| line |
true |
false |
branch |
|
72
|
0 |
0 |
unless ref $seq or $seq and $db |
|
76
|
0 |
0 |
if defined $start and not defined $offset |
|
79
|
0 |
0 |
$end > $start ? : |
|
|
0 |
0 |
if defined $end and not defined $length |
|
83
|
0 |
0 |
ref $seq ? : |
|
84
|
0 |
0 |
unless ($obj) |
|
92
|
0 |
0 |
unless $parent |
|
98
|
0 |
0 |
if $strand < 0 |
|
101
|
0 |
0 |
if $obj->can('smapped') |
|
104
|
0 |
0 |
$obj->can('smapped') ? : |
|
120
|
0 |
0 |
if defined $refseq |
|
139
|
0 |
0 |
$end > $start ? : |
|
147
|
0 |
0 |
if @_ |
|
155
|
0 |
0 |
if (@_) |
|
159
|
0 |
0 |
unless defined $refseq |
|
162
|
0 |
0 |
if (ref $refseq and ref $refseq eq 'ARRAY') |
|
167
|
0 |
0 |
if (ref $refseq and $refseq->can('smapped')) |
|
168
|
0 |
0 |
unless $self->parent eq $refseq->parent |
|
180
|
0 |
0 |
unless $refseq->isa('Ace::Object') |
|
182
|
0 |
0 |
unless $refseq |
|
186
|
0 |
0 |
unless $r_parent eq $$self{'parent'} |
|
194
|
0 |
0 |
unless $prev |
|
195
|
0 |
0 |
if $self->absolute |
|
196
|
0 |
0 |
wantarray ? : |
|
205
|
0 |
0 |
if $self->absolute |
|
206
|
0 |
0 |
if (my($ref, $r_offset, $r_strand) = $self->refseq) { } |
|
223
|
0 |
0 |
if @_ |
|
234
|
0 |
0 |
unless defined $abs |
|
235
|
0 |
0 |
if $abs |
|
237
|
0 |
0 |
if ($self->refseq) { } |
|
239
|
0 |
0 |
$r_strand < 0 ? : |
|
252
|
0 |
0 |
$$self{'length'} > 0 ? : |
|
253
|
0 |
0 |
if ($abs and $self->refseq ne $self->parent) |
|
255
|
0 |
0 |
if $r_strand < 0 or $$self{'strand'} < 0 or $$self{'length'} < 0 |
|
259
|
0 |
0 |
if $self->r_strand eq $$self{'strand'} |
|
267
|
0 |
0 |
if defined $_[0] |
|
274
|
0 |
0 |
if ($self->absolute) { } |
|
|
0 |
0 |
elsif (my $ref = $self->refseq) { } |
|
277
|
0 |
0 |
$ref->isa('Ace::Sequence::Feature') ? : |
|
287
|
0 |
0 |
if (ref $arg and $arg->isa('Ace::Sequence')) |
|
290
|
0 |
0 |
$reversed ? : |
|
293
|
0 |
0 |
$reversed ? : |
|
299
|
0 |
0 |
if $$self{'dna'} |
|
305
|
0 |
0 |
$self->end >= $self->start ? : |
|
306
|
0 |
0 |
if $self->r_strand ne $effective_strand |
|
314
|
0 |
0 |
unless defined $abs |
|
321
|
0 |
0 |
if $self->debug |
|
323
|
0 |
0 |
unless $abs |
|
331
|
0 |
0 |
unless require GFF |
|
339
|
0 |
0 |
if $gff |
|
355
|
0 |
0 |
if ($self->automerge) |
|
358
|
0 |
0 |
if ($types{'transcript'}) |
|
362
|
0 |
0 |
if $types{'clone'} |
|
363
|
0 |
0 |
if ($types{'similarity'}) |
|
370
|
0 |
0 |
wantarray ? : |
|
379
|
0 |
0 |
$curated ? : |
|
380
|
0 |
0 |
$curated ? : |
|
381
|
0 |
0 |
$curated ? : |
|
383
|
0 |
0 |
unless @features |
|
396
|
0 |
0 |
unless $transcript |
|
397
|
0 |
0 |
if ($feature->type =~ /^(exon|intron|cds)$/) { } |
|
|
0 |
0 |
elsif ($feature->type eq 'Sequence') { } |
|
407
|
0 |
0 |
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 = $self->_query('seqfeatures -version 2 -list') |
|
521
|
0 |
0 |
if ($ref_strand > 0) { } |
|
522
|
0 |
0 |
defined $ref_offset ? : |
|
530
|
0 |
0 |
defined $ref_offset ? : |
|
559
|
0 |
0 |
if $obj->isa('Ace::Sequence') |
|
564
|
0 |
0 |
if $obj->isa('Ace::Object') |
|
574
|
0 |
0 |
if exists $CACHE{$obj} |
|
576
|
0 |
0 |
unless $p |
|
584
|
0 |
0 |
if @pieces |
|
603
|
0 |
0 |
$tl_start < $tl_end ? : |
|
605
|
0 |
0 |
$strand < 0 ? : |
|
|
0 |
0 |
if $length |
|
631
|
0 |
0 |
if ($automerge and lc $type eq 'transcript') { } |
|
|
0 |
0 |
elsif ($automerge and lc $type eq 'clone') { } |
|
644
|
0 |
0 |
if (%filter) { } |
|
649
|
0 |
0 |
if ($type ne '') { } |
|
651
|
0 |
0 |
defined $st ? : |
|
657
|
0 |
0 |
unless defined $st |
|
666
|
0 |
0 |
if $@ |
|
670
|
0 |
0 |
$promiscuous ? : |
|
681
|
0 |
0 |
if ($abs) |
|
709
|
0 |
0 |
if $start > $end |
|
719
|
0 |
0 |
if $self->debug |
|
734
|
0 |
0 |
unless $features |
|
736
|
0 |
0 |
if ref $features eq 'ARRAY' and @$features |
|
737
|
0 |
0 |
unless ref $features |