| line |
true |
false |
branch |
|
244
|
0 |
0 |
unless my $dbh = 'DBI'->connect($dsn, $username, $password)
|
|
269
|
0 |
0 |
unless my $sth = $self->dbh->prepare($cvterm_query)
|
|
272
|
0 |
0 |
unless $sth->execute($self->sofa_id)
|
|
290
|
0 |
0 |
if (defined $name2term{$$hashref{'name'}}) { }
|
|
292
|
0 |
0 |
if (ref $name2term{$$hashref{'name'}} ne 'ARRAY')
|
|
312
|
0 |
0 |
$arg{-'recursivMapping'} ? :
|
|
314
|
0 |
0 |
$arg{-'inferCDS'} ? :
|
|
315
|
0 |
0 |
$arg{-'allow_obsolete'} ? :
|
|
317
|
0 |
0 |
if (exists $arg{-'enable_seqscan'} and not $arg{-'enable_seqscan'})
|
|
321
|
0 |
0 |
defined $arg{-'srcfeatureslice'} ? :
|
|
322
|
0 |
0 |
$arg{-'do2Level'} ? :
|
|
324
|
0 |
0 |
if ($arg{-'organism'})
|
|
402
|
0 |
0 |
unless my($coverage, $tag) = $self->coverage_array(-'seqid', $seq_name, -'start', $start, -'end', $end, -'type', $types, -'bins', $bins)
|
|
420
|
0 |
0 |
$iterator ? :
|
|
474
|
0 |
0 |
unless my $segment = $self->segment(-'name', $seq_name)
|
|
482
|
0 |
0 |
unless $seqid
|
|
512
|
0 |
0 |
if (ref $types eq 'ARRAY') { }
|
|
531
|
0 |
0 |
unless $sth->execute(@args)
|
|
539
|
0 |
0 |
unless %bins
|
|
553
|
0 |
0 |
if $bin > $last_bin
|
|
561
|
0 |
0 |
wantarray ? :
|
|
570
|
0 |
0 |
if (ref $type and $type->isa('Bio::DB::GFF::Typename')) { }
|
|
577
|
0 |
0 |
if (defined $source_tag) { }
|
|
578
|
0 |
0 |
if (length $primary_tag) { }
|
|
618
|
0 |
0 |
if defined @_
|
|
619
|
0 |
0 |
if defined $tripal
|
|
652
|
0 |
0 |
if defined @_
|
|
653
|
0 |
0 |
if defined $fulltext
|
|
683
|
0 |
0 |
if defined @_
|
|
684
|
0 |
0 |
if defined $refclass
|
|
703
|
0 |
0 |
if defined $flag
|
|
705
|
0 |
0 |
if defined $$self{'use_all_feature_names'}
|
|
713
|
0 |
0 |
unless $exists->execute
|
|
716
|
0 |
0 |
if ($kind and $kind eq 'r' || $kind eq 'v') { }
|
|
|
0 |
0 |
elsif ($kind) { }
|
|
748
|
0 |
0 |
unless ($organism_name)
|
|
755
|
0 |
0 |
if ($organism_name =~ /(\S+?)\s+(.+)/)
|
|
760
|
0 |
0 |
unless $species_query->execute($genus, $species)
|
|
763
|
0 |
0 |
if ($species_query->rows == 1)
|
|
766
|
0 |
0 |
if ($organism_id)
|
|
776
|
0 |
0 |
unless $org_query->execute($organism_name)
|
|
779
|
0 |
0 |
if ($org_query->rows > 1) { }
|
|
|
0 |
0 |
elsif ($org_query->rows == 0) { }
|
|
789
|
0 |
0 |
if ($organism_id)
|
|
798
|
0 |
0 |
unless $abbrev_query->execute($organism_name)
|
|
800
|
0 |
0 |
if ($abbrev_query->rows > 1) { }
|
|
|
0 |
0 |
elsif ($abbrev_query->rows == 0) { }
|
|
809
|
0 |
0 |
if ($organism_id)
|
|
839
|
0 |
0 |
if defined $flag
|
|
860
|
0 |
0 |
if defined @_
|
|
861
|
0 |
0 |
if defined $allow_obsolete
|
|
878
|
0 |
0 |
unless @_
|
|
886
|
0 |
0 |
unless $sth->execute
|
|
892
|
0 |
0 |
if $sofa_id
|
|
900
|
0 |
0 |
unless $sth->execute
|
|
906
|
0 |
0 |
if $sofa_id
|
|
926
|
0 |
0 |
if @_
|
|
944
|
0 |
0 |
if @_
|
|
960
|
0 |
0 |
if @_
|
|
979
|
0 |
0 |
if @_
|
|
980
|
0 |
0 |
if defined $$self{'dbh'}
|
|
987
|
0 |
0 |
unless my $dbh = 'DBI'->connect($dsn, $username, $password)
|
|
991
|
0 |
0 |
if (exists $$self{-'enable_seqscan'} and not $$self{-'enable_seqscan'})
|
|
1018
|
0 |
0 |
if (ref $arg eq 'HASH') { }
|
|
|
0 |
0 |
elsif ($arg) { }
|
|
1049
|
0 |
0 |
if (ref $cvnames eq 'HASH')
|
|
1050
|
0 |
0 |
if (ref $arg eq 'HASH') { }
|
|
|
0 |
0 |
elsif ($arg) { }
|
|
1287
|
0 |
0 |
if (@args == 1)
|
|
1334
|
0 |
0 |
if (@args == 1)
|
|
1365
|
0 |
0 |
if ($name =~ /^id:(\d+)/)
|
|
1371
|
0 |
0 |
if (scalar @temp_array == 2)
|
|
1372
|
0 |
0 |
if ($self->source2dbxref($temp_array[0]) > 0)
|
|
1382
|
0 |
0 |
if $self->fulltext
|
|
1386
|
0 |
0 |
if ($name =~ /\*/)
|
|
1405
|
0 |
0 |
if ($class)
|
|
1407
|
0 |
0 |
$class eq 'CDS' && $self->inferCDS ? :
|
|
1410
|
0 |
0 |
unless $type
|
|
1412
|
0 |
0 |
if (ref $type eq 'