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])