Core

Problem

class pym2sa.core.problem.MSAProblem

Bases: jmetal.core.problem.Problem

Class representing MSA problems

evaluate(solution: pym2sa.core.solution.MSASolution) → pym2sa.core.solution.MSASolution

get_name() → str

Solution

class pym2sa.core.solution.MSASolution(problem, msa: list) → None

Bases: jmetal.core.solution.Solution

Class representing MSA solutions.

add_gap_to_sequence_at_index(seq_index: int, gap_position: int)

Add one gap to an specific sequence.

Parameters:

• seq_index – Index of the sequence on the alignment.
• gap_position – Index of the gap.

decode_alignment_as_list_of_pairs() → list

decode_alignment_as_list_of_sequences() → list

decode_sequence_at_index(seq_index: int)

get_char_position_in_original_sequence(seq_index: int, position: int)

get_gap_columns_from_alignment() → list

Get index of gap columns in the alignment.

get_length_of_alignment() → int

Get length of the alignment (i.e., length of the first sequence).

get_length_of_gaps(seq_index: int) → int

get_length_of_sequence(seq_index: int) → int

Get length of an specific sequence.

Parameters:seq_index – Index of the sequence in the alignment.

get_next_char_position_after_gap(seq_index: int, gap_position: int)

get_number_of_gaps_groups_of_sequence(seq_index: int) → float

Get number of gaps groups of an specific sequence.

get_number_of_gaps_of_sequence_at_index(seq_index: int)

Get number of gaps of an specific sequence.

Parameters:seq_index – Index of the sequence in the alignment.

get_original_char_position_in_aligned_sequence(seq_index: int, position: int)

get_total_number_of_gaps() → int

Get total number of gaps in the alignment.

is_gap_char_at_sequence(seq_index: int, index: int) → bool

is_gap_column(column: int) → bool

Check if an specific column in the alignment is in all gaps groups (i.e., column consist only of gaps).

Parameters:column – Index of the column in the alignment.

is_valid_msa() → bool

Check if all sequences of the alignment have the same length.

merge_gaps_groups() → None

Merge consecutive gaps groups in the alignment.

remove_full_of_gaps_columns() → None

Remove columns that consist only of gaps.

remove_gap_column(column: int) → None

remove_gap_from_sequence(seq_index: int, position: int)

remove_gap_group_from_sequence_at_column(seq_index: int, column_index: int) → None

split_gap_column(column: int) → None