def __find_original_positions_in_aligned_sequences(
self, solution: MSASolution,
column_positions_in_first_parent: list):
positions = [-1 for _ in range(solution.number_of_variables)]
for i in range(solution.number_of_variables):
pos = column_positions_in_first_parent[i]
positions[
i] = solution.get_original_char_position_in_aligned_sequence(
i, pos)
return positions
def test_should_get_original_char_position_in_aligned_sequence(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', '-ABC'), ('seq2', 'ABCD'),
('seq3', '--AB')])
# check
self.assertEqual(
1,
msa.get_original_char_position_in_aligned_sequence(seq_index=0,
position=0))
self.assertEqual(
2,
msa.get_original_char_position_in_aligned_sequence(seq_index=0,
position=1))
self.assertEqual(
3,
msa.get_original_char_position_in_aligned_sequence(seq_index=0,
position=2))
self.assertEqual(
0,
msa.get_original_char_position_in_aligned_sequence(seq_index=1,
position=0))
self.assertEqual(
1,
msa.get_original_char_position_in_aligned_sequence(seq_index=1,
position=1))
self.assertEqual(
2,
msa.get_original_char_position_in_aligned_sequence(seq_index=1,
position=2))
self.assertEqual(
2,
msa.get_original_char_position_in_aligned_sequence(seq_index=2,
position=0))
self.assertEqual(
3,
msa.get_original_char_position_in_aligned_sequence(seq_index=2,
position=1))
