| line |
!l |
l&&!r |
l&&r |
condition |
|
606
|
0 |
0 |
0 |
$len == 1 and $refstring =~ /[^\.\-\*\?]/ |
|
|
0 |
0 |
0 |
$len == 1 and $refstring =~ /[^\.\-\*\?]/ and $varstring =~ /[^\.\-\*\?]/ |
|
|
0 |
0 |
0 |
$refstring =~ /^[^\.\-\*\?]+$/ and not $varstring =~ /^[^\.\-\*\?]+$/ |
|
|
0 |
0 |
0 |
not $refstring =~ /^[^\.\-\*\?]+$/ and $varstring =~ /^[^\.\-\*\?]+$/ |
|
696
|
4 |
1 |
0 |
$self->gene->get_DNA->alphabet eq 'rna' and $self->numbering eq 'gene' |
|
702
|
1 |
0 |
0 |
$transnumber and $transnumber >= 0 |
|
|
1 |
0 |
0 |
$transnumber and $transnumber >= 0 and $transnumber <= $#transcripts |
|
790
|
0 |
0 |
0 |
$seqDiff->offset != 0 and $dnamut->region ne 'intron' |
|
1004
|
0 |
5 |
0 |
$strand == 1 and $self->mutation->postlabel <= $RNAstart |
|
|
5 |
0 |
0 |
$strand != 1 and $self->mutation->postlabel >= $RNAstart |
|
|
0 |
5 |
0 |
$strand == 1 and $self->mutation->prelabel >= $RNAend |
|
|
5 |
0 |
0 |
$strand != 1 and $self->mutation->prelabel <= $RNAend |
|
1028
|
0 |
4 |
0 |
$strand == 1 and $self->mutation->prelabel < $before |
|
|
4 |
0 |
0 |
$strand == -1 and $self->mutation->prelabel > $before |
|
1053
|
0 |
0 |
14 |
$strand == 1 and $self->mutation->prelabel >= $before |
|
|
0 |
14 |
0 |
$strand == 1 and $self->mutation->prelabel >= $before and $self->mutation->postlabel <= $after |
|
|
14 |
0 |
0 |
$strand == -1 and $self->mutation->prelabel <= $before |
|
|
14 |
0 |
0 |
$strand == -1 and $self->mutation->prelabel <= $before and $self->mutation->postlabel >= $after |
|
|
0 |
2 |
12 |
$strand == 1 and $exons[$i]->start < $self->mutation->prelabel |
|
|
2 |
10 |
2 |
$strand == 1 and $exons[$i]->start < $self->mutation->prelabel and $exons[$i]->end > $self->mutation->prelabel |
|
|
0 |
0 |
12 |
$strand == 1 and $exons[$i]->start < $self->mutation->postlabel |
|
|
0 |
10 |
2 |
$strand == 1 and $exons[$i]->start < $self->mutation->postlabel and $exons[$i]->end > $self->mutation->postlabel |
|
|
10 |
0 |
0 |
$strand == -1 and $exons[$i]->start > $self->mutation->prelabel |
|
|
10 |
0 |
0 |
$strand == -1 and $exons[$i]->start > $self->mutation->prelabel and $exons[$i]->end < $self->mutation->prelabel |
|
|
10 |
0 |
0 |
$strand == -1 and $exons[$i]->start > $self->mutation->postlabel |
|
|
10 |
0 |
0 |
$strand == -1 and $exons[$i]->start > $self->mutation->postlabel and $exons[$i]->end < $self->mutation->postlabel |
|
1341
|
0 |
0 |
5 |
$self->rnachange and $self->rnachange->region eq 'coding' |
|
1365
|
0 |
0 |
5 |
$rlenori == 1 and $rlenmut == 1 |
|
|
0 |
0 |
5 |
$rlenori == 1 and $rlenmut == 1 and $aachange->allele_ori->seq ne '*' |
|
|
0 |
0 |
0 |
$rlenori == $rlenmut and $aachange->allele_ori->seq ne '*' |
|
1382
|
0 |
0 |
0 |
$aachange->RNAChange->allele_mut->seq and $aachange->RNAChange->allele_ori->seq |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
177
|
2 |
4 |
0 |
$value =~ /(coding)( )?(\d+)?/ or $value eq 'entry' |
