| line |
!l |
l&&!r |
l&&r |
condition |
|
424
|
0 |
0 |
0 |
ref $seq and $seq->isa('Bio::Seq::RichSeqI') |
|
500
|
0 |
0 |
0 |
not $name and $seq->can('attributes') |
|
504
|
0 |
0 |
0 |
$seq->can('accession_number') and defined $seq->accession_number |
|
|
0 |
0 |
0 |
$seq->can('accession_number') and defined $seq->accession_number and $seq->accession_number ne 'unknown' |
|
|
0 |
0 |
0 |
$seq->can('accession') and defined $seq->accession |
|
|
0 |
0 |
0 |
$seq->can('accession') and defined $seq->accession and $seq->accession ne 'unknown' |
|
519
|
0 |
0 |
0 |
$seq->can('molecule') and defined($gb_type = $seq->molecule) |
|
557
|
0 |
0 |
0 |
$self->suppress_residues and $self->allow_residues eq $ftype |
|
623
|
0 |
0 |
0 |
$seq->can('is_circular') and $seq->is_circular |
|
659
|
0 |
0 |
0 |
$seq->can('division') and defined $seq->division |
|
680
|
0 |
0 |
0 |
$seq->can('desc') and defined $seq->desc |
|
700
|
0 |
0 |
0 |
defined $temp and $temp ne '.' |
|
|
0 |
0 |
0 |
defined $temp and $temp ne '.' and $temp ne '' |
|
769
|
0 |
0 |
0 |
$seq->can('accession_number') and defined $seq->accession_number |
|
|
0 |
0 |
0 |
$seq->can('accession_number') and defined $seq->accession_number and $seq->accession_number ne 'unknown' |
|
780
|
0 |
0 |
0 |
$seq->isa('Bio::Seq::RichSeqI') and defined $seq->get_secondary_accessions |
|
794
|
0 |
0 |
0 |
$seq->isa('Bio::Seq::RichSeqI') and defined $seq->pid |
|
992
|
0 |
0 |
0 |
$ref->start == 1 and $ref->end == $len |
|
1039
|
0 |
0 |
0 |
$gb_type eq 'gene' || $gb_type eq 'DNA' and not $nounflatten |
|
1147
|
0 |
0 |
0 |
$ftype eq 'mRNA' && $feat->primary_tag eq 'gene' |
|
1171
|
0 |
0 |
0 |
$ftype eq 'mRNA' and %finaldatahash |
|
1214
|
0 |
0 |
0 |
$ult eq 'pub' and $mh{'type_id'}{'name'} eq 'journal' |
|
|
0 |
0 |
0 |
$ult eq 'pub' and not defined $mh{'uniquename'} |
|
1245
|
0 |
0 |
0 |
index($chadotables, $xx) < 0 and index($chadotables, $yy) < 0 |
|
1308
|
0 |
0 |
0 |
$seq->molecule eq 'protein' and $acc =~ /^[a-zA-z]\d{5}/ |
|
|
0 |
0 |
0 |
$seq->molecule eq 'protein' and $acc =~ /^\d{6,7}[a-zA-Z]/ |
|
|
0 |
0 |
0 |
$acc =~ /\d+/ and not $acc =~ /[a-zA-Z]/ |
|
1410
|
0 |
0 |
0 |
$seqtype eq 'mRNA' and $sftype eq 'gene' |
|
1442
|
0 |
0 |
0 |
$tag ne 'gene' and $tag ne 'symbol' |
|
|
0 |
0 |
0 |
$tag ne 'gene' and $tag ne 'symbol' and $tag ne 'Name' |
|
|
0 |
0 |
0 |
$tag ne 'gene' and $tag ne 'symbol' and $tag ne 'Name' and $tag ne 'Parent' |
|
1523
|
0 |
0 |
0 |
$seqtype eq 'mRNA' and $sftype eq 'gene' |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
557
|
0 |
0 |
0 |
