Subroutine Coverage

Bio/SimpleAlign.pm
Criterion Covered Total %
subroutine 80 96 83.3
pod 70 78 89.7


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