| line |
true |
false |
branch |
|
150
|
0 |
0 |
if (defined $value) { } |
|
|
0 |
0 |
elsif (not defined $obj->{'_annotation'}) { } |
|
151
|
0 |
0 |
unless $value->isa('Bio::AnnotationCollectionI') |
|
162
|
0 |
0 |
if ($species) { } |
|
169
|
0 |
0 |
unless (shift())->{'segments'} |
|
178
|
0 |
0 |
$source ne '' ? : |
|
192
|
0 |
3 |
if CORE::ref $class |
|
198
|
3 |
0 |
if ($arg{-'strand'} =~ /^[\+\-\.]$/) { } |
|
199
|
1 |
2 |
if $arg{-'strand'} eq '+' |
|
200
|
1 |
2 |
if $arg{-'strand'} eq '-' |
|
201
|
1 |
2 |
if $arg{-'strand'} eq '.' |
|
203
|
0 |
0 |
$arg{-'strand'} >= 0 ? : |
|
|
0 |
0 |
$arg{-'strand'} ? : |
|
208
|
0 |
3 |
if exists $arg{-'subtype'} |
|
210
|
0 |
3 |
if exists $arg{-'score'} |
|
212
|
1 |
2 |
exists $arg{-'end'} ? : |
|
216
|
0 |
18 |
if exists $arg{"-$option"} |
|
223
|
0 |
3 |
if (defined $self->{'stop'} and defined $self->{'start'} and $self->{'stop'} < $self->{'start'}) |
|
230
|
0 |
3 |
if (my $s = $arg{-'segments'}) |
|
255
|
0 |
0 |
if (CORE::ref $seg eq 'ARRAY') { } |
|
|
0 |
0 |
elsif (CORE::ref $seg) { } |
|
257
|
0 |
0 |
unless defined $start and defined $stop |
|
260
|
0 |
0 |
if ($start > $stop) |
|
277
|
0 |
0 |
if $start < $min_start |
|
278
|
0 |
0 |
if $stop > $max_stop |
|
283
|
0 |
0 |
if $seg->start and $seg->start < $min_start |
|
284
|
0 |
0 |
if $seg->end and $seg->end > $max_stop |
|
287
|
0 |
0 |
if (@segments) |
|
298
|
0 |
0 |
wantarray ? : |
|
|
0 |
0 |
unless my $s = $self->{'segments'} |
|
304
|
0 |
0 |
if @_ |
|
310
|
0 |
0 |
if @_ |
|
316
|
0 |
0 |
if @_ |
|
323
|
0 |
0 |
if @_ |
|
329
|
0 |
0 |
if @_ |
|
330
|
0 |
0 |
if (my $rs = $self->{'refseq'}) { } |
|
332
|
0 |
0 |
$strand >= 0 ? : |
|
340
|
0 |
2 |
if @_ |
|
341
|
0 |
2 |
if (my $rs = $self->{'refseq'}) |
|
343
|
0 |
0 |
$strand >= 0 ? : |
|
350
|
0 |
3 |
if @_ |
|
351
|
0 |
3 |
if (my $rs = $self->{'refseq'}) |
|
353
|
0 |
0 |
unless $d |
|
354
|
0 |
0 |
if $rstrand == $d |
|
355
|
0 |
0 |
if $rstrand != $d |
|
364
|
0 |
0 |
if @_ |
|
393
|
0 |
0 |
if @_ |
|
400
|
0 |
0 |
exists $self->{'seq'} ? : |
|
406
|
0 |
0 |
if CORE::ref $seq |
|
503
|
0 |
0 |
if @_ |
|
509
|
0 |
0 |
if (@_) { } |
|
512
|
0 |
0 |
$self->{'attributes'} ? : |
|
519
|
0 |
0 |
if @_ |
|
528
|
0 |
0 |
if defined $notes |
|
539
|
0 |
0 |
$self->start < $self->end ? : |
|
544
|
0 |
0 |
$self->start > $self->end ? : |
|
560
|
0 |
0 |
unless 'Bio::Location::Split'->can('new') |
|
562
|
0 |
0 |
if (my(@segments) = $self->segments) { } |
|
575
|
0 |
0 |
unless 'Bio::Location::Simple'->can('new') |
|
576
|
0 |
0 |
if (my(@segments) = $self->segments) { } |
|
607
|
0 |
0 |
unless my(@segments) = $self->segments |
|
612
|
0 |
0 |
unless 'Bio::Location::WidestCoordPolicy'->can('new') |
|
627
|
0 |
0 |
defined $strand && $strand < 0 ? : |
|
628
|
0 |
0 |
if (my $id = $self->seq_id) |
|
636
|
0 |
0 |
if @_ |
|
643
|
0 |
0 |
if @_ |
|
644
|
0 |
0 |
defined $d ? : |
|
651
|
0 |
0 |
if @_ |
|
658
|
0 |
0 |
if ($self->version == 3) |
|
665
|
0 |
0 |
if $name |
|
668
|
0 |
0 |
defined $self->score ? : |
|
|
0 |
0 |
defined $self->phase ? : |
|
677
|
0 |
0 |
if ($recurse) |
|
695
|
0 |
0 |
if ($recurse) |
|
696
|
0 |
0 |
unless %$parent_tree |
|
697
|
0 |
0 |
defined $force_id ? : |
|
699
|
0 |
0 |
if $seenit->{$primary_id}++ |
|
702
|
0 |
0 |
if (@rsf) |
|
707
|
0 |
0 |
if (@types == 1 and $types[0] eq $self->primary_tag) |
|
720
|
0 |
0 |
defined $self->score ? : |
|
|
0 |
0 |
defined $self->phase ? : |
|
738
|
0 |
0 |
if defined $id |
|
747
|
0 |
0 |
unless defined $id |
|
748
|
0 |
0 |
if $parent |
|
757
|
0 |
0 |
if @_ |
|
801
|
0 |
0 |
unless my $value = $self->{'attributes'}{$tag} |
|
804
|
0 |
0 |
$ref && $ref eq 'ARRAY' ? : |
|
811
|
0 |
0 |
if @values == 1 |
|
824
|
0 |
0 |
if @values |
|
830
|
0 |
0 |
if (@$parent) |
|
835
|
0 |
0 |
if defined $id |
|
836
|
0 |
0 |
if defined $parent_id |
|
837
|
0 |
0 |
if defined $name |
|
886
|
0 |
0 |
if (@_) |
|
888
|
0 |
0 |
unless $newref->seq_id eq $self->seq_id |