| line |
true |
false |
branch |
|
153
|
1 |
0 |
unless (defined $self->sequence_factory) |
|
160
|
1 |
0 |
if ($self->_fh) |
|
194
|
0 |
1 |
if $self->{'_end_of_data'} |
|
219
|
0 |
58 |
if @_ |
|
249
|
1 |
62 |
if @_ |
|
268
|
0 |
1 |
unless (defined $seq) |
|
272
|
0 |
1 |
unless (ref $seq and $seq->isa('Bio::SeqI')) |
|
286
|
1 |
0 |
$seq->can('seq_version') ? : |
|
289
|
1 |
0 |
if ($version) |
|
293
|
1 |
0 |
if ($accversion) { } |
|
302
|
1 |
0 |
unless ($seq_chaos_feature_id =~ /:/) |
|
311
|
0 |
1 |
if ($seq->desc =~ /haplotype(.*)/i) |
|
320
|
1 |
0 |
if (my $spec = $seq->species) |
|
323
|
0 |
1 |
if (my $ssp = $spec->sub_species) |
|
327
|
1 |
0 |
if ($spec->common_name) |
|
333
|
0 |
1 |
if ($common =~ /\((.*)\)/) |
|
339
|
1 |
0 |
if ($OS) |
|
342
|
0 |
1 |
if ($haplotype) |
|
366
|
5 |
0 |
if $seq->can($_) |
|
368
|
1 |
0 |
if $seq->can('get_dates') |
|
379
|
0 |
1 |
if $haplotype |
|
384
|
1 |
0 |
if ($OS) |
|
394
|
0 |
1 |
if @sources > 1 |
|
396
|
1 |
0 |
if ($source) |
|
429
|
1 |
114 |
if @_ |
|
437
|
1 |
114 |
if @_ |
|
445
|
1 |
58 |
if @_ |
|
476
|
0 |
58 |
$loc->is_remote ? : |
|
480
|
0 |
58 |
if ($CREATE_SPLIT_SFS and $loc->isa('Bio::Location::SplitLocationI')) { } |
|
|
0 |
58 |
elsif ($loc->isa('Bio::Location::RemoteLocationI')) { } |
|
494
|
0 |
0 |
if ($_->is_remote) |
|
517
|
0 |
58 |
unless ($strand) |
|
536
|
0 |
58 |
if $props{'id'} |
|
540
|
11 |
47 |
unless $props{'db_xref'} |
|
541
|
14 |
44 |
if ($pid) |
|
545
|
1 |
57 |
$props{'organism'} ? : |
|
546
|
57 |
1 |
if (not $org and $self->organismstr) |
|
549
|
55 |
3 |
$name ? : |
|
550
|
55 |
3 |
if ($self->genus_species and $name) |
|
553
|
0 |
58 |
unless ($uname) |
|
576
|
55 |
3 |
$name ? : |
|
|
14 |
44 |
$tn ? : |
|
|
58 |
0 |
$org ? : |
|
584
|
0 |
58 |
if (@subsfs) { } |
|
602
|
0 |
0 |
if ($ssf->primary_tag eq 'CDS') |
|
616
|
58 |
0 |
unless $props{'parent'} |
|
662
|
0 |
58 |
if ($ob->isa('Bio::SeqI')) { } |
|
663
|
0 |
0 |
$ob->can('seq_version') ? : |
|
666
|
0 |
58 |
unless $ob->isa('Bio::SeqFeatureI') |
|
668
|
0 |
58 |
if ($ob->primary_id) { } |
|
675
|
0 |
58 |
if ($@) |
|
682
|
0 |
58 |
unless ($id) |
|
683
|
0 |
0 |
if ($ob->isa('Bio::SeqFeatureI')) { } |
|
690
|
58 |
0 |
if ($id) |
|
691
|
0 |
58 |
$self->context_namespace ? : |
|
701
|
0 |
58 |
ref $loc eq 'ARRAY' ? : |
|
704
|
26 |
32 |
if ($str < 0) |