def find_cutting_points_in_first_parent(self, solution: MSASolution,
position: int) -> list:
""" Find the real cutting points in a solution. If the column is a gap then the next non-gap
symbol must be found """
positions = [-1 for _ in range(solution.number_of_variables)]
for i in range(solution.number_of_variables):
if solution.is_gap_char_at_sequence(i, position):
positions[i] = solution.get_next_char_position_after_gap(
i, position)
else:
positions[i] = position
return positions
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
def test_should_get_next_char_position_after_gap(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa_1 = MSASolution(problem, msa=[('seq1', '-ABC'), ('seq2', 'AB-C')])
problem = MSA(score_list=[])
problem.identifiers = ['seq1']
problem.number_of_variables = 1
msa_2 = MSASolution(problem, msa=[('seq1', 'A--BC')])
msa_extra_gaps = MSASolution(problem,
msa=[('seq1', '---A---BC--D---')])
# check
self.assertEqual(
1,
msa_1.get_next_char_position_after_gap(seq_index=0,
gap_position=0))
self.assertEqual(
3,
msa_1.get_next_char_position_after_gap(seq_index=1,
gap_position=2))
self.assertEqual(
3,
msa_2.get_next_char_position_after_gap(seq_index=0,
gap_position=1))
self.assertEqual(
3,
msa_2.get_next_char_position_after_gap(seq_index=0,
gap_position=2))
self.assertEqual(
3,
msa_extra_gaps.get_next_char_position_after_gap(seq_index=0,
gap_position=0))
self.assertEqual(
3,
msa_extra_gaps.get_next_char_position_after_gap(seq_index=0,
gap_position=1))
self.assertEqual(
7,
msa_extra_gaps.get_next_char_position_after_gap(seq_index=0,
gap_position=4))
self.assertEqual(
7,
msa_extra_gaps.get_next_char_position_after_gap(seq_index=0,
gap_position=6))
self.assertEqual(
11,
msa_extra_gaps.get_next_char_position_after_gap(seq_index=0,
gap_position=9))
self.assertEqual(
11,
msa_extra_gaps.get_next_char_position_after_gap(seq_index=0,
gap_position=10))
self.assertEqual(
-1,
msa_extra_gaps.get_next_char_position_after_gap(seq_index=0,
gap_position=12))
