| line |
true |
false |
branch |
|
97
|
0 |
5 |
if (defined $file) |
|
99
|
0 |
0 |
if (@{$self->{'errors'};}) |
|
113
|
0 |
0 |
if $self->{'line_no'} |
|
114
|
0 |
0 |
if $self->{'file_name'} |
|
121
|
0 |
4 |
if $self->{'parsed'} |
|
122
|
0 |
4 |
if $self->{'seen_header'} |
|
123
|
0 |
4 |
if $self->{'seen_symbol'} |
|
124
|
0 |
4 |
if $like and not $like =~ /^(RNA|DNA|PROTEIN)$/iu |
|
126
|
4 |
0 |
$like ? : |
|
138
|
0 |
92 |
if $self->{'parsed'} |
|
139
|
0 |
0 |
unless $self->{'seen_header'} or $self->{'seen_symbol'} |
|
140
|
0 |
92 |
if (defined $self->{'sym_lookup'}{$sym}) |
|
144
|
16 |
76 |
if $sym ge 'a' and $sym le 'z' |
|
145
|
60 |
32 |
if $sym ge 'A' and $sym le 'Z' |
|
147
|
8 |
84 |
if (defined $aliases) |
|
150
|
60 |
32 |
if (defined $comprise) { } |
|
156
|
0 |
160 |
if (not defined $csym) { } |
|
|
0 |
160 |
elsif (defined $csym->{'comprise'}) { } |
|
165
|
0 |
60 |
if ($sym eq '?' and length $symbol->{'comprise'} < scalar @{$self->{'core_syms'};}) |
|
169
|
0 |
32 |
if $sym eq '?' |
|
170
|
0 |
32 |
if $self->{'seen_ambig'} |
|
180
|
0 |
0 |
if $self->{'parsed'} |
|
184
|
0 |
0 |
unless $line =~ /\S/u |
|
185
|
0 |
0 |
if ($line =~ /$HEADER_RE/u) { } |
|
|
0 |
0 |
elsif ($line =~ /$CORE_PAIR_RE/u) { } |
|
|
0 |
0 |
elsif ($line =~ /$CORE_SINGLE_RE/u) { } |
|
|
0 |
0 |
elsif ($line =~ /$AMBIG_RE/u) { } |
|
202
|
36 |
70 |
if ($both_case) |
|
203
|
34 |
2 |
if ($character ge 'A' and $character le 'Z') { } |
|
|
0 |
4 |
elsif ($character ge 'a' and $character le 'z') { } |
|
213
|
0 |
4 |
if $self->{'parsed'} |
|
218
|
2 |
2 |
if (scalar @{$self->{'ambig_syms'};} == 0 or length $self->{'ambig_syms'}[0]{'comprise'} != scalar @{$self->{'core_syms'};}) |
|
239
|
0 |
62 |
if (defined $real) { } |
|
261
|
0 |
32 |
unless (defined $sym->{'complement'}) |
|
272
|
0 |
184 |
unless defined $target |
|
277
|
0 |
62 |
unless defined $complement |
|
300
|
22 |
40 |
if ($both_case and $prime_sym =~ /^[A-Za-z]$/u) |
|
307
|
2 |
6 |
if ($both_case and $alias_sym =~ /^[A-Za-z]$/u) |
|
327
|
8 |
24 |
if ($both_case and $prime_sym =~ /^[A-Za-z]$/u) |
|
338
|
2 |
2 |
if ($both_case and $alias_sym =~ /^[A-Za-z]$/u) |
|
356
|
22 |
40 |
if ($both_case and $prime_sym =~ /^[A-Za-z]$/u) |
|
367
|
2 |
6 |
if ($both_case and $alias_sym =~ /^[A-Za-z]$/u) |
|
386
|
58 |
4 |
if ($i != $self->{'ncore'}) |
|
391
|
22 |
40 |
if ($both_case and $prime_sym =~ /^[A-Za-z]$/u) |
|
402
|
2 |
6 |
if ($both_case and $alias_sym =~ /^[A-Za-z]$/u) |
|
418
|
140 |
236 |
if (defined $self->{'lookup'}{chr $i}) |
|
419
|
38 |
102 |
if ($i > $range_start + 1) { } |
|
|
12 |
90 |
elsif ($i == $range_start + 1) { } |
|
428
|
0 |
4 |
$wildcard eq '-' || $wildcard eq '/' ? : |
|
432
|
4 |
0 |
if ($self->{'like'}) |
|
434
|
0 |
4 |
if ($self->{'like'} eq 'RNA') { } |
|
|
4 |
0 |
elsif ($self->{'like'} eq 'DNA') { } |
|
|
0 |
0 |
elsif ($self->{'like'} eq 'PROTEIN') { } |
|
445
|
4 |
0 |
