def setUp(self):
"""Setup for ScoreMatrix tests."""
self.score_matrix = ScoreMatrix('AACGU','ACAGU')
def fill():
pass
def traceback():
pass
self.score_matrix.fill = fill
self.score_matrix.traceback = traceback
self.empty_score_matrix = ScoreMatrix('','')
def test_init(self):
"""Tests for ScoreMatrix __init__ function."""
#Test empty ScoreMatrix
self.empty_score_matrix = ScoreMatrix('', '')
self.assertEqual(self.empty_score_matrix.First, '')
self.assertEqual(self.empty_score_matrix.Second, '')
self.assertEqual(self.empty_score_matrix.Cols, 1)
self.assertEqual(self.empty_score_matrix.Rows, 1)
self.assertEqual(self.empty_score_matrix.GapScore, -1)
self.assertEqual(self.empty_score_matrix.GapSymbol, '-')
self.assertEqual(self.empty_score_matrix.FirstAlign, [])
self.assertEqual(self.empty_score_matrix.SecondAlign, [])
def setUp(self):
"""Setup for ScoreMatrix tests."""
self.score_matrix = ScoreMatrix('AACGU', 'ACAGU')
def fill():
pass
def traceback():
pass
self.score_matrix.fill = fill
self.score_matrix.traceback = traceback
self.empty_score_matrix = ScoreMatrix('', '')
class ScoreMatrixTests(TestCase):
"""Tests for ScoreCell class.
"""
def setUp(self):
"""Setup for ScoreMatrix tests."""
self.score_matrix = ScoreMatrix("AACGU", "ACAGU")
def fill():
pass
def traceback():
pass
self.score_matrix.fill = fill
self.score_matrix.traceback = traceback
self.empty_score_matrix = ScoreMatrix("", "")
def test_init(self):
"""Tests for ScoreMatrix __init__ function."""
# Test empty ScoreMatrix
self.empty_score_matrix = ScoreMatrix("", "")
self.assertEqual(self.empty_score_matrix.First, "")
self.assertEqual(self.empty_score_matrix.Second, "")
self.assertEqual(self.empty_score_matrix.Cols, 1)
self.assertEqual(self.empty_score_matrix.Rows, 1)
self.assertEqual(self.empty_score_matrix.GapScore, -1)
self.assertEqual(self.empty_score_matrix.GapSymbol, "-")
self.assertEqual(self.empty_score_matrix.FirstAlign, [])
self.assertEqual(self.empty_score_matrix.SecondAlign, [])
def test_str(self):
"""Tests for ScoreMatrix __str__ function."""
# Test empty ScoreMatrix
self.assertEqual(self.empty_score_matrix.__str__(), "Empty Score Matrix")
# Test full ScoreMatrix
self.assertEqual(
self.score_matrix.__str__(),
"""\t\tA\tA\tC\tG\tU\n\t0\t0\t0\t0\t0\t0\nA\t0\t0\t0\t0\t0\t0\nC\t0\t0\t0\t0\t0\t0\nA\t0\t0\t0\t0\t0\t0\nG\t0\t0\t0\t0\t0\t0\nU\t0\t0\t0\t0\t0\t0""",
)
def test_alignment(self):
"""Tests for ScoreMatrix alignment function."""
# Should not align since ScoreMatrix base object does not have fill()
# or traceback() methods. For testing purposes fill() and traceback()
# for self.score_matrix do nothing.
self.assertEqual(self.score_matrix.alignment(), ("", ""))
class ScoreMatrixTests(TestCase):
"""Tests for ScoreCell class.
"""
def setUp(self):
"""Setup for ScoreMatrix tests."""
self.score_matrix = ScoreMatrix('AACGU', 'ACAGU')
def fill():
pass
def traceback():
pass
self.score_matrix.fill = fill
self.score_matrix.traceback = traceback
self.empty_score_matrix = ScoreMatrix('', '')
def test_init(self):
"""Tests for ScoreMatrix __init__ function."""
#Test empty ScoreMatrix
self.empty_score_matrix = ScoreMatrix('', '')
self.assertEqual(self.empty_score_matrix.First, '')
self.assertEqual(self.empty_score_matrix.Second, '')
self.assertEqual(self.empty_score_matrix.Cols, 1)
self.assertEqual(self.empty_score_matrix.Rows, 1)
self.assertEqual(self.empty_score_matrix.GapScore, -1)
self.assertEqual(self.empty_score_matrix.GapSymbol, '-')
self.assertEqual(self.empty_score_matrix.FirstAlign, [])
self.assertEqual(self.empty_score_matrix.SecondAlign, [])
def test_str(self):
"""Tests for ScoreMatrix __str__ function."""
#Test empty ScoreMatrix
self.assertEqual(self.empty_score_matrix.__str__(),
"Empty Score Matrix")
#Test full ScoreMatrix
self.assertEqual(self.score_matrix.__str__(),\
"""\t\tA\tA\tC\tG\tU\n\t0\t0\t0\t0\t0\t0\nA\t0\t0\t0\t0\t0\t0\nC\t0\t0\t0\t0\t0\t0\nA\t0\t0\t0\t0\t0\t0\nG\t0\t0\t0\t0\t0\t0\nU\t0\t0\t0\t0\t0\t0""")
def test_alignment(self):
"""Tests for ScoreMatrix alignment function."""
#Should not align since ScoreMatrix base object does not have fill()
#or traceback() methods. For testing purposes fill() and traceback()
#for self.score_matrix do nothing.
self.assertEqual(self.score_matrix.alignment(), ('', ''))
def test_init(self):
"""Tests for ScoreMatrix __init__ function."""
# Test empty ScoreMatrix
self.empty_score_matrix = ScoreMatrix("", "")
self.assertEqual(self.empty_score_matrix.First, "")
self.assertEqual(self.empty_score_matrix.Second, "")
self.assertEqual(self.empty_score_matrix.Cols, 1)
self.assertEqual(self.empty_score_matrix.Rows, 1)
self.assertEqual(self.empty_score_matrix.GapScore, -1)
self.assertEqual(self.empty_score_matrix.GapSymbol, "-")
self.assertEqual(self.empty_score_matrix.FirstAlign, [])
self.assertEqual(self.empty_score_matrix.SecondAlign, [])
