| line |
true |
false |
branch |
|
312
|
0 |
0 |
unless (defined $self->sequence_factory) |
|
319
|
0 |
0 |
if defined $args{'-suppress_residues'} |
|
322
|
0 |
0 |
if defined $args{'-allow_residues'} |
|
420
|
0 |
0 |
unless (defined $seq) |
|
424
|
0 |
0 |
unless (ref $seq and $seq->isa('Bio::Seq::RichSeqI')) |
|
430
|
0 |
0 |
unless ($srcfeature) |
|
431
|
0 |
0 |
if ($seq->can('seq_id')) |
|
432
|
0 |
0 |
if $seq->seq_id ne $seq->display_name |
|
437
|
0 |
0 |
if (defined $srcfeature) |
|
439
|
0 |
0 |
if ($srcfeature =~ /[a-zA-Z]/) { } |
|
447
|
0 |
0 |
if (not defined $srcfeattype) { } |
|
452
|
0 |
0 |
if ($srcfeattype =~ /\S+/) { } |
|
466
|
0 |
0 |
if $seq->can('display_id') |
|
467
|
0 |
0 |
if $seq->can('display_name') |
|
500
|
0 |
0 |
if (not $name and $seq->can('attributes')) |
|
504
|
0 |
0 |
if ($seq->can('accession_number') and defined $seq->accession_number and $seq->accession_number ne 'unknown') { } |
|
|
0 |
0 |
elsif ($seq->can('accession') and defined $seq->accession and $seq->accession ne 'unknown') { } |
|
|
0 |
0 |
elsif ($seq->can('attributes')) { } |
|
514
|
0 |
0 |
if ($len == 0) |
|
519
|
0 |
0 |
unless ($seq->can('molecule') and defined($gb_type = $seq->molecule)) |
|
520
|
0 |
0 |
$seq->can('alphabet') ? : |
|
522
|
0 |
0 |
if $ftype eq 'dna' |
|
523
|
0 |
0 |
if $ftype eq 'rna' |
|
525
|
0 |
0 |
if (length $seq_so_type > 0) { } |
|
526
|
0 |
0 |
if (defined $seq_so_type) { } |
|
|
0 |
0 |
elsif ($seq->type) { } |
|
530
|
0 |
0 |
$seq->type =~ /(.*):/ ? : |
|
544
|
0 |
0 |
if ($species) { } |
|
549
|
0 |
0 |
if (not defined $spec) { } |
|
557
|
0 |
0 |
if (not $self->suppress_residues or $self->suppress_residues and $self->allow_residues eq $ftype) { } |
|
559
|
0 |
0 |
$seq->seq->isa('Bio::PrimarySeq') ? : |
|
569
|
0 |
0 |
if ($ftype eq 'gene' or $ftype eq 'mRNA' or $ftype eq 'exon' or $ftype eq 'protein' or $ftype eq 'polypeptide') |
|
571
|
0 |
0 |
unless defined $isanal |
|
584
|
0 |
0 |
if (defined $srcfeature) |
|
590
|
0 |
0 |
if ($seq->can('phase')) |
|
594
|
0 |
0 |
if ($seq->can('strand')) |
|
611
|
0 |
0 |
unless (defined $srcfeature) |
|
617
|
0 |
0 |
unless (defined $datasource) |
|
621
|
0 |
0 |
if ($datasource =~ /GenBank/i) |
|
623
|
0 |
0 |
if ($seq->can('is_circular') and $seq->is_circular) { } |
|
659
|
0 |
0 |
if ($seq->can('division') and defined $seq->division) |
|
680
|
0 |
0 |
if ($seq->can('desc') and defined $seq->desc) |
|
697
|
0 |
0 |
if ($seq->can('keywords')) |
|
700
|
0 |
0 |
if (defined $temp and $temp ne '.' and $temp ne '') |
|
716
|
0 |
0 |
if ($seq->can('annotation')) |
|
737
|
0 |
0 |
if ($seq->can('attributes')) |
|
740
|
0 |
0 |
if $key eq 'parent_id' |
|
741
|
0 |
0 |
if $key eq 'load_id' |
|
743
|
0 |
0 |
if ($key eq 'Alias') { } |
|
|
0 |
0 |
elsif ($key eq 'Ontology_term') { } |
|
|
0 |
0 |
elsif ($key eq 'dbxref' or $key eq 'Dbxref') { } |
|
|
0 |
0 |
elsif ($key =~ /^[a-z]/) { } |
