def test_should_get_the_right_char_position_in_the_original_sequence(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1']
problem.number_of_variables = 1
msa_1 = MSASolution(problem, msa=[('seq1', '-ABC')])
msa_2 = MSASolution(problem, msa=[('seq1', 'A--B-C')])
# check
self.assertEqual(
0,
msa_1.get_char_position_in_original_sequence(seq_index=0,
position=1))
self.assertEqual(1, msa_1.get_char_position_in_original_sequence(0, 2))
self.assertEqual(2, msa_1.get_char_position_in_original_sequence(0, 3))
self.assertEqual(0, msa_2.get_char_position_in_original_sequence(0, 0))
self.assertEqual(1, msa_2.get_char_position_in_original_sequence(0, 3))
self.assertEqual(2, msa_2.get_char_position_in_original_sequence(0, 5))
def __find_symbol_position_in_original_sequence(self,
solution: MSASolution,
seq_index: int,
position: int):
""" Given a symbol position, finds the corresponding position of the symbol in the original
sequence if gaps are not taken into account. If the symbol is a gap the returned value is -1 """
if position > solution.get_length_of_alignment():
raise Exception(
'Position {0} is larger than the sequence size {1}'.format(
position, solution.get_length_of_alignment()))
if not solution.is_gap_char_at_sequence(seq_index, position):
symbol_position = solution.get_char_position_in_original_sequence(
seq_index, position)
else:
position = solution.get_next_char_position_after_gap(
seq_index, position)
if position < 0:
symbol_position = -1
else:
symbol_position = solution.get_char_position_in_original_sequence(
seq_index, position)
return symbol_position
