| line |
true |
false |
branch |
|
227
|
0 |
4 |
if ($enc) { } |
|
270
|
4 |
4 |
if (not $enc) { } |
|
|
0 |
4 |
elsif (ref $enc eq 'HASH') { } |
|
|
4 |
0 |
elsif (not ref $enc) { } |
|
277
|
0 |
0 |
if (ref $locs eq 'ARRAY') { } |
|
|
0 |
0 |
elsif (UNIVERSAL::isa($locs, 'Bio::LocationI')) { } |
|
285
|
1 |
3 |
if not defined $exp and $enc =~ /[DEJKV]/o |
|
287
|
1 |
3 |
if ($enc =~ /\d/o) |
|
292
|
2 |
2 |
unless $num |
|
297
|
0 |
4 |
if (defined $exp and $exp == 0 and $enc =~ /([^CIUGFB])/) { } |
|
|
0 |
4 |
elsif ($enc =~ /[^CDEIJKUVGFB]/) { } |
|
303
|
1 |
3 |
if ($loc) { } |
|
308
|
0 |
1 |
if $loc->location_type eq 'EXACT' and $loc->length != $ct |
|
315
|
0 |
1 |
if ($start < $self->start) |
|
320
|
0 |
1 |
if ($end > $self->end) |
|
332
|
1 |
0 |
if ($currseq) |
|
334
|
1 |
0 |
if $self->strand < 0 |
|
335
|
1 |
0 |
$loc->location_type eq 'IN-BETWEEN' ? : |
|
336
|
1 |
0 |
$loc->location_type eq 'IN-BETWEEN' ? : |
|
346
|
1 |
0 |
if $self->strand < 0 |
|
347
|
1 |
0 |
$loc->location_type eq 'IN-BETWEEN' ? : |
|
|
0 |
1 |
$self->strand >= 0 ? : |
|
349
|
1 |
0 |
if $self->strand < 0 |
|
355
|
1 |
0 |
if $self->strand < 0 |
|
357
|
1 |
0 |
if $self->strand < 0 |
|
359
|
0 |
1 |
$exp ? : |
|
376
|
2 |
5 |
$exp ? : |
|
398
|
7 |
5 |
if $self->strand and $self->strand < 0 |
|
401
|
4 |
8 |
unless @enc |
|
408
|
5 |
96 |
if ($nt[$i] =~ /[\.\-]/o and not $enc[$i] =~ /[GB]/o) { } |
|
|
10 |
110 |
elsif (not $nt[$i] =~ /[\.\-]/o and $enc[$i] =~ /[GB]/o) { } |
|
414
|
0 |
12 |
if ($i < @enc) { } |
|
|
3 |
9 |
elsif ($i < @nt) { } |
|
417
|
0 |
0 |
if ($enc[$i] =~ /[GB]/o) { } |
|
425
|
2 |
6 |
if ($nt[$i] =~ /[\.\-]/o) { } |
|
438
|
68 |
41 |
if ($enc[$i] =~ /[CDE]/o) { } |
|
|
0 |
41 |
elsif ($enc[$i] =~ /[IJK]/o) { } |
|
|
0 |
41 |
elsif ($enc[$i] =~ /[UV]/o) { } |
|
|
4 |
37 |
elsif ($enc[$i] eq 'B') { } |
|
|
37 |
0 |
elsif ($enc[$i] eq 'G') { } |
|
442
|
0 |
68 |
if $Vct and not $Vwarned++ |
|
447
|
0 |
0 |
if $Vct and not $Vwarned++ |
|
450
|
0 |
0 |
if ($Uct == 1) |
|
461
|
7 |
5 |
if $self->strand and $self->strand < 0 |
|
487
|
0 |
2 |
unless defined $nogaps |
|
489
|
2 |
0 |
$self->strand < 0 ? : |
|
494
|
0 |
2 |
if ($loc) |
|
496
|
0 |
0 |
if $loc->location_type eq 'IN-BETWEEN' |
|
503
|
0 |
0 |
if $self->strand < 0 |
|
508
|
0 |
20 |
if ($enc[$i] eq 'I' or $enc[$i] eq 'U' or $enc[$i] eq 'F') { } |
|
|
8 |
12 |
elsif ($enc[$i] eq 'G' or $enc[$i] eq 'B') { } |
|
513
|
8 |
0 |
$nogaps ? : |
|
518
|
2 |
0 |
$self->can_call_new ? : |
|
595
|
1 |
0 |
if $self->strand < 0 |
|
597
|
1 |
0 |
if $self->strand < 0 |