|
|
6 |
0 |
0 |
$value =~ /(coding)( )?(\d+)?/ or $value eq 'entry' or $value eq 'gene' |
|
214
|
5 |
0 |
0 |
$value->seq or $value->len |
|
293
|
5 |
0 |
0 |
$value->isa('Bio::LiveSeq::DNA') || $value->isa('Bio::LiveSeq::Transcript') |
|
898
|
0 |
5 |
0 |
$self->mutation->len == 0 || $self->mutation->len == 1 |
|
927
|
4 |
0 |
1 |
$seqDiff->numbering eq 'entry' or $seqDiff->numbering eq 'gene' |
|
969
|
0 |
0 |
5 |
$self->mutation->prelabel > $DNAend or $self->mutation->postlabel > $DNAend |
|
974
|
0 |
0 |
0 |
$self->mutation->postlabel == $RNAstart or follows($self->mutation->postlabel, $RNAstart) |
|
|
0 |
0 |
0 |
$RNAend == $self->mutation->prelabel or follows($RNAend, $self->mutation->prelabel) |
|
990
|
0 |
0 |
0 |
follows($self->mutation->prelabel, $before) or $after == $self->mutation->prelabel |
|
|
0 |
0 |
0 |
follows($self->mutation->prelabel, $before) or $after == $self->mutation->prelabel or follows($after, $self->mutation->prelabel) |
|
|
0 |
0 |
0 |
follows($self->mutation->prelabel, $before) or $after == $self->mutation->prelabel or follows($after, $self->mutation->prelabel) or follows($after, $self->mutation->postlabel) |
|
1004
|
0 |
0 |
5 |
$strand == 1 and $self->mutation->postlabel <= $RNAstart or $strand != 1 and $self->mutation->postlabel >= $RNAstart |
|
|
0 |
0 |
5 |
$strand == 1 and $self->mutation->prelabel >= $RNAend or $strand != 1 and $self->mutation->prelabel <= $RNAend |
|
1028
|
0 |
0 |
4 |
$strand == 1 and $self->mutation->prelabel < $before or $strand == -1 and $self->mutation->prelabel > $before |
|
1053
|
0 |
0 |
14 |
$strand == 1 and $self->mutation->prelabel >= $before and $self->mutation->postlabel <= $after or $strand == -1 and $self->mutation->prelabel <= $before and $self->mutation->postlabel >= $after |
|
|
2 |
2 |
10 |
$strand == 1 and $exons[$i]->start < $self->mutation->prelabel and $exons[$i]->end > $self->mutation->prelabel or $strand == 1 and $exons[$i]->start < $self->mutation->postlabel and $exons[$i]->end > $self->mutation->postlabel |
|
|
2 |
0 |
10 |
$strand == 1 and $exons[$i]->start < $self->mutation->prelabel and $exons[$i]->end > $self->mutation->prelabel or $strand == 1 and $exons[$i]->start < $self->mutation->postlabel and $exons[$i]->end > $self->mutation->postlabel or $strand == -1 and $exons[$i]->start > $self->mutation->prelabel and $exons[$i]->end < $self->mutation->prelabel |
|
|
0 |
0 |
10 |
$strand == 1 and $exons[$i]->start < $self->mutation->prelabel and $exons[$i]->end > $self->mutation->prelabel or $strand == 1 and $exons[$i]->start < $self->mutation->postlabel and $exons[$i]->end > $self->mutation->postlabel or $strand == -1 and $exons[$i]->start > $self->mutation->prelabel and $exons[$i]->end < $self->mutation->prelabel or $strand == -1 and $exons[$i]->start > $self->mutation->postlabel and $exons[$i]->end < $self->mutation->postlabel |