5, _sim_nw) self.assertEqual(sw5.dist_abs('CGATATCAG', 'TGACGSTGC'), 0) self.assertEqual(sw5.dist_abs('AGACTAGTTAC', 'TGACGSTGC'), 1) self.assertEqual(sw5.dist_abs('AGACTAGTTAC', 'CGAGACGT'), 0) # Test wrapper self.assertEqual( smith_waterman('AGACTAGTTAC', 'CGAGACGT', 5, _sim_wikipedia), 26 )
def test_smith_waterman_dist_abs_nialls(self): """Test abydos.distance.SmithWaterman.dist_abs (Nialls set).""" sw_vals = (5, 1, 1, 3, 2, 1, 1, 0, 0, 1, 1, 2, 2, 1, 0, 0) sw2 = SmithWaterman(2, _sim_nw) for i in range(len(NIALL)): self.assertEqual(sw2.dist_abs(NIALL[0], NIALL[i]), sw_vals[i])