class DirectionsMatrixTest(unittest.TestCase):
def setUp(self):
self.solver = NeedlemanWunschSolver(
CellCostComputer(same_cost=5, diff_cost=-5, gap_penalty=-2))
@parameterized.expand([[[[[], [], []],
[[], [Direction.DIAGONAL],
[Direction.LEFT, Direction.DIAGONAL]],
[[], [Direction.UP],
[Direction.LEFT, Direction.UP]]], "AD", "AA"],
[[[[], [], [], []],
[[], [Direction.DIAGONAL],
[Direction.LEFT, Direction.DIAGONAL],
[Direction.LEFT]],
[[], [Direction.UP],
[Direction.LEFT, Direction.UP],
[Direction.LEFT, Direction.UP]],
[[], [Direction.DIAGONAL, Direction.UP],
[Direction.DIAGONAL], [Direction.LEFT]]], "ADA",
"AAS"], [[[[]]], "", ""],
[[[[]], [[]], [[]]], "AA", ""],
[[[[], [], []]], "", "AA"]])
def test_directions_matrix(self, expected_result, a_seq, b_seq):
_, result = self.solver.compute_cost_direction_matrices(a_seq=a_seq,
b_seq=b_seq)
self.assertListEqual(result, expected_result)
class CostMatrixTests(unittest.TestCase):
def setUp(self):
self.solver = NeedlemanWunschSolver(
CellCostComputer(same_cost=5, diff_cost=-5, gap_penalty=-2))
@parameterized.expand([[[[0, -2, -4, -6], [-2, 5, 3, 1], [-4, 3, 10, 8],
[-6, 1, 8, 15], [-8, -1, 6, 13]], "acca", "acc"],
[
[[0]],
"",
"",
], [[[0, -2, -4, -6]], "", "ala"],
[[[0], [-2], [-4], [-6]], "ala", ""],
[[[0, -2, -4, -6, -8], [-2, -4, 3, 1, -1],
[-4, 3, 1, -1, 6], [-6, 1, 8, 6, 4],
[-8, -1, 6, 13, 11], [-10, -3, 4, 11, 9]],
"alaaa", "laal"],
[[[0, -2, -4], [-2, 5, 3], [-4, 3, 10], [-6, 1, 8],
[-8, -1, 6]], "adad", "ad"]])
def test_cost_matrix(self, expected_matrix, a_seq, b_seq):
result, _ = self.solver.compute_cost_direction_matrices(a_seq=a_seq,
b_seq=b_seq)
self.assertListEqual(result, expected_matrix)