| line |
!l |
l&&!r |
l&&r |
condition |
|
171
|
0 |
0 |
3 |
UNIVERSAL::can($value, 'isa') and $value->isa('Bio::Polloc::GroupCriteria::operator')
|
|
261
|
0 |
0 |
0 |
defined $self->locigroup and not defined $$self{'_features'}
|
|
264
|
0 |
0 |
0 |
$$self{'_reorder'} and $self->source ne $self->target
|
|
496
|
0 |
0 |
0 |
defined $loci and ref $loci
|
|
|
0 |
0 |
0 |
defined $loci and ref $loci and UNIVERSAL::can($loci, 'isa')
|
|
508
|
0 |
0 |
0 |
$$ext{'-detectstrand'} and $$ext{'-upstream'} || $$ext{'-downstream'}
|
|
527
|
0 |
0 |
0 |
$$ext{'-upstream'} and $$ext{'-downstream'}
|
|
536
|
0 |
0 |
0 |
$$br[0] ne $$_[0] and $$br[3] == $$_[3]
|
|
|
0 |
0 |
0 |
$$br[0] ne $$_[0] and $$br[3] == $$_[3] and $$br[3] * $$_[1] < $$br[3] * $$br[2]
|
|
579
|
0 |
0 |
0 |
$$item[1] < $locus->to and $$item[2] > $locus->from
|
|
839
|
0 |
0 |
0 |
$up_pos and $down_pos
|
|
843
|
0 |
0 |
0 |
defined $$us[0] and defined $$us[4]
|
|
849
|
0 |
0 |
0 |
defined $$ds[0] and defined $$ds[4]
|
|
852
|
0 |
0 |
0 |
defined $found and abs $$us[2] - $$ds[2] > $found
|
|
929
|
0 |
0 |
0 |
defined $seq and UNIVERSAL::can($seq, 'isa')
|
|
|
0 |
0 |
0 |
defined $seq and UNIVERSAL::can($seq, 'isa') and $seq->isa('Bio::Seq')
|
|
1040
|
0 |
0 |
0 |
$alg eq 'blast' and $hsp->frac_identical('query') >= $$ext{'-similarity'}
|
|
|
0 |
0 |
0 |
$alg eq 'blast' and $hsp->frac_identical('query') >= $$ext{'-similarity'} and $hsp->score >= $$ext{'-score'}
|
|
|
0 |
0 |
0 |
$alg eq 'hmmer' and $hsp->score >= $$ext{'-score'}
|
|
|
0 |
0 |
0 |
$alg eq 'hmmer' and $hsp->score >= $$ext{'-score'} and $hsp->evalue <= $$ext{'-e'}
|
|
1133
|
3 |
0 |
0 |
defined $features and not defined $loci
|
| line |
l |
!l&&r |
!l&&!r |
condition |
|
508
|
0 |
0 |
0 |
$$ext{'-upstream'} || $$ext{'-downstream'}
|
|
587
|
0 |
0 |
0 |
$id eq $acc or $id =~ /\|$acc(\.\d+)?(\||\s*$)/
|
|
852
|
0 |
0 |
0 |
$$us[0] ne $$ds[0] or $$us[3] == $$ds[3]
|
|
|
0 |
0 |
0 |
$$us[0] ne $$ds[0] or $$us[3] == $$ds[3] or abs $$ds[2] - $$us[2] > $max_len
|
|
|
0 |
0 |
0 |
$$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'}
|
|
|
0 |
0 |
0 |
$$us[0] ne $$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] - $$ds[2] > $found
|
|
974
|
0 |
0 |
0 |
$alg eq 'blast' or $alg eq 'hmmer'
|
|
1040
|
0 |
0 |
0 |
$alg eq 'blast' and $hsp->frac_identical('query') >= $$ext{'-similarity'} and $hsp->score >= $$ext{'-score'} or $alg eq 'hmmer' and $hsp->score >= $$ext{'-score'} and $hsp->evalue <= $$ext{'-e'}
|