|
764
|
0 |
0 |
if ($seq->can('source')) |
|
769
|
0 |
0 |
if ($seq->can('accession_number') and defined $seq->accession_number and $seq->accession_number ne 'unknown') |
|
780
|
0 |
0 |
if ($seq->isa('Bio::Seq::RichSeqI') and defined $seq->get_secondary_accessions) |
|
794
|
0 |
0 |
if ($seq->isa('Bio::Seq::RichSeqI') and defined $seq->pid) |
|
808
|
0 |
0 |
if (defined $ann) |
|
818
|
0 |
0 |
if (index($location, ' ==') >= 0) |
|
830
|
0 |
0 |
if ($location =~ /Unpublished/) { } |
|
|
0 |
0 |
elsif ($location =~ /Submitted/) { } |
|
|
0 |
0 |
elsif ($location =~ /\D+\s\d+\s\((\d+|\d+-\d+)\),\s(\d+-\d+|\d+--\d+)\s\(\d\d\d\d\)$/) { } |
|
852
|
0 |
0 |
if (defined $pyear) |
|
937
|
0 |
0 |
if (defined $autref) { } |
|
942
|
0 |
0 |
if ($pubtype eq 'submitted') |
|
944
|
0 |
0 |
if (defined $autref) |
|
953
|
0 |
0 |
if (defined $ref->comment or defined $refhash->{'comment'}) |
|
964
|
0 |
0 |
if (defined $fbrf) |
|
967
|
0 |
0 |
if (defined($temp = $ref->medline)) |
|
972
|
0 |
0 |
if (defined($temp = $ref->pubmed)) |
|
981
|
0 |
0 |
if (not defined $pubhash{'uniquename'} or $pubhash{'uniquename'} eq '') |
|
982
|
0 |
0 |
if (defined $fbrf) |
|
992
|
0 |
0 |
if ($ref->start == 1 and $ref->end == $len or not defined $ref->start || defined $ref->end) { } |
|
1026
|
0 |
0 |
if (defined $srcfeature) |
|
1039
|
0 |
0 |
if ($gb_type eq 'gene' || $gb_type eq 'DNA' and not $nounflatten) |
|
1050
|
0 |
0 |
if ($datasource =~ /GenBank/i) { } |
|
|
0 |
0 |
elsif ($datasource =~ /GFF/i) { } |
|
1066
|
0 |
0 |
if ($prim_tag eq 'source') |
|
1069
|
0 |
0 |
if ($tag eq 'db_xref' or $tag eq 'Dbxref' or $tag eq 'dbxref') { } |
|
|
0 |
0 |
elsif ($tag eq 'Ontology_term') { } |
|
|
0 |
0 |
elsif ($tag ne 'gene') { } |
|
1104
|
0 |
0 |
if ($feat->can('source')) |
|
1120
|
0 |
0 |
if ($feat->can('phase')) |
|
1147
|
0 |
0 |
if (not $ftype eq 'mRNA' && $feat->primary_tag eq 'gene') { } |
|
1155
|
0 |
0 |
if (@top_dbxrefs) |
|
1159
|
0 |
0 |
if (@top_featureprops) |
|
1163
|
0 |
0 |
if (@top_featrels) |
|
1167
|
0 |
0 |
if (@top_featurecvterms) |
|
1171
|
0 |
0 |
if ($ftype eq 'mRNA' and %finaldatahash) { } |
|
1201
|
0 |
0 |
if @_ |
|
1203
|
0 |
0 |
unless (defined $self->{'writer'}) |
|
1214
|
0 |
0 |
if ($ult eq 'pub' and $mh{'type_id'}{'name'} eq 'journal') { } |
|
|
0 |
0 |
elsif ($ult eq 'pub' and not defined $mh{'uniquename'}) { } |
|
|
0 |
0 |
elsif ($ult eq 'cvterm' or $ult eq 'cv') { } |
|
|
0 |
0 |
elsif ($isMatch) { } |
|
1245
|
0 |
0 |
if (index($chadotables, $xx) < 0 and index($chadotables, $yy) < 0) |
|
1247
|
0 |
0 |
if ($isMatch) { } |
|
1255
|
0 |
0 |
if (defined $fkey{$x}) { } |
|
1276
|
0 |
0 |
if (index($chadotables, $xx) > 0 or index($chadotables, $yy) > 0) |
|
1281
|
0 |
0 |
if (ref($ntref) =~ /HASH/) { } |
|
|
0 |
0 |
elsif (ref($ntref) =~ /ARRAY/) { } |
|
1308
|
0 |
0 |
if ($acc =~ /^NM_\d{6}/ or $acc =~ /^NP_\d{6}/ or $acc =~ /^NT_\d{6}/ or $acc =~ /^NC_\d{6}/) { } |
