| line |
true |
false |
branch |
|
115
|
0 |
0 |
if not defined $self->{'_sequences'} or scalar @{$self->{'_sequences'};} < 1 |
|
126
|
0 |
0 |
$end5 < $end3 ? : |
|
135
|
0 |
0 |
if ($start < 0) { } |
|
|
0 |
0 |
elsif ($end > length $self->{'_assembly'}{'seq'}) { } |
|
|
0 |
0 |
elsif ($start >= $end) { } |
|
146
|
0 |
0 |
if ($end5 > $end3) |
|
153
|
0 |
0 |
if $feat->primary_tag ne 'CDS' |
|
170
|
0 |
0 |
if $self->verbose > 0 |
|
177
|
0 |
0 |
unless $seq->display_id |
|
190
|
0 |
0 |
if ($line =~ /<\?xml\s+version\s+=\s+"\d+\.\d+"\?>/o) { } |
|
|
0 |
0 |
elsif ($line =~ //o) { } |
|
|
0 |
0 |
elsif ($line =~ //o) { } |
|
|
0 |
0 |
elsif ($line =~ //o) { } |
|
|
0 |
0 |
elsif ($line =~ m[]o) { } |
|
193
|
0 |
0 |
if $1 ne 'TIGR' |
|
218
|
0 |
0 |
unless ($line =~ //o) |
|
224
|
0 |
0 |
if ($line =~ //o) { } |
|
|
0 |
0 |
elsif ($line =~ //o) { } |
|
239
|
0 |
0 |
unless $line =~ //o |
|
243
|
0 |
0 |
if ($line =~ //o) { } |
|
254
|
0 |
0 |
if ($line =~ //o) { } |
|
262
|
0 |
0 |
if ($line =~ m[]) |
|
275
|
0 |
0 |
unless ($line =~ /]*)>/o) |
|
287
|
0 |
0 |
if (($attr, $val) = $line =~ m[]*)>([^<]*)]o) { } |
|
296
|
0 |
0 |
if ($line =~ //o) { } |
|
308
|
0 |
0 |
if ($line =~ / |
|
316
|
0 |
0 |
if ($line =~ //o) |
|
322
|
0 |
0 |
if ($line =~ //o) { } |
|
330
|
0 |
0 |
if ($line =~ //o) |
|
336
|
0 |
0 |
if ($line =~ //o) |
|
342
|
0 |
0 |
if ($line =~ //o) { } |
|
350
|
0 |
0 |
if ($line =~ m[]o) |
|
362
|
0 |
0 |
unless ($line =~ //o) |
|
372
|
0 |
0 |
unless $line |
|
375
|
0 |
0 |
if (($seq) = $line =~ /^\s*(\w+)\s*$/o) { } |
|
|
0 |
0 |
elsif (($seq) = $line =~ m[^\s*(\w+)\s*$]o) { } |
|
394
|
0 |
0 |
if ($line =~ //o) { } |
|
398
|
0 |
0 |
unless (defined $h->{'end5'} and defined $h->{'end3'}) |
|
413
|
0 |
0 |
unless ($line =~ / |
|
419
|
0 |
0 |
if ($line =~ m[([^>]+)]o) { } |
|
426
|
0 |
0 |
if ($line =~ //o) { } |
|
433
|
0 |
0 |
if ($line =~ m[([^<]*)]o) { } |
|
440
|
0 |
0 |
if ($line =~ m[\s*(.+)\s*]o) { } |
|
445
|
0 |
0 |
if scalar @ss > 0 |
|
452
|
0 |
0 |
if ($line =~ m[([^<]*)]o) { } |
|
462
|
0 |
0 |
if ($line =~ m[([^<]*)]o) { } |
|
484
|
0 |
0 |
if (my(%h) = $line =~ //o) { } |
|
495
|
0 |
0 |
if ($line =~ m[]o) |
|
508
|
0 |
0 |
unless ($line =~ //o) |
|
514
|
0 |
0 |
if ($line =~ //o) { } |
|
522
|
0 |
0 |
if ($line =~ //o) { } |
|
530
|
0 |
0 |
if ($line =~ m[]o) |
|
542
|
0 |
0 |
unless ($line =~ //o) |
|
559
|
0 |
0 |
unless defined $one and defined $two |
|
565
|
0 |
0 |
if ($line =~ m[]o) |
|
578
|
0 |
0 |
if ($line =~ //o) { } |
|
593
|
0 |
0 |
if ($line =~ //o) { } |
|
608
|
0 |
0 |
if ($line =~ //o) { } |
|
624
|
0 |
0 |
if ($line =~ //o) { } |
|
641
|
0 |
0 |
unless $line =~ //o |
|
659
|
0 |
0 |
unless ($line =~ //o) |
|
664
|
0 |
0 |
if ($line =~ m[([\w\.]+)]o) { } |
|
682
|
0 |
0 |
if ($line =~ m[([^>]*)]o) { } |
|
683
|
0 |
0 |
if $1 and not $1 =~ /^\s*$/o |
|
689
|
0 |
0 |
if ($line =~ //o) { } |
|
700
|
0 |
0 |
if ($line =~ //o) { } |
