| line |
true |
false |
branch |
|
94
|
0 |
0 |
if $parent
|
|
109
|
0 |
0 |
if ($srcseq and not $parent)
|
|
116
|
0 |
0 |
if ref $parent and $parent->can('srcfeature_id')
|
|
171
|
0 |
0 |
if defined @_
|
|
172
|
0 |
0 |
if defined $organism
|
|
207
|
0 |
0 |
if @_
|
|
225
|
0 |
0 |
if @_
|
|
252
|
0 |
0 |
if @_
|
|
281
|
0 |
0 |
if defined $_[0]
|
|
299
|
0 |
0 |
if @_
|
|
316
|
0 |
0 |
if @_
|
|
332
|
0 |
0 |
if defined $_[0]
|
|
484
|
0 |
0 |
unless $attribute
|
|
488
|
0 |
0 |
if ($recurse)
|
|
556
|
0 |
0 |
if @_
|
|
557
|
0 |
0 |
if defined $$self{'seq_id'}
|
|
562
|
0 |
0 |
unless $feature_id
|
|
651
|
0 |
0 |
if @_
|
|
728
|
0 |
0 |
if @_
|
|
746
|
0 |
0 |
if @_
|
|
789
|
0 |
0 |
if ($$hashref{'name'})
|
|
887
|
0 |
0 |
if @_
|
|
931
|
0 |
0 |
if (defined $refclass_feature_id)
|
|
938
|
0 |
0 |
if (@type > 0)
|
|
944
|
0 |
0 |
if ($inferCDS and grep {'CDS|UTR';} @type)
|
|
964
|
0 |
0 |
unless $partof
|
|
965
|
0 |
0 |
if ref $partof eq 'ARRAY'
|
|
966
|
0 |
0 |
if ref $derivesfrom eq 'ARRAY'
|
|
972
|
0 |
0 |
unless ($self->factory->tripal)
|
|
1014
|
0 |
0 |
if ($self->factory->recursivMapping)
|
|
1057
|
0 |
0 |
unless $subfeature_query->execute
|
|
1063
|
0 |
0 |
if $rows < 1
|
|
1069
|
0 |
0 |
if $$hashref{'is_obsolete'} and not $self->factory->allow_obsolete
|
|
1070
|
0 |
0 |
unless $$hashref{'srcfeature_id'} == $self->srcfeature_id
|
|
1111
|
0 |
0 |
if ($inferCDS and $feat->type =~ /exon/ || $feat->type =~ /polypeptide/)
|
|
1122
|
0 |
0 |
if @p_e_cache > 0
|
|
1128
|
0 |
0 |
if (@type and $inferCDS)
|
|
1133
|
0 |
0 |
if ($feat->method =~ /$type_str/)
|
|
1198
|
0 |
0 |
unless $b->type cmp $a->type
|
|
1206
|
0 |
0 |
if ($poly->type->method =~ /poly/) { }
|
|
1226
|
0 |
0 |
if ($feat->start < $start and $feat->end < $start) { }
|
|
|
0 |
0 |
elsif ($feat->start > $stop and $feat->end > $stop) { }
|
|
|
0 |
0 |
elsif ($feat->start >= $start and $feat->end <= $stop) { }
|
|
1228
|
0 |
0 |
if ($feat->strand) { }
|
|
1229
|
0 |
0 |
if ($feat->strand > 0) { }
|
|
|
0 |
0 |
elsif ($feat->strand < 0) { }
|
|
1243
|
0 |
0 |
if ($feat->strand) { }
|
|
1244
|
0 |
0 |
if ($feat->strand > 0) { }
|
|
|
0 |
0 |
elsif ($feat->strand < 0) { }
|
|
1265
|
0 |
0 |
if ($feat->start < $start and $feat->end >= $start) { }
|
|
|
0 |
0 |
elsif ($feat->start >= $start and $feat->end > $stop) { }
|
|
1267
|
0 |
0 |
if ($utr->strand) { }
|
|
1268
|
0 |
0 |
if ($utr->strand > 0) { }
|
|
|
0 |
0 |
elsif ($utr->strand < 0) { }
|
|
1285
|
0 |
0 |
if ($utr->strand) { }
|
|
1286
|
0 |
0 |
if ($feat->strand > 0) { }
|
|
|
0 |
0 |
elsif ($feat->strand < 0) { }
|
|
1309
|
0 |
0 |
unless @coding_array > 0 or @noncoding_array > 0
|
|
1312
|
0 |
0 |
if (defined $coding_array[0]->phase) { }
|
|
1349
|
0 |
0 |
unless defined $exons[$i]
|
|
1397
|
0 |
0 |
unless ref $subfeature
|
|
1398
|
0 |
0 |
unless $subfeature->isa('Bio::DB::Das::Chado::Segment::Feature')
|
|
1417
|
0 |
0 |
unless 'Bio::Location::Split'->can('new')
|
|
1418
|
0 |
0 |
unless 'Bio::Location::Simple'->can('new')
|
|
1421
|
0 |
0 |
if (my(@segments) = $self->sub_SeqFeature) { }
|
|
1454
|
0 |
0 |
if (ref(my $t = $clone->type))
|
|
1455
|
0 |
0 |
$t->can('clone') ? :
|
|
1459
|
0 |
0 |
if (ref(my $g = $clone->group))
|
|
1460
|
0 |
0 |
$g->can('clone') ? :
|
|
1464
|
0 |
0 |
if (my $merged = $$self{'merged_segs'})
|
|
1490
|
0 |
0 |
unless my $subfeat = $self->subfeatures
|
|
1521
|
0 |
0 |
if $func_name eq 'DESTROY'
|
|
1525
|
0 |
0 |
if $func_name =~ /^[A-Z]/
|
|
1554
|
0 |
0 |
if (my $subfeat = $self->subfeatures)
|
|
1560
|
0 |
0 |
unless defined $$self{'strand'}
|
|
1561
|
0 |
0 |
if ($start <= $stop) { }
|
|
1562
|
0 |
0 |
if not defined $$self{'start'} or $start < $$self{'start'}
|
|
1563
|
0 |
0 |
if not defined $$self{'stop'} or $stop > $$self{'stop'}
|
|
1565
|
0 |
0 |
if not defined $$self{'start'} or $start > $$self{'start'}
|
|
1566
|
0 |
0 |
if not defined $$self{'stop'} or $stop < $$self{'stop'}
|
|
1609
|
0 |
0 |
if $$self{'sorted'}++
|
|
1610
|
0 |
0 |
unless my $strand = $self->strand
|
|
1611
|
0 |
0 |
unless my $subfeat = $self->subfeatures
|
|
1616
|
0 |
0 |
if $strand > 0
|
|
1620
|
0 |
0 |
if $strand < 0
|
|
1643
|
0 |
0 |
if $name
|
|
1670
|
0 |
0 |
if ($self->factory->use_all_feature_names) { }
|
|
1682
|
0 |
0 |
unless $sth->execute($self->feature_id)
|
|
1687
|
0 |
0 |
if $$hashref{'name'} ne $name
|
|
1735
|
0 |
0 |
unless $sth->execute($self->feature_id)
|
|
1738
|
0 |
0 |
if (my $hashref = $sth->fetchrow_hashref)
|