| line |
true |
false |
branch |
|
101
|
0 |
150 |
if ($@) { } |
|
238
|
67 |
61 |
if ($self->has_tag($arg)) |
|
377
|
0 |
0 |
unless $formatter |
|
398
|
1 |
0 |
unless (defined $static_gff_formatter) |
|
460
|
122 |
16 |
if ($self->entire_seq->is_circular) |
|
465
|
7 |
131 |
!grep({$_ =~ /(?:nosort|db|phase)/;} @args) ? : |
|
466
|
0 |
138 |
if (@args and $old_api) |
|
469
|
0 |
0 |
if @args |
|
470
|
0 |
0 |
if @args |
|
471
|
0 |
0 |
if @args |
|
474
|
2 |
3 |
if (defined $phase and $phase < 0 || $phase > 2) |
|
479
|
0 |
138 |
if ($db and ref $db and not $db->isa('Bio::DB::RandomAccessI')) { } |
|
|
0 |
138 |
elsif (defined $db and $Bio::SeqFeatureI::HasInMemory and $db->isa('Bio::DB::InMemoryCache')) { } |
|
488
|
114 |
24 |
unless ($self->location->isa('Bio::Location::SplitLocationI')) |
|
489
|
2 |
112 |
if ($phase) { } |
|
503
|
0 |
24 |
unless ($self->location->isa('Bio::Location::SplitLocationI')) |
|
518
|
0 |
24 |
if ($self->isa('Bio::Das::SegmentI') and not $self->absolute) |
|
526
|
2 |
22 |
if (not $nosort) { } |
|
535
|
2 |
3 |
unless defined $fstrand |
|
536
|
0 |
5 |
if defined $_->strand and $fstrand != $_->strand |
|
538
|
5 |
0 |
if (defined $_->seq_id) |
|
539
|
2 |
3 |
if $_->seq_id ne $seqid |
|
545
|
1 |
1 |
if ($fstrand == 1) { } |
|
|
1 |
0 |
elsif ($fstrand == -1) { } |
|
554
|
0 |
2 |
if ($mixed) |
|
575
|
0 |
107 |
unless ($loc->isa('Bio::Location::Atomic')) |
|
579
|
0 |
107 |
if ($fstrand != $loc->strand) |
|
584
|
105 |
2 |
if (defined $loc->seq_id) { } |
|
588
|
2 |
103 |
if ($loc_seq_id ne $seqid) { } |
|
592
|
0 |
2 |
if (defined $db) { } |
|
598
|
0 |
0 |
if ($@) |
|
609
|
2 |
0 |
unless (defined $called_seq) |
|
618
|
23 |
80 |
unless (defined($last_id && $last_id eq $loc_seq_id)) |
|
636
|
103 |
2 |
if (defined $called_seq_seq) { } |
|
644
|
0 |
105 |
if ($called_seq_len < $loc->end) |
|
653
|
0 |
105 |
if ($self->isa('Bio::Das::SegmentI')) { } |
|
661
|
103 |
2 |
if (defined $called_seq_seq) { } |
|
670
|
105 |
0 |
if (defined $self->location->guide_strand) { } |
|
674
|
0 |
0 |
defined $loc->strand ? : |
|
677
|
0 |
0 |
if ($strand == -1) { } |
|
688
|
103 |
2 |
if defined $loc_seq_id |
|
692
|
24 |
0 |
defined $self->location->guide_strand ? : |
|
693
|
11 |
13 |
if ($guide_strand == -1) |
|
698
|
0 |
24 |
if (defined $phase) |
|
753
|
58 |
58 |
if (@_) |
|
754
|
0 |
58 |
if ($self->has_tag('ID')) |
|
802
|
3 |
3 |
if (@_) |
|
803
|
0 |
3 |
if $self->has_tag('phase') |
|
805
|
0 |
3 |
unless not defined $newphase or $newphase == 0 or $newphase == 1 or $newphase == 2 |
|
811
|
2 |
1 |
$self->has_tag('phase') ? : |