| line |
true |
false |
branch |
| 72 |
0 |
25 |
unless ref $seq or $seq and $db |
| 76 |
0 |
25 |
if defined $start and not defined $offset |
| 79 |
0 |
0 |
$end > $start ? : |
| |
0 |
25 |
if defined $end and not defined $length |
| 83 |
24 |
1 |
ref $seq ? : |
| 84 |
0 |
25 |
unless ($obj) |
| 92 |
0 |
25 |
unless $parent |
| 98 |
4 |
21 |
if $strand < 0 |
| 101 |
16 |
9 |
if $obj->can('smapped') |
| 104 |
16 |
9 |
$obj->can('smapped') ? : |
| 120 |
17 |
8 |
if defined $refseq |
| 139 |
5 |
1 |
$end > $start ? : |
| 147 |
0 |
10 |
if @_ |
| 155 |
18 |
1000 |
if (@_) |
| 159 |
0 |
18 |
unless defined $refseq |
| 162 |
0 |
18 |
if (ref $refseq and ref $refseq eq 'ARRAY') |
| 167 |
16 |
2 |
if (ref $refseq and $refseq->can('smapped')) |
| 168 |
0 |
16 |
unless $self->parent eq $refseq->parent |
| 180 |
2 |
0 |
unless $refseq->isa('Ace::Object') |
| 182 |
0 |
2 |
unless $refseq |
| 186 |
0 |
2 |
unless $r_parent eq $$self{'parent'} |
| 194 |
0 |
1018 |
unless $prev |
| 195 |
0 |
1018 |
if $self->absolute |
| 196 |
534 |
484 |
wantarray ? : |
| 205 |
0 |
134 |
if $self->absolute |
| 206 |
134 |
0 |
if (my($ref, $r_offset, $r_strand) = $self->refseq) { } |
| 223 |
0 |
24 |
if @_ |
| 234 |
389 |
36 |
unless defined $abs |
| 235 |
36 |
389 |
if $abs |
| 237 |
389 |
0 |
if ($self->refseq) { } |
| 239 |
34 |
355 |
$r_strand < 0 ? : |
| 252 |
47 |
59 |
$$self{'length'} > 0 ? : |
| 253 |
17 |
89 |
if ($abs and $self->refseq ne $self->parent) |
| 255 |
9 |
8 |
if $r_strand < 0 or $$self{'strand'} < 0 or $$self{'length'} < 0 |
| 259 |
82 |
7 |
if $self->r_strand eq $$self{'strand'} |
| 267 |
0 |
1611 |
if defined $_[0] |
| 274 |
0 |
59 |
if ($self->absolute) { } |
| |
59 |
0 |
elsif (my $ref = $self->refseq) { } |
| 277 |
0 |
59 |
$ref->isa('Ace::Sequence::Feature') ? : |
| 287 |
0 |
3 |
if (ref $arg and $arg->isa('Ace::Sequence')) |
| 290 |
0 |
0 |
$reversed ? : |
| 293 |
0 |
3 |
$reversed ? : |
| 299 |
0 |
12 |
if $$self{'dna'} |
| 305 |
9 |
3 |
$self->end >= $self->start ? : |
| 306 |
8 |
4 |
if $self->r_strand ne $effective_strand |
| 314 |
6 |
0 |
unless defined $abs |
| 321 |
0 |
6 |
if $self->debug |
| 323 |
6 |
0 |
unless $abs |
| 331 |
0 |
0 |
unless require GFF |
| 339 |
0 |
0 |
if $gff |
| 355 |
5 |
0 |
if ($self->automerge) |
| 358 |
0 |
5 |
if ($types{'transcript'}) |
| 362 |
0 |
5 |
if $types{'clone'} |
| 363 |
0 |
5 |
if ($types{'similarity'}) |
| 370 |
5 |
0 |
wantarray ? : |
| 379 |
0 |
1 |
$curated ? : |
| 380 |
0 |
1 |
$curated ? : |
| 381 |
0 |
1 |
$curated ? : |
| 383 |
0 |
1 |
unless @features |
| 396 |
2 |
102 |
unless $transcript |
| 397 |
83 |
19 |
if ($feature->type =~ /^(exon|intron|cds)$/) { } |
| |
19 |
0 |
elsif ($feature->type eq 'Sequence') { } |
| 407 |
8 |
11 |
unless exists $transcripts{$_}{'exon'} |
| 419 |
0 |
0 |
unless @clones |
| 428 |
0 |
0 |
$self->strand < 0 ? : |
| 429 |
0 |
0 |
$self->strand < 0 ? : |
| 431 |
0 |
0 |
if $feature->type eq 'Clone_left_end' |
| 432 |
0 |
0 |
if $feature->type eq 'Clone_right_end' |
| 434 |
0 |
0 |
if ($feature->type eq 'Sequence') |
| 436 |
0 |
0 |
if $info =~ /LINK|CHROMOSOME|\.\w+$/ |
| 437 |
0 |
0 |
if ($info->Genomic_canonical(0)) |
| 438 |
0 |
0 |
if $info->Clone |
| 451 |
0 |
0 |
if ($abs) |
| 475 |
0 |
0 |
unless @types |
| 492 |
0 |
0 |
unless $feature->type eq 'similarity' |
| 505 |
0 |
0 |
if $$self{'feature_list'} |
| 506 |
0 |
0 |
unless my $raw = $self->_query('seqfeatures -version 2 -list') |
| 521 |
5 |
1 |
if ($ref_strand > 0) { } |
| 522 |
5 |
0 |
defined $ref_offset ? : |
| 530 |
1 |
0 |
defined $ref_offset ? : |
| 559 |
16 |
11 |
if $obj->isa('Ace::Sequence') |
| 564 |
11 |
0 |
if $obj->isa('Ace::Object') |
| 574 |
0 |
0 |
if exists $CACHE{$obj} |
| 576 |
0 |
0 |
unless $p |
| 584 |
0 |
0 |
if @pieces |
| 603 |
6 |
5 |
$tl_start < $tl_end ? : |
| 605 |
5 |
6 |
$strand < 0 ? : |
| |
11 |
0 |
if $length |
| 631 |
0 |
7 |
if ($automerge and lc $type eq 'transcript') { } |
| |
0 |
7 |
elsif ($automerge and lc $type eq 'clone') { } |
| 644 |
5 |
0 |
if (%filter) { } |
| 649 |
7 |
0 |
if ($type ne '') { } |
| 651 |
0 |
7 |
defined $st ? : |
| 657 |
0 |
0 |
unless defined $st |
| 666 |
0 |
5 |
if $@ |
| 670 |
0 |
5 |
$promiscuous ? : |
| 681 |
0 |
5 |
if ($abs) |
| 709 |
5 |
13 |
if $start > $end |
| 719 |
0 |
18 |
if $self->debug |
| 734 |
1 |
5 |
unless $features |
| 736 |
5 |
0 |
if ref $features eq 'ARRAY' and @$features |
| 737 |
0 |
5 |
unless ref $features |