| line |
true |
false |
branch |
|
132
|
110 |
395 |
if defined $fstrand and $fstrand eq '-' |
|
133
|
505 |
0 |
$group ? : |
|
203
|
48 |
276 |
if defined $fstrand and $fstrand eq '-' |
|
205
|
324 |
0 |
$group ? : |
|
253
|
107 |
869 |
if @_ |
|
274
|
107 |
759 |
if @_ |
|
295
|
0 |
280 |
if @_ |
|
315
|
26 |
0 |
if @_ |
|
335
|
26 |
0 |
if @_ |
|
356
|
85 |
564 |
unless $self->{'fstrand'} |
|
357
|
0 |
564 |
if ($self->absolute) |
|
380
|
107 |
1311 |
if @_ |
|
438
|
0 |
0 |
unless my $group = $self->group |
|
439
|
0 |
0 |
unless $group->can('start') |
|
463
|
0 |
0 |
unless $t->can('start') |
|
470
|
0 |
0 |
if ($v == 2.5) { } |
|
|
0 |
0 |
elsif ($v == 3) { } |
|
488
|
0 |
283 |
if (@_) |
|
566
|
107 |
0 |
if (ref(my $t = $clone->type)) |
|
567
|
107 |
0 |
$t->can('clone') ? : |
|
571
|
107 |
0 |
if (ref(my $g = $clone->group)) |
|
572
|
107 |
0 |
$g->can('clone') ? : |
|
576
|
0 |
107 |
if (my $merged = $self->{'merged_segs'}) |
|
600
|
107 |
0 |
if @_ |
|
625
|
0 |
30 |
unless my $subfeat = $self->{'subfeatures'} |
|
628
|
30 |
0 |
if ($type) { } |
|
629
|
0 |
30 |
unless my $features = $$subfeat{lc $type} |
|
688
|
0 |
0 |
unless 'Bio::Location::Split'->can('new') |
|
689
|
0 |
0 |
unless 'Bio::Location::Simple'->can('new') |
|
692
|
0 |
0 |
if (my(@segments) = $self->segments) { } |
|
753
|
0 |
0 |
if exists $self->{'merged_segs'}{$type} |
|
755
|
0 |
0 |
unless $Bio::DB::GFF::Feature::a->[1] <=> $Bio::DB::GFF::Feature::b->[1] |
|
762
|
0 |
0 |
if @merged |
|
764
|
0 |
0 |
if (defined $previous and $previous->stop + 1 >= $s->start and $pscore == $score and $previous->method eq $s->method) { } |
|
|
0 |
0 |
elsif (defined $previous and $previous->start == $s->start and $previous->stop == $s->stop and $previous->method eq $s->method) { } |
|
769
|
0 |
0 |
if ($self->absolute and $self->strand < 0) { } |
|
776
|
0 |
0 |
if (ref $g and $g->isa('Bio::DB::GFF::Homol')) |
|
815
|
0 |
0 |
unless my $subfeat = $self->{'subfeatures'} |
|
848
|
0 |
20 |
unless defined(my $id = $self->id) |
|
953
|
0 |
0 |
if $CONSTANT_TAGS{$tag} |
|
956
|
0 |
0 |
if $atts and $atts->{$tag} |
|
968
|
0 |
30 |
if $func_name eq 'DESTROY' |
|
972
|
30 |
0 |
if $func_name =~ /^[A-Z]/ |
|
1002
|
59 |
250 |
if (my $subfeat = $self->{'subfeatures'}) |
|
1008
|
202 |
0 |
if (defined $self->{'fstrand'}) { } |
|
1009
|
202 |
0 |
if $self->{'fstrand'} ne $strand |
|
1014
|
166 |
36 |
$start < $stop ? : |
|
1015
|
0 |
202 |
if ($shrink and not $first++) { } |
|
1017
|
0 |
0 |
$self->{'fstrand'} ne '-' ? : |
|
1018
|
0 |
0 |
$self->{'fstrand'} ne '-' ? : |
|
1020
|
166 |
36 |
if ($self->{'fstrand'} ne '-') { } |
|
1022
|
1 |
165 |
if not defined $self->{'start'} or $low < $self->{'start'} |
|
1024
|
4 |
162 |
if not defined $self->{'stop'} or $high > $self->{'stop'} |
|
1027
|
4 |
32 |
if not defined $self->{'start'} or $high > $self->{'start'} |
|
1029
|
0 |
36 |
if not defined $self->{'stop'} or $low < $self->{'stop'} |
|
1035
|
202 |
0 |
unless $h and $h->isa('Bio::DB::GFF::Homol') |
|
1036
|
0 |
0 |
unless $g and $g->isa('Bio::DB::GFF::Homol') |
|
1039
|
0 |
0 |
if ($shrink and not $tfirst++) { } |
|
1043
|
0 |
0 |
if ($start <= $stop) { } |
|
1044
|
0 |
0 |
if not defined $g->{'start'} or $start < $g->{'start'} |
|
1045
|
0 |
0 |
if not defined $g->{'stop'} or $stop > $g->{'stop'} |
|
1047
|
0 |
0 |
if not defined $g->{'start'} or $start > $g->{'start'} |
|
1048
|
0 |
0 |
if not defined $g->{'stop'} or $stop < $g->{'stop'} |
|
1079
|
15 |
15 |
if $self->{'sorted'}++ |
|
1080
|
0 |
15 |
unless my $strand = $self->strand |
|
1081
|
0 |
15 |
unless my $subfeat = $self->{'subfeatures'} |
|
1086
|
20 |
5 |
if $strand > 0 |
|
1090
|
5 |
20 |
if $strand < 0 |
|
1112
|
80 |
0 |
if $name |
|
1140
|
0 |
0 |
if $version == 3 |
|
1146
|
0 |
0 |
if defined $start and defined $stop and $start > $stop |
|
1153
|
0 |
0 |
if (my $t = $self->target) { } |
|
|
0 |
0 |
elsif (my $g = $self->group) { } |
|
1154
|
0 |
0 |
$version == 2.5 ? : |
|
1160
|
0 |
0 |
$name =~ /\S\s\S/ ? : |
|
1167
|
0 |
0 |
if $v =~ /\S\s+\S/ |
|
1174
|
0 |
0 |
ref $ref ? : |
|
1176
|
0 |
0 |
unless defined $phase |
|
1177
|
0 |
0 |
defined $start ? : |
|
|
0 |
0 |
defined $stop ? : |
|
|
0 |
0 |
defined $self->score ? : |
|
|
0 |
0 |
defined $strand ? : |
|
1207
|
0 |
0 |
if defined $start and defined $stop and $start > $stop |
|
1211
|
0 |
0 |
ref $ref ? : |
|
1213
|
0 |
0 |
unless defined $phase |
|
1217
|
0 |
0 |
if (my $g = $self->group) |
|
1220
|
0 |
0 |
if defined $class |
|
1221
|
0 |
0 |
if not defined $parent or $name ne $parent |
|
1224
|
0 |
0 |
if defined $parent and $parent ne '' |
|
1226
|
0 |
0 |
if (my $t = $self->target) |
|
1227
|
0 |
0 |
if $t->stop < $t->start |
|
1239
|
0 |
0 |
if ($recurse) |
|
1260
|
0 |
0 |
if $version |
|
1302
|
0 |
0 |
if ($factory->can('create_cmap_viewer_link')) |
|
1309
|
0 |
0 |
unless $link_str |