| line |
count |
pod |
subroutine |
|
2
|
48 |
n/a |
BEGIN |
|
3
|
48 |
n/a |
BEGIN |
|
4
|
48 |
n/a |
BEGIN |
|
5
|
48 |
n/a |
BEGIN |
|
6
|
48 |
n/a |
BEGIN |
|
8
|
48 |
n/a |
BEGIN |
|
186
|
291 |
Yes |
new |
|
265
|
0 |
No |
addSeq |
|
271
|
2420 |
Yes |
add_seq |
|
312
|
0 |
n/a |
__ANON__ |
|
342
|
0 |
No |
removeSeq |
|
348
|
13 |
Yes |
remove_seq |
|
411
|
1 |
Yes |
purge |
|
477
|
1 |
Yes |
sort_alphabetically |
|
508
|
1 |
Yes |
sort_by_list |
|
548
|
2 |
Yes |
set_new_reference |
|
577
|
7 |
n/a |
_in_aln |
|
606
|
1 |
Yes |
uniq_seq |
|
674
|
15 |
n/a |
_check_uniq |
|
695
|
26 |
n/a |
_convert_leading_ending_gaps |
|
726
|
0 |
No |
eachSeq |
|
732
|
7623 |
Yes |
each_seq |
|
757
|
2 |
Yes |
each_alphabetically |
|
772
|
94 |
n/a |
_alpha_startend |
|
797
|
0 |
No |
eachSeqWithId |
|
803
|
89 |
Yes |
each_seq_with_id |
|
831
|
258 |
Yes |
get_seq_by_pos |
|
855
|
18 |
Yes |
get_seq_by_id |
|
903
|
0 |
Yes |
seq_with_features |
|
969
|
1 |
Yes |
select |
|
1012
|
8 |
Yes |
select_noncont |
|
1053
|
1 |
Yes |
select_noncont_by_name |
|
1083
|
31 |
Yes |
slice |
|
1189
|
4 |
Yes |
remove_columns |
|
1222
|
6 |
Yes |
remove_gaps |
|
1255
|
9 |
n/a |
_remove_col |
|
1319
|
1 |
n/a |
_remove_columns_by_type |
|
1365
|
3 |
n/a |
_remove_columns_by_num |
|
1409
|
0 |
Yes |
splice_by_seq_pos |
|
1449
|
4 |
Yes |
map_chars |
|
1477
|
1 |
Yes |
uppercase |
|
1505
|
1 |
Yes |
cigar_line |
|
1581
|
6 |
Yes |
match_line |
|
1668
|
14 |
Yes |
gap_line |
|
1695
|
2 |
Yes |
all_gap_line |
|
1729
|
0 |
Yes |
gap_col_matrix |
|
1765
|
1 |
Yes |
match |
|
1809
|
5 |
Yes |
unmatch |
|
1854
|
142 |
Yes |
id |
|
1874
|
16 |
Yes |
accession |
|
1894
|
25 |
Yes |
description |
|
1916
|
32 |
Yes |
missing_char |
|
1939
|
18 |
Yes |
match_char |
|
1961
|
11242 |
Yes |
gap_char |
|
1984
|
5 |
Yes |
symbol_chars |
|
2017
|
26 |
Yes |
score |
|
2037
|
11 |
Yes |
consensus_string |
|
2061
|
1 |
Yes |
consensus_conservation |
|
2074
|
2100 |
n/a |
_consensus_aa |
|
2097
|
2522 |
n/a |
_consensus_counts |
|
2130
|
1 |
Yes |
consensus_iupac |
|
2148
|
10 |
n/a |
_consensus_iupac |
|
2252
|
56 |
Yes |
consensus_meta |
|
2272
|
54 |
Yes |
is_flush |
|
2311
|
0 |
No |
length_aln |
|
2317
|
2217 |
Yes |
length |
|
2345
|
0 |
Yes |
maxname_length |
|
2352
|
0 |
No |
maxnse_length |
|
2359
|
21 |
Yes |
maxdisplayname_length |
|
2387
|
2 |
Yes |
max_metaname_length |
|
2428
|
2 |
Yes |
num_residues |
|
2452
|
2553 |
Yes |
num_sequences |
|
2473
|
9 |
Yes |
average_percentage_identity |
|
2530
|
5 |
Yes |
percentage_identity |
|
2551
|
18 |
Yes |
overall_percentage_identity |
|
2666
|
27 |
Yes |
column_from_residue_number |
|
2702
|
550 |
Yes |
displayname |
|
2720
|
0 |
No |
get_displayname |
|
2726
|
0 |
No |
set_displayname |
|
2744
|
1 |
Yes |
set_displayname_count |
|
2780
|
11 |
Yes |
set_displayname_flat |
|
2802
|
1 |
Yes |
set_displayname_normal |
|
2824
|
123 |
Yes |
source |
|
2847
|
1 |
Yes |
set_displayname_safe |
|
2884
|
1 |
Yes |
restore_displayname |
|
2913
|
1 |
Yes |
sort_by_start |
|
2929
|
3 |
n/a |
_startend |
|
2983
|
14 |
Yes |
bracket_string |
|
3031
|
4 |
Yes |
get_SeqFeatures |
|
3058
|
9 |
Yes |
add_SeqFeature |
|
3098
|
0 |
Yes |
remove_SeqFeatures |
|
3117
|
2 |
Yes |
feature_count |
|
3158
|
87 |
Yes |
annotation |
|
3186
|
0 |
Yes |
no_residues |
|
3205
|
0 |
Yes |
no_sequences |
|
3233
|
6 |
Yes |
mask_columns |