| line |
true |
false |
branch |
|
212
|
0 |
203 |
if ref $package |
|
213
|
0 |
203 |
unless $factory |
|
216
|
35 |
168 |
if (ref $name and $name->isa('Bio::DB::GFF::Segment')) |
|
217
|
5 |
30 |
unless defined $start |
|
218
|
5 |
30 |
unless defined $stop |
|
225
|
0 |
168 |
if (ref $name and $name->can('class')) |
|
239
|
0 |
168 |
if ($nocheck) |
|
247
|
0 |
168 |
$force_absolute ? : |
|
|
8 |
160 |
unless my $result = $factory->abscoords($name, $class, $force_absolute ? $name : ()) |
|
253
|
0 |
160 |
unless defined $sname |
|
261
|
0 |
160 |
if ($absstart > $absstop) |
|
263
|
0 |
0 |
$absstrand eq '+' ? : |
|
267
|
0 |
160 |
if (defined $offset) |
|
268
|
0 |
0 |
if defined $this_start |
|
272
|
0 |
160 |
if (defined $this_length) |
|
273
|
0 |
0 |
if defined $this_stop |
|
279
|
25 |
55 |
if $absref eq $sname and not defined $this_start and not defined $this_stop |
|
281
|
75 |
85 |
unless defined $this_start |
|
282
|
80 |
80 |
unless defined $this_stop |
|
286
|
0 |
160 |
if ($force_absolute) { } |
|
|
140 |
20 |
elsif ($absstrand eq '+') { } |
|
300
|
5 |
5 |
if ($factory->strict_bounds_checking and $this_start < $absstart || $this_stop > $absstop) |
|
303
|
0 |
5 |
unless $this_start <= $absstop and $this_stop >= $absstart |
|
304
|
5 |
0 |
if (my $a = $factory->abscoords($absref, 'Sequence')) |
|
307
|
0 |
5 |
if ($this_start < $refstart) |
|
311
|
5 |
0 |
if ($this_stop > $refstop) |
|
322
|
0 |
160 |
if (defined $refseq) { } |
|
323
|
0 |
0 |
if $refseq->can('class') |
|
326
|
0 |
0 |
unless ($refref eq $absref) |
|
330
|
0 |
0 |
if $refstrand eq '-' |
|
333
|
20 |
140 |
if $absstrand eq '-' |
|
339
|
160 |
0 |
wantarray ? : |
|
346
|
0 |
5 |
$self->strand < 0 ? : |
|
|
5 |
1586 |
if $self->absolute |
|
351
|
0 |
0 |
$self->strand < 0 ? : |
|
|
0 |
697 |
if $self->absolute |
|
358
|
0 |
35 |
unless defined $self->abs_end |
|
364
|
0 |
120 |
if ($self->absolute) { } |
|
366
|
0 |
0 |
$a < $b ? : |
|
374
|
0 |
140 |
if ($self->absolute) { } |
|
376
|
0 |
0 |
$a > $b ? : |
|
411
|
50 |
322 |
if (@_) |
|
413
|
10 |
40 |
if (@_ == 2) { } |
|
421
|
0 |
50 |
unless defined $newref |
|
424
|
30 |
20 |
if ref $newref and $newref->can('class') |
|
430
|
30 |
20 |
if ($newref->isa('Bio::DB::GFF::RelSegment')) { } |
|
431
|
25 |
5 |
$newref->abs_strand >= 0 ? : |
|
437
|
15 |
5 |
if $refsource eq $self->{'sourceseq'} |
|
442
|
5 |
45 |
unless $refsource eq $self->{'sourceseq'} |
|
447
|
5 |
362 |
$self->absolute ? : |
|
468
|
0 |
0 |
$a < $b ? : |
|
488
|
0 |
0 |
$a > $b ? : |
|
512
|
0 |
10 |
if $self->absolute |
|
516
|
5 |
5 |
if (ref $label and overload::StrVal($self) eq overload::StrVal($label->ref)) |
|
552
|
60 |
6407 |
if @_ |
|
699
|
5 |
0 |
defined $_[0] && $_[0] =~ /^-/ ? : |
|
862
|
10 |
75 |
if defined $strand and $strand eq '-' |
|
868
|
55 |
30 |
unless $whole |
|
870
|
70 |
15 |
if (@_) |
|
871
|
45 |
25 |
if ($_[0] =~ /^-/) { } |
|
906
|
0 |
15 |
if $strand eq '-' |
|
909
|
0 |
15 |
if (@_ and not $_[0] =~ /^-/) { } |
|
943
|
35 |
0 |
if ref $package |
|
969
|
0 |
2283 |
unless defined $_[0] |
|
971
|
0 |
2283 |
if ($self->absolute) { } |
|
976
|
161 |
2122 |
defined $refstrand && $refstrand eq '-' ? : |
|
980
|
2203 |
80 |
if @result == 1 and not wantarray |
|
1002
|
0 |
0 |
if ($self->absolute) { } |
|
1007
|
0 |
0 |
$abs_strand < 0 ? : |
|
1011
|
0 |
0 |
if @result == 1 and not wantarray |
|
1033
|
0 |
0 |
if ($self->absolute) { } |
|
1038
|
0 |
0 |
$abs_strand < 0 ? : |
|
1042
|
0 |
0 |
if @result == 1 and not wantarray |
|
1054
|
10 |
617 |
if ($self->absolute) |
|
1059
|
0 |
617 |
unless defined $start and defined $stop |
|
1065
|
5 |
5 |
if $s eq '-' |
|
1066
|
5 |
0 |
if $s eq '+' |
|
1081
|
0 |
0 |
if ref $self |
|
1082
|
0 |
0 |
unless $ranges[0]->isa('Bio::DB::GFF::RelSegment') |
|
1088
|
0 |
0 |
unless $_->can('abs_ref') |
|
1089
|
0 |
0 |
unless $ref eq $_->abs_ref |
|
1090
|
0 |
0 |
if not defined $low or $low < $_->abs_low |
|
1091
|
0 |
0 |
if not defined $high or $high > $_->abs_high |
|
1094
|
0 |
0 |
unless $low < $high |
|
1105
|
0 |
0 |
unless $other->isa('Bio::DB::GFF::RelSegment') |
|
1106
|
0 |
0 |
if $self->abs_ref ne $other->abs_ref |
|
1107
|
0 |
0 |
if $self->abs_low > $other->abs_high |
|
1108
|
0 |
0 |
if $self->abs_high < $other->abs_low |
|
1115
|
0 |
0 |
unless $other->isa('Bio::DB::GFF::RelSegment') |
|
1116
|
0 |
0 |
if $self->abs_ref ne $other->abs_ref |
|
1117
|
0 |
0 |
unless $self->abs_low <= $other->abs_low |
|
1118
|
0 |
0 |
unless $self->abs_high >= $other->abs_high |
|
1125
|
0 |
0 |
if ref $self |
|
1126
|
0 |
0 |
unless $ranges[0]->isa('Bio::DB::GFF::RelSegment') |
|
1132
|
0 |
0 |
unless $_->can('abs_ref') |
|
1133
|
0 |
0 |
unless $ref eq $_->abs_ref |
|
1134
|
0 |
0 |
if not defined $low or $low > $_->abs_low |
|
1135
|
0 |
0 |
if not defined $high or $high < $_->abs_high |