|
|
0 |
0 |
elsif ($acc =~ /^XM_\d{6}/ or $acc =~ /^XP_\d{6}/ or $acc =~ /^XR_\d{6}/) { } |
|
|
0 |
0 |
elsif ($acc =~ /^[a-zA-Z]{1,2}\d{5,6}/) { } |
|
|
0 |
0 |
elsif ($seq->molecule eq 'protein' and $acc =~ /^[a-zA-z]\d{5}/) { } |
|
|
0 |
0 |
elsif ($seq->molecule eq 'protein' and $acc =~ /^\d{6,7}[a-zA-Z]/) { } |
|
|
0 |
0 |
elsif ($acc =~ /\d+/ and not $acc =~ /[a-zA-Z]/) { } |
|
|
0 |
0 |
elsif ($acc =~ /^CG\d+/ or $acc =~ /^FB[a-z][a-z]\d+/) { } |
|
1343
|
0 |
0 |
if ($feat->has_tag('symbol')) { } |
|
|
0 |
0 |
elsif ($feat->has_tag('label')) { } |
|
1353
|
0 |
0 |
if ($feat->has_tag('Name')) |
|
1358
|
0 |
0 |
if (defined $feattype_args2so{$prim_tag}) { } |
|
1364
|
0 |
0 |
if ($prim_tag eq 'mutation') |
|
1365
|
0 |
0 |
if ($feat->start == $feat->end) { } |
|
1374
|
0 |
0 |
if ($sftype eq 'gene' or $sftype eq 'mRNA' or $sftype eq 'exon' or $sftype eq 'protein' or $sftype eq 'polypeptide') |
|
1405
|
0 |
0 |
if ($feat->can('phase')) |
|
1410
|
0 |
0 |
if ($seqtype eq 'mRNA' and $sftype eq 'gene') { } |
|
1412
|
0 |
0 |
if ($feat->location->isa('Bio::Location::FuzzyLocationI')) |
|
1413
|
0 |
0 |
if ($feat->location->start_pos_type ne 'EXACT') |
|
1416
|
0 |
0 |
if ($feat->location->end_pos_type ne 'EXACT') |
|
1442
|
0 |
0 |
if ($tag eq 'db_xref' or $tag eq 'dbxref' or $tag eq 'Dbxref') { } |
|
|
0 |
0 |
elsif ($tag eq 'Alias') { } |
|
|
0 |
0 |
elsif ($tag eq 'Ontology_term') { } |
|
|
0 |
0 |
elsif ($tag ne 'gene' and $tag ne 'symbol' and $tag ne 'Name' and $tag ne 'Parent') { } |
|
1464
|
0 |
0 |
if $tag eq 'parent_id' |
|
1465
|
0 |
0 |
if $tag eq 'load_id' |
|
1477
|
0 |
0 |
if ($feat->can('source')) |
|
1481
|
0 |
0 |
if (@sub_featureprops) |
|
1484
|
0 |
0 |
if (@sfdbxrefs) |
|
1487
|
0 |
0 |
if (@sub_featuresyns) |
|
1490
|
0 |
0 |
if (@sub_featurecvterms) |
|
1495
|
0 |
0 |
if ($feat->has_tag('locus_tag')) { } |
|
|
0 |
0 |
elsif ($feat->has_tag('gene')) { } |
|
1504
|
0 |
0 |
if (defined $rref) |
|
1509
|
0 |
0 |
if (@ssfeatrel) |
|
1523
|
0 |
0 |
if ($seqtype eq 'mRNA' and $sftype eq 'gene') { } |
|
1541
|
0 |
0 |
if ($feat->has_tag('locus_tag')) { } |
|
|
0 |
0 |
elsif ($feat->has_tag('gene')) { } |
|
1576
|
0 |
0 |
if ($temp ne '.') { } |
|
1577
|
0 |
0 |
if (index($temp, ' and ') > 0) { } |
|
1593
|
0 |
0 |
if (index($a, ',') > 0) { } |
|
|
0 |
0 |
elsif (index($a, ' ') > 0) { } |
|
1621
|
0 |
0 |
if (not $citation =~ /Submitted/) { } |
|
1640
|
0 |
0 |
if (not $citation =~ /Submitted/) { } |
|
1646
|
0 |
0 |
if (defined $a) { } |
|
1673
|
0 |
0 |
if @_ |
|
1674
|
0 |
0 |
if defined $suppress_residues |
|
1698
|
0 |
0 |
if @_ |
|
1699
|
0 |
0 |
if defined $allow_residues |
|
1741
|
0 |
0 |
if ($sftype eq 'protein' or $sftype eq 'polypeptide') { } |
|
1903
|
0 |
0 |
if ($term =~ /(\S+):(\S+)/) |
|
1941
|
0 |
0 |
if ($term =~ /(\S+):(\S+)/) { } |
|
1945
|
0 |
0 |
if ($acc =~ /(\S+)\.(\S+)/) |
|
1982
|
0 |
0 |
unless $source |