| line |
count |
pod |
subroutine |
|
2
|
13 |
n/a |
BEGIN |
|
3
|
13 |
n/a |
BEGIN |
|
4
|
13 |
n/a |
BEGIN |
|
5
|
13 |
n/a |
BEGIN |
|
6
|
13 |
n/a |
BEGIN |
|
7
|
13 |
n/a |
BEGIN |
|
8
|
13 |
n/a |
BEGIN |
|
9
|
13 |
n/a |
BEGIN |
|
10
|
13 |
n/a |
BEGIN |
|
11
|
13 |
n/a |
BEGIN |
|
12
|
13 |
n/a |
BEGIN |
|
13
|
13 |
n/a |
BEGIN |
|
14
|
13 |
n/a |
BEGIN |
|
148
|
38 |
Yes |
new |
|
153
|
0 |
No |
__ANON__ |
|
153
|
0 |
No |
accession |
|
153
|
0 |
No |
add_seq |
|
153
|
0 |
No |
annotation |
|
153
|
0 |
No |
average_percentage_identity |
|
153
|
0 |
No |
column_from_residue_number |
|
153
|
0 |
No |
consensus_iupac |
|
153
|
0 |
No |
consensus_meta |
|
153
|
0 |
No |
consensus_string |
|
153
|
0 |
No |
datatype |
|
153
|
0 |
No |
description |
|
153
|
0 |
No |
displayname |
|
153
|
0 |
No |
each_alphabetically |
|
153
|
0 |
No |
each_seq |
|
153
|
0 |
No |
each_seq_with_id |
|
153
|
0 |
No |
gap_char |
|
153
|
0 |
No |
get_SeqFeatures |
|
153
|
0 |
No |
get_seq_by_pos |
|
153
|
0 |
No |
id |
|
153
|
0 |
No |
is_flush |
|
153
|
0 |
No |
length |
|
153
|
0 |
No |
map_chars |
|
153
|
0 |
No |
match |
|
153
|
0 |
No |
match_char |
|
153
|
0 |
No |
match_line |
|
153
|
0 |
No |
max_metaname_length |
|
153
|
0 |
No |
maxdisplayname_length |
|
153
|
0 |
No |
maxname_length |
|
153
|
0 |
No |
missing_char |
|
153
|
0 |
No |
no_residues |
|
153
|
0 |
No |
no_sequences |
|
153
|
0 |
No |
num_sequences |
|
153
|
0 |
No |
overall_percentage_identity |
|
153
|
0 |
No |
percentage_identity |
|
153
|
0 |
No |
purge |
|
153
|
0 |
No |
remove_seq |
|
153
|
0 |
No |
score |
|
153
|
0 |
No |
select |
|
153
|
0 |
No |
select_noncont |
|
153
|
0 |
No |
set_displayname_count |
|
153
|
0 |
No |
set_displayname_flat |
|
153
|
0 |
No |
set_displayname_normal |
|
153
|
0 |
No |
slice |
|
153
|
0 |
No |
sort_alphabetically |
|
153
|
0 |
No |
source |
|
153
|
0 |
No |
symbol_chars |
|
153
|
0 |
No |
unmatch |
|
153
|
0 |
n/a |
uppercase |
|
165
|
13 |
n/a |
BEGIN |
|
185
|
0 |
Yes |
new_from_bioperl |
|
258
|
0 |
Yes |
set_special_symbols |
|
335
|
4 |
Yes |
set_charlabels |
|
385
|
12 |
Yes |
set_raw |
|
435
|
0 |
Yes |
get_special_symbols |
|
457
|
4 |
Yes |
get_charlabels |
|
478
|
214 |
Yes |
get_nchar |
|
502
|
16 |
Yes |
get_ntax |
|
520
|
5 |
Yes |
get_raw |
|
544
|
1 |
Yes |
get_ungapped_columns |
|
574
|
2 |
Yes |
get_invariant_columns |
|
617
|
0 |
Yes |
calc_indel_sizes |
|
718
|
1 |
Yes |
calc_prop_invar |
|
757
|
4 |
Yes |
calc_state_counts |
|
789
|
2 |
Yes |
calc_state_frequencies |
|
846
|
1 |
Yes |
calc_distinct_site_patterns |
|
897
|
1 |
Yes |
calc_gc_content |
|
935
|
0 |
Yes |
calc_median_sequence |
|
1007
|
4 |
Yes |
keep_chars |
|
1039
|
3 |
Yes |
prune_chars |
|
1066
|
1 |
Yes |
prune_invariant |
|
1101
|
1 |
Yes |
prune_uninformative |
|
1152
|
0 |
Yes |
prune_missing_and_gaps |
|
1161
|
0 |
n/a |
__ANON__ |
|
1197
|
0 |
n/a |
bootstrap |
|
1198
|
0 |
n/a |
__ANON__ |
|
1232
|
0 |
Yes |
jackknife |
|
1237
|
0 |
n/a |
__ANON__ |
|
1270
|
0 |
Yes |
replicate |
|
1299
|
0 |
n/a |
_replicate_dna |
|
1472
|
0 |
n/a |
_replicate_binary |
|
1551
|
0 |
n/a |
__ANON__ |
|
1581
|
120 |
Yes |
insert |
|
1628
|
0 |
n/a |
__ANON__ |
|
1628
|
73 |
n/a |
_validate |
|
1645
|
0 |
Yes |
compress_lookup |
|
1678
|
48 |
Yes |
check_taxa |
|
1724
|
1 |
Yes |
make_taxa |
|
1766
|
0 |
Yes |
to_xml |
|
1826
|
0 |
n/a |
_normalize_symbols |
|
1892
|
1 |
Yes |
to_nexus |
|
2067
|
0 |
Yes |
to_dom |
|
2137
|
0 |
n/a |
_package_char_labels |
|
2151
|
6 |
n/a |
_tag |
|
2152
|
634 |
n/a |
_type |
|
2153
|
18 |
n/a |
_container |
|
2156
|
137 |
n/a |
_update_characters |