not $self->suppress_residues or $self->suppress_residues and $self->allow_residues eq $ftype |
|
569
|
0 |
0 |
0 |
$ftype eq 'gene' or $ftype eq 'mRNA' |
|
|
0 |
0 |
0 |
$ftype eq 'gene' or $ftype eq 'mRNA' or $ftype eq 'exon' |
|
|
0 |
0 |
0 |
$ftype eq 'gene' or $ftype eq 'mRNA' or $ftype eq 'exon' or $ftype eq 'protein' |
|
|
0 |
0 |
0 |
$ftype eq 'gene' or $ftype eq 'mRNA' or $ftype eq 'exon' or $ftype eq 'protein' or $ftype eq 'polypeptide' |
|
743
|
0 |
0 |
0 |
$key eq 'dbxref' or $key eq 'Dbxref' |
|
814
|
0 |
0 |
0 |
$ref->location || $refhash->{'location'} |
|
833
|
0 |
0 |
0 |
$ref->title || $refhash->{'title'} |
|
844
|
0 |
0 |
0 |
$ref->title || $refhash->{'title'} |
|
890
|
0 |
0 |
0 |
$ref->title || $refhash->{'title'} |
|
926
|
0 |
0 |
0 |
$ref->title || $refhash->{'title'} |
|
953
|
0 |
0 |
0 |
defined $ref->comment or defined $refhash->{'comment'} |
|
954
|
0 |
0 |
0 |
$ref->comment || $refhash->{'comment'} |
|
981
|
0 |
0 |
0 |
not defined $pubhash{'uniquename'} or $pubhash{'uniquename'} eq '' |
|
992
|
0 |
0 |
0 |
defined $ref->start || defined $ref->end |
|
|
0 |
0 |
0 |
$ref->start == 1 and $ref->end == $len or not defined $ref->start || defined $ref->end |
|
1039
|
0 |
0 |
0 |
$gb_type eq 'gene' || $gb_type eq 'DNA' |
|
1069
|
0 |
0 |
0 |
$tag eq 'db_xref' or $tag eq 'Dbxref' |
|
|
0 |
0 |
0 |
$tag eq 'db_xref' or $tag eq 'Dbxref' or $tag eq 'dbxref' |
|
1214
|
0 |
0 |
0 |
$ult eq 'cvterm' or $ult eq 'cv' |
|
1276
|
0 |
0 |
0 |
index($chadotables, $xx) > 0 or index($chadotables, $yy) > 0 |
|
1308
|
0 |
0 |
0 |
$acc =~ /^NM_\d{6}/ or $acc =~ /^NP_\d{6}/ |
|
|
0 |
0 |
0 |
$acc =~ /^NM_\d{6}/ or $acc =~ /^NP_\d{6}/ or $acc =~ /^NT_\d{6}/ |
|
|
0 |
0 |
0 |
$acc =~ /^NM_\d{6}/ or $acc =~ /^NP_\d{6}/ or $acc =~ /^NT_\d{6}/ or $acc =~ /^NC_\d{6}/ |
|
|
0 |
0 |
0 |
$acc =~ /^XM_\d{6}/ or $acc =~ /^XP_\d{6}/ |
|
|
0 |
0 |
0 |
$acc =~ /^XM_\d{6}/ or $acc =~ /^XP_\d{6}/ or $acc =~ /^XR_\d{6}/ |
|
|
0 |
0 |
0 |
$acc =~ /^CG\d+/ or $acc =~ /^FB[a-z][a-z]\d+/ |
|
1374
|
0 |
0 |
0 |
$sftype eq 'gene' or $sftype eq 'mRNA' |
|
|
0 |
0 |
0 |
$sftype eq 'gene' or $sftype eq 'mRNA' or $sftype eq 'exon' |
|
|
0 |
0 |
0 |
$sftype eq 'gene' or $sftype eq 'mRNA' or $sftype eq 'exon' or $sftype eq 'protein' |
|
|
0 |
0 |
0 |
$sftype eq 'gene' or $sftype eq 'mRNA' or $sftype eq 'exon' or $sftype eq 'protein' or $sftype eq 'polypeptide' |
|
1442
|
0 |
0 |
0 |
$tag eq 'db_xref' or $tag eq 'dbxref' |
|
|
0 |
0 |
0 |
$tag eq 'db_xref' or $tag eq 'dbxref' or $tag eq 'Dbxref' |
|
1741
|
0 |
0 |
0 |
$sftype eq 'protein' or $sftype eq 'polypeptide' |