|
729
|
0 |
0 |
$strand == 1 ? : |
|
736
|
0 |
0 |
if ($line =~ /]*>/o) { } |
|
748
|
0 |
0 |
if ($line =~ //o) |
|
758
|
0 |
0 |
if ($line =~ //o) |
|
766
|
0 |
0 |
if ($line =~ m[]o) { } |
|
785
|
0 |
0 |
unless $line =~ //o |
|
788
|
0 |
0 |
if ($line =~ m[\s*([\w\.]+)\s*]o) { } |
|
|
0 |
0 |
elsif ($line =~ m[.*]o) { } |
|
800
|
0 |
0 |
if ($line =~ m[\s*([\w\.]+)\s*]o) |
|
806
|
0 |
0 |
if ($line =~ m[\s*([\w\.]+)\s*]o) { } |
|
|
0 |
0 |
elsif ($line =~ m[.*]o) { } |
|
815
|
0 |
0 |
if ($line =~ m[.*]o) |
|
820
|
0 |
0 |
if (my($attr, $value) = $line =~ m[]*)>([^>]+)]o) { } |
|
847
|
0 |
0 |
if ($line =~ m[([\w\-\\\.]+)]o) |
|
852
|
0 |
0 |
if ($line =~ m[\s*([^<]+)\s*]o) |
|
857
|
0 |
0 |
if ($line =~ m[([^>]+)]o) { } |
|
864
|
0 |
0 |
if ($line =~ /
|
|
868
|
0 |
0 |
if ($line =~ m[([^>]+)]o) |
|
883
|
0 |
0 |
if (defined $type and defined $assignment and defined $term) |
|
893
|
0 |
0 |
if ($line =~ m[
|
|
910
|
0 |
0 |
if ($start < 1) { } |
|
|
0 |
0 |
elsif ($end > $length) { } |
|
|
0 |
0 |
elsif ($start > $end) { } |
|
938
|
0 |
0 |
unless ($line =~ /]+)>/o) |
|
946
|
0 |
0 |
if ($line =~ m[\s*([\w\.]+)\s*]o) { } |
|
954
|
0 |
0 |
if ($line =~ m[\s*([\w\.]+)\s*]o) { } |
|
962
|
0 |
0 |
if ($line =~ //o) |
|
973
|
0 |
0 |
if ($line =~ m[([^>]+)]o) { } |
|
979
|
0 |
0 |
if ($line =~ //o) { } |
|
1008
|
0 |
0 |
if ($line =~ //o) { } |
|
1027
|
0 |
0 |
if $model and $model->start >= 1 |
|
1028
|
0 |
0 |
if $exon and scalar $exon->location->each_Location >= 1 |
|
1029
|
0 |
0 |
if $cds and scalar $cds->location->each_Location >= 1 |
|
1040
|
0 |
0 |
unless ($line =~ //o) |
|
1062
|
0 |
0 |
if ($line =~ m[]o) |
|
1074
|
0 |
0 |
unless ($line =~ //o) |
|
1080
|
0 |
0 |
if ($line =~ m[([^<]+)]o) { } |
|
1087
|
0 |
0 |
if ($line =~ m[([^<]+)]o) { } |
|
1094
|
0 |
0 |
if ($line =~ //o) { } |
|
1104
|
0 |
0 |
if ($line =~ //o) |
|
1110
|
0 |
0 |
if ($line =~ //o) |
|
1116
|
0 |
0 |
if ($line =~ m[]o) |
|
1128
|
0 |
0 |
unless ($line =~ //o) |
|
1134
|
0 |
0 |
if ($line =~ m[([^<]+)]o) { } |
|
1141
|
0 |
0 |
if ($line =~ m[([^<]+)]o) { } |
|
1148
|
0 |
0 |
if ($line =~ //o) { } |
|
1158
|
0 |
0 |
if ($line =~ m[]o) |
|
1170
|
0 |
0 |
unless ($line =~ /
|
|
1178
|
0 |
0 |
if ($line =~ //o) { } |
|
|
0 |
0 |
elsif ($line =~ //o) { } |
|
|
0 |
0 |
elsif ($line =~ //o) { } |
|
1191
|
0 |
0 |
if ($line =~ m[]o) |
|
1203
|
0 |
0 |
unless ($line =~ //o) |
|
1209
|
0 |
0 |
if ($line =~ //o) { } |
|
1227
|
0 |
0 |
if ($line =~ m[]o) |
|
1239
|
0 |
0 |
unless ($line =~ //o) |
|
1245
|
0 |
0 |
if ($line =~ //o) { } |
|
1265
|
0 |
0 |
if ($line =~ m[]o) |
|
1277
|
0 |
0 |
unless ($line =~ //o) |
|
1283
|
0 |
0 |
if ($line =~ //o) { } |
|
1301
|
0 |
0 |
if ($line =~ m[]o) |
|
1314
|
0 |
0 |
if (($tag) = $line =~ m[^[^<]*
|
|
1315
|
0 |
0 |
if $line =~ m[(.+)$] |
|
1328
|
0 |
0 |
if (my($val) = $line =~ m[(<$tag.*>.*?)]s) |
|
1329
|
0 |
0 |
if ($line =~ m[\s*(\w+[\s\w]*?)\s*$]s) |