| line |
true |
false |
branch |
|
112
|
3 |
1 |
if defined $value
|
|
130
|
3 |
1 |
if defined $value
|
|
149
|
0 |
3 |
if (defined $value)
|
|
170
|
3 |
1 |
if (defined $value)
|
|
171
|
0 |
3 |
unless UNIVERSAL::can($value, 'isa') and $value->isa('Bio::Polloc::GroupCriteria::operator')
|
|
216
|
0 |
0 |
unless $feat1->isa('Bio::Polloc::LocusI')
|
|
219
|
0 |
0 |
unless $feat2->isa('Bio::Polloc::LocusI')
|
|
222
|
0 |
0 |
unless defined $self->condition
|
|
225
|
0 |
0 |
unless $self->condition->type eq 'bool'
|
|
228
|
0 |
0 |
unless defined $self->source
|
|
229
|
0 |
0 |
unless defined $self->target
|
|
232
|
0 |
0 |
unless $feat1->family eq $self->source
|
|
233
|
0 |
0 |
unless $feat2->family eq $self->target
|
|
261
|
0 |
0 |
if defined $self->locigroup and not defined $$self{'_features'}
|
|
263
|
0 |
0 |
unless defined $$self{'_features'}
|
|
264
|
0 |
0 |
if ($$self{'_reorder'} and $self->source ne $self->target)
|
|
269
|
0 |
0 |
if ($ft->family eq $self->source) { }
|
|
|
0 |
0 |
elsif ($ft->family eq $self->target) { }
|
|
309
|
0 |
0 |
unless defined $index
|
|
310
|
0 |
0 |
unless defined $$self{'_features'}
|
|
433
|
17 |
3 |
unless $#args >= 0
|
|
434
|
3 |
0 |
if $#args == 0
|
|
435
|
0 |
3 |
unless $#args % 2
|
|
446
|
0 |
3 |
defined $f{'-lensd'} ? :
|
|
447
|
3 |
0 |
defined $f{'-maxlen'} ? :
|
|
448
|
0 |
3 |
defined $f{'-minlen'} ? :
|
|
449
|
3 |
0 |
defined $f{'-similarity'} ? :
|
|
450
|
3 |
0 |
defined $f{'-score'} ? :
|
|
451
|
3 |
0 |
defined $f{'-consensusperc'} ? :
|
|
452
|
3 |
0 |
defined $f{'-e'} ? :
|
|
453
|
0 |
3 |
unless defined $f{'-p'}
|
|
495
|
0 |
0 |
unless defined $ext
|
|
496
|
0 |
0 |
unless defined $loci and ref $loci and UNIVERSAL::can($loci, 'isa')
|
|
498
|
0 |
0 |
unless $loci->isa('Bio::Polloc::LociGroup')
|
|
500
|
0 |
0 |
unless $#{$loci->loci;} >= 0
|
|
506
|
0 |
0 |
if (lc $$ext{'-function'} eq 'context') { }
|
|
508
|
0 |
0 |
if $$ext{'-detectstrand'} and $$ext{'-upstream'} || $$ext{'-downstream'}
|
|
511
|
0 |
0 |
$$ext{'-feature'} ? :
|
|
512
|
0 |
0 |
if $$ext{'-upstream'}
|
|
514
|
0 |
0 |
if $$ext{'-downstream'}
|
|
516
|
0 |
0 |
if $$ext{'-feature'}
|
|
519
|
0 |
0 |
unless ($max_len)
|
|
522
|
0 |
0 |
if $#{$self->locigroup->loci;} < 1
|
|
527
|
0 |
0 |
if ($$ext{'-upstream'} and $$ext{'-downstream'}) { }
|
|
|
0 |
0 |
elsif ($eval_feature) { }
|
|
530
|
0 |
0 |
if ($eval_feature)
|
|
536
|
0 |
0 |
if $$br[0] ne $$_[0] and $$br[3] == $$_[3] and $$br[3] * $$_[1] < $$br[3] * $$br[2]
|
|
566
|
0 |
0 |
if defined $locus->id
|
|
570
|
0 |
0 |
if defined $loci->name
|
|
571
|
0 |
0 |
if defined $loci->featurename
