| line |
true |
false |
branch |
|
375
|
0 |
11271 |
if ($self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq')) { } |
|
401
|
0 |
11337 |
if ($alphabet eq 'protein') |
|
404
|
0 |
11337 |
if ($alphabet ne 'dna' and $alphabet ne 'rna') |
|
407
|
0 |
0 |
if ($self->can('warn')) { } |
|
415
|
1 |
11336 |
if ($alphabet eq 'rna') |
|
424
|
1 |
11336 |
if ($alphabet eq 'rna') |
|
447
|
2 |
322 |
if (defined $start and ref $start and $start->isa('Bio::LocationI')) { } |
|
|
0 |
322 |
elsif (not $end) { } |
|
|
0 |
322 |
elsif ($end < $start) { } |
|
465
|
8 |
316 |
if ($self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq') or $self->isa('Bio::Seq::RichSeq')) { } |
|
585
|
24 |
263 |
if ($args[0] and $args[0] =~ /^-[A-Z]+/i) { } |
|
606
|
283 |
4 |
unless defined $terminator and $terminator ne '' |
|
607
|
286 |
1 |
unless defined $unknown and $unknown ne '' |
|
608
|
267 |
20 |
unless defined $frame and $frame ne '' |
|
609
|
267 |
20 |
unless defined $codonTableId and $codonTableId ne '' |
|
613
|
1 |
286 |
if ($codonTable) { } |
|
614
|
0 |
1 |
unless $codonTable->isa('Bio::Tools::CodonTable') |
|
624
|
0 |
287 |
if $self->alphabet =~ /protein/i |
|
628
|
1 |
286 |
if ($start_codon) |
|
629
|
0 |
1 |
unless $start_codon =~ /^[A-Z]{3}$/i |
|
634
|
0 |
287 |
if ($offset) { } |
|
635
|
0 |
0 |
unless $offset =~ /^[123]$/ |
|
644
|
12 |
275 |
if ($orf) { } |
|
645
|
2 |
10 |
$orf eq 'longest' ? : |
|
649
|
0 |
13 |
unless $frame == 0 or $frame == 1 or $frame == 2 |
|
661
|
9 |
277 |
if ($complete) |
|
664
|
9 |
0 |
if (substr($output, -1, 1) eq $terminator) { } |
|
667
|
0 |
0 |
if $throw |
|
671
|
2 |
7 |
if ($output =~ /\Q$terminator\E/) |
|
673
|
2 |
0 |
if $throw |
|
677
|
3 |
4 |
if (substr($output, 0, 1) ne 'M') |
|
678
|
3 |
0 |
if ($codonTable->is_start_codon(substr($seq, 0, 3))) { } |
|
|
0 |
0 |
elsif ($throw) { } |
|
692
|
3 |
281 |
if ($self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq')) { } |
|
728
|
1 |
1 |
unless $self->alphabet eq 'dna' |
|
737
|
0 |
1 |
if ($self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq')) { } |
|
774
|
0 |
1 |
unless $self->alphabet eq 'rna' |
|
783
|
0 |
1 |
if ($self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq')) { } |
|
897
|
1 |
13 |
if $start_codon |
|
901
|
1 |
13 |
$start_codon ? : |
|
920
|
530 |
709 |
if ($current_orf_start[$frame] >= 0) { } |
|
|
44 |
665 |
elsif (&$is_start($this_codon)) { } |
|
921
|
44 |
486 |
if ($codon_table->is_ter_codon($this_codon) or my $is_last_codon_in_frame = $j >= $seqlen - 5) |
|
926
|
10 |
34 |
if ($first_only and $frame == $start_frame_order[0]) |
|
927
|
4 |
6 |
if $is_last_codon_in_frame |
|
950
|
0 |
4 |
CORE::length $seq > 200 ? : |
|
956
|
0 |
15 |
unless $orf |
|
975
|
0 |
0 |
if ($main::main::{'Bio::PrimarySeq'}) { } |
|
981
|
0 |
0 |
if ($@) |
|
1000
|
11 |
0 |
if ($self->can_call_new) { } |
|
1007
|
0 |
11 |
if ($seqclass eq 'Bio::PrimarySeq') |