if (defined $req_core) |
|
449
|
0 |
16 |
unless (defined $symobj) |
|
452
|
0 |
16 |
unless ($symobj->{'index'} < $self->{'ncore'}) |
|
455
|
16 |
0 |
if (defined $req_comp) { } |
|
458
|
0 |
16 |
unless (defined $compobj or not defined $symobj->{'complement'} || $symobj->{'complement'} != $compobj) |
|
475
|
0 |
0 |
if $self->{'parsed'} |
|
491
|
0 |
0 |
if (defined $sym->{'name'}) |
|
495
|
0 |
0 |
if (defined $sym->{'colour'}) |
|
507
|
0 |
0 |
unless defined $options{'print_header'} |
|
508
|
0 |
0 |
unless defined $options{'print_footer'} |
|
510
|
0 |
0 |
if ($options{'print_header'}) |
|
512
|
0 |
0 |
$self->{'like'} ? : |
|
518
|
0 |
0 |
if (defined $csym and $sym->{'index'} < $csym->{'index'}) |
|
525
|
0 |
0 |
unless (defined $sym->{'complement'}) |
|
532
|
0 |
0 |
if (scalar @{$sym->{'comprise'};} == 0) |
|
553
|
0 |
0 |
if ($gap) |
|
560
|
0 |
0 |
if ($options{'print_footer'}) |
|
571
|
0 |
0 |
if $self->{'like'} |
|
579
|
0 |
0 |
if scalar @{$sym->{'aliases'};} > 0 |
|
580
|
0 |
0 |
if defined $sym->{'name'} |
|
581
|
0 |
0 |
if defined $sym->{'colour'} and $sym->{'colour'} > 0 |
|
582
|
0 |
0 |
if ($i < $self->{'ncore'}) { } |
|
583
|
0 |
0 |
if defined $sym->{'complement'} |
|
610
|
0 |
0 |
if ($should_encode) { } |
|
619
|
0 |
5 |
unless $self->{'parsed'} |
|
638
|
7 |
1 |
if (wantarray) { } |
|
655
|
0 |
0 |
unless ($self->is_core($sym)) |
|
689
|
24 |
53 |
if ($self->is_core($sym)) |
|
758
|
0 |
0 |
if $index < 0 or $index > scalar @{$self->{'syms'};} |
|
771
|
0 |
0 |
unless defined $sym |
|
784
|
0 |
0 |
unless defined $sym |
|
796
|
0 |
0 |
if (defined $sym->{'comprise'}) { } |
|
815
|
0 |
0 |
if (defined $sym) { } |
|
832
|
0 |
0 |
unless ($set->{$a}) |
|
848
|
0 |
0 |
if ($seq =~ /($not_valid)/u) { } |
|
860
|
0 |
1 |
unless $self->has_complement |
|
880
|
0 |
0 |
defined $options{'NO_ALIASES'} ? : |
|
881
|
0 |
0 |
defined $options{'NO_AMBIGS'} ? : |
|
882
|
0 |
0 |
defined $options{'NO_UNKNOWN'} ? : |
|
884
|
0 |
0 |
if ($no_aliases) { } |
|
|
0 |
0 |
elsif ($no_ambigs) { } |
|
887
|
0 |
0 |
if ($no_ambigs) { } |
|
898
|
0 |
0 |
if ($no_unknown) |
|
935
|
0 |
2 |
if $self->size_core != $other->size_core |
|
936
|
0 |
2 |
if $self->size_full != $other->size_full |
|
937
|
0 |
2 |
if $self->has_complement != $other->has_complement |
|
938
|
0 |
2 |
if defined $self->{'name'} != defined $other->{'name'} |
|
939
|
2 |
0 |
if (defined $self->{'name'} and defined $other->{'name'}) |
|
940
|
0 |
2 |
if $self->{'name'} ne $other->{'name'} |
|
946
|
0 |
47 |
if $self_sym->{'sym'} ne $other_sym->{'sym'} |
|
947
|
0 |
47 |
if defined $self_sym->{'name'} != defined $other_sym->{'name'} |
|
948
|
46 |
1 |
if (defined $self_sym->{'name'} and defined $other_sym->{'name'}) |
|
949
|
0 |
46 |
if $self_sym->{'name'} ne $other_sym->{'name'} |
|
951
|
0 |
47 |
if defined $self_sym->{'colour'} != defined $other_sym->{'colour'} |
|
952
|
16 |
31 |
if (defined $self_sym->{'colour'} and defined $other_sym->{'colour'}) |
|
953
|
0 |
16 |
if $self_sym->{'colour'} != $other_sym->{'colour'} |
|
955
|
0 |
47 |
if scalar @{$self_sym->{'aliases'};} != scalar @{$other_sym->{'aliases'};} |
|
958
|
0 |
6 |
if $self_sym->{'aliases'}[$j] ne $other_sym->{'aliases'}[$j] |
|
965
|
0 |
16 |
if defined $self_sym->{'complement'} != defined $other_sym->{'complement'} |
|
966
|
16 |
0 |
if (defined $self_sym->{'complement'} and defined $other_sym->{'complement'}) |
|
967
|
0 |
16 |
if $self_sym->{'complement'}{'sym'} ne $other_sym->{'complement'}{'sym'} |
|
974
|
0 |
31 |
if scalar @{$self_sym->{'comprise'};} != scalar @{$other_sym->{'comprise'};} |
|
976
|
0 |
92 |
if $self_sym->{'comprise'}[$j]{'sym'} ne $other_sym->{'comprise'}[$j]{'sym'} |
|
984
|
1 |
0 |
unless defined $self->{'cached_is_dna'} |
|
990
|
1 |
0 |
unless defined $self->{'cached_is_moddna'} |
|
996
|
0 |
0 |
unless defined $self->{'cached_is_rna'} |
|
1002
|
0 |
0 |
unless defined $self->{'cached_is_protein'} |
|
1012
|
0 |
0 |
unless defined $text |
|
1048
|
0 |
0 |
unless defined $text |
|
1059
|
470 |
56 |
if (length $a == length $b) { } |
|
|
14 |
42 |
elsif (length $a > length $b) { } |
|
1068
|
438 |
66 |
if ($is_letter_a) { } |
|
|
18 |
48 |
elsif ($is_letter_b) { } |
|
1069
|
394 |
44 |
if ($is_letter_b) { } |
|
1070
|
168 |
226 |
if ($sym_a < $sym_b) { } |
|
|
192 |
34 |
elsif ($sym_b < $sym_a) { } |
|
1087
|
48 |
0 |
if ($is_num_a) { } |
|
|
0 |
0 |
elsif ($is_num_b) { } |
|
1088
|
48 |
0 |
if ($is_num_b) { } |
|
1089
|
16 |
32 |
if ($sym_a < $sym_b) { } |
|
|
32 |
0 |
elsif ($sym_b < $sym_a) { } |
|
1103
|
0 |
0 |
if ($sym_a < $sym_b) { } |
|
|
0 |
0 |
elsif ($sym_b < $sym_a) { } |
|
1123
|
150 |
66 |
if (defined $sym1->{'comprise'} and defined $sym2->{'comprise'}) { } |
|
|
0 |
66 |
elsif (defined $sym1->{'comprise'}) { } |
|
|
0 |
66 |
elsif (defined $sym2->{'comprise'}) { } |
|
1125
|
150 |
0 |
if $ret != 0 |
|
1134
|
66 |
0 |
if $ret != 0 |
|
1137
|
0 |
0 |
if (defined $sym1->{'complement'} and defined $sym2->{'complement'}) { } |
|
|
0 |
0 |
elsif (defined $sym1->{'complement'}) { } |
|
|
0 |
0 |
elsif (defined $sym2->{'complement'}) { } |
|
1139
|
0 |
0 |
if $ret != 0 |
|
1147
|
0 |
0 |
if (scalar @{$sym1->{'aliases'};} != scalar @{$sym2->{'aliases'};}) |
|
1153
|
0 |
0 |
if $ret != 0 |
|
1157
|
0 |
0 |
if (defined $sym1->{'name'} and defined $sym2->{'name'}) { } |
|
|
0 |
0 |
elsif (defined $sym1->{'name'}) { } |
|
|
0 |
0 |
elsif (defined $sym2->{'name'}) { } |
|
1159
|
0 |
0 |
if $ret != 0 |
|
1167
|
0 |
0 |
if (defined $sym1->{'colour'} and defined $sym2->{'colour'}) { } |
|
|
0 |
0 |
elsif (defined $sym1->{'colour'}) { } |
|
|
0 |
0 |
elsif (defined $sym2->{'colour'}) { } |
|
1208
|
0 |
0 |
if $alph->has_errors |
|
1263
|
0 |
2 |
if $alph->has_errors |
|
1303
|
0 |
2 |
if $alph->has_errors |
|
1348
|
0 |
0 |
if $alph->has_errors |