class SmithWatermanMatrixTests(TestCase):
"""Tests for SmithWatermanMatrix class.
"""
def setUp(self):
"""Setup for SmithWatermanMatrix tests."""
self.sw_matrix = SmithWatermanMatrix('ACGU', 'CAGU')
def test_fill(self):
"""Tests for SmithWatermanMatrix fill function."""
filled_sw_matrix = copy(self.sw_matrix)
filled_sw_matrix.fill()
matrix_scores_filled = [[0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 1, 0, 0, 0], [0, 0, 0, 1, 0],
[0, 0, 0, 0, 2]]
matrix_pointers_filled = [[None, None, None, None, None],
[None, None, 'diag', None, None],
[None, 'diag', None, None, None],
[None, None, None, 'diag', None],
[None, None, None, None, 'diag']]
for i in range(len(filled_sw_matrix)):
for j in range(len(filled_sw_matrix[i])):
self.assertEqual(filled_sw_matrix[i][j].Score,\
matrix_scores_filled[i][j])
self.assertEqual(filled_sw_matrix[i][j].Pointer,\
matrix_pointers_filled[i][j])
self.assertEqual(filled_sw_matrix.MaxScore, (2, 4, 4))
def test_traceback(self):
"""Tests for SmithWatermanMatrix traceback function."""
self.sw_matrix.fill()
self.sw_matrix.traceback()
self.assertEqual(self.sw_matrix.FirstAlign, ['G', 'U'])
self.assertEqual(self.sw_matrix.SecondAlign, ['G', 'U'])
class SmithWatermanMatrixTests(TestCase):
"""Tests for SmithWatermanMatrix class.
"""
def setUp(self):
"""Setup for SmithWatermanMatrix tests."""
self.sw_matrix = SmithWatermanMatrix("ACGU", "CAGU")
def test_fill(self):
"""Tests for SmithWatermanMatrix fill function."""
filled_sw_matrix = copy(self.sw_matrix)
filled_sw_matrix.fill()
matrix_scores_filled = [[0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 1, 0, 0, 0], [0, 0, 0, 1, 0], [0, 0, 0, 0, 2]]
matrix_pointers_filled = [
[None, None, None, None, None],
[None, None, "diag", None, None],
[None, "diag", None, None, None],
[None, None, None, "diag", None],
[None, None, None, None, "diag"],
]
for i in range(len(filled_sw_matrix)):
for j in range(len(filled_sw_matrix[i])):
self.assertEqual(filled_sw_matrix[i][j].Score, matrix_scores_filled[i][j])
self.assertEqual(filled_sw_matrix[i][j].Pointer, matrix_pointers_filled[i][j])
self.assertEqual(filled_sw_matrix.MaxScore, (2, 4, 4))
def test_traceback(self):
"""Tests for SmithWatermanMatrix traceback function."""
self.sw_matrix.fill()
self.sw_matrix.traceback()
self.assertEqual(self.sw_matrix.FirstAlign, ["G", "U"])
self.assertEqual(self.sw_matrix.SecondAlign, ["G", "U"])
def setUp(self):
"""Setup for SmithWatermanMatrix tests."""
self.sw_matrix = SmithWatermanMatrix('ACGU', 'CAGU')
def setUp(self):
"""Setup for SmithWatermanMatrix tests."""
self.sw_matrix = SmithWatermanMatrix("ACGU", "CAGU")
def setUp(self):
"""Setup for SmithWatermanMatrix tests."""
self.sw_matrix = SmithWatermanMatrix('ACGU','CAGU')