|
|
572
|
0 |
0 |
if defined $loci->genomes
|
|
576
|
0 |
0 |
unless ($$ext{'-alldetected'})
|
|
579
|
0 |
0 |
if $$item[1] < $locus->to and $$item[2] > $locus->from
|
|
587
|
0 |
0 |
if ($id eq $acc or $id =~ /\|$acc(\.\d+)?(\||\s*$)/)
|
|
591
|
0 |
0 |
unless defined $seq
|
|
592
|
0 |
0 |
unless defined $self->genomes->[$$seq[0]]->get_sequences->[$$seq[1]]
|
|
595
|
0 |
0 |
defined $id ? :
|
|
|
0 |
0 |
$$item[3] == -1 ? :
|
|
651
|
0 |
0 |
$complete ? :
|
|
698
|
0 |
0 |
if ($$bin[$f][$$groups[$g][$m]])
|
|
767
|
0 |
0 |
unless $l_max >= 0
|
|
771
|
0 |
0 |
if defined $advance
|
|
772
|
0 |
0 |
unless $self->evaluate($$loci[$i], $$loci[$j])
|
|
779
|
0 |
0 |
if ($j == $$groups[$g][$m])
|
|
797
|
0 |
0 |
unless defined $locus
|
|
823
|
0 |
0 |
if defined $value
|
|
825
|
0 |
0 |
unless defined $self->locigroup
|
|
839
|
0 |
0 |
unless $up_pos and $down_pos
|
|
843
|
0 |
0 |
unless defined $$us[0] and defined $$us[4]
|
|
849
|
0 |
0 |
unless defined $$ds[0] and defined $$ds[4]
|
|
852
|
0 |
0 |
if $$us[0] ne $$ds[0] or $$us[3] == $$ds[3] or abs $$ds[2] - $$us[2] > $max_len or abs $$ds[2] - $$us[2] < $$ext{'-minlen'} or defined $found and abs $$us[2] - $$ds[2] > $found
|
|
862
|
0 |
0 |
if $#$pair > 1
|
|
929
|
0 |
0 |
unless defined $seq and UNIVERSAL::can($seq, 'isa') and $seq->isa('Bio::Seq')
|
|
934
|
0 |
0 |
unless $start != $end
|
|
939
|
0 |
0 |
unless length $cleanstr > 0
|
|
941
|
0 |
0 |
if $from < $to
|
|
969
|
0 |
0 |
unless defined $ext
|
|
970
|
0 |
0 |
unless defined $self->genomes
|
|
972
|
0 |
0 |
unless defined $aln
|
|
974
|
0 |
0 |
if ($alg eq 'blast' or $alg eq 'hmmer') { }
|
|
976
|
0 |
0 |
unless (defined $$self{'_seqsdb'})
|
|
984
|
0 |
0 |
if ($alg eq 'blast')
|
|
994
|
0 |
0 |
if ($alg eq 'blast') { }
|
|
|
0 |
0 |
elsif ($alg eq 'hmmer') { }
|
|
1015
|
0 |
0 |
if ($alg eq 'blast') { }
|
|
|
0 |
0 |
elsif ($alg eq 'hmmer') { }
|
|
1016
|
0 |
0 |
if $query->seq =~ tr/N// > 0.25 * $query->length
|
|
1040
|
0 |
0 |
if ($alg eq 'blast' and $hsp->frac_identical('query') >= $$ext{'-similarity'} and $hsp->score >= $$ext{'-score'} or $alg eq 'hmmer' and $hsp->score >= $$ext{'-score'} and $hsp->evalue <= $$ext{'-e'})
|
|
1051
|
0 |
0 |
$hsp->strand('hit') != $hsp->strand('query') ? :
|
|
|
0 |
0 |
$hsp->strand('hit') != $hsp->strand('query') ? :
|
|
|
0 |
0 |
$hsp->strand('hit') != $hsp->strand('query') ? :
|
|
1109
|
0 |
0 |
if (defined $$self{'_seqsdb'})
|
|
1111
|
0 |
0 |
unless $self->genomes
|
|
1113
|
0 |
0 |
unless unlink $_
|
|
1115
|
0 |
0 |
unless unlink "$tmp/$k"
|
|
1133
|
0 |
3 |
if defined $features and not defined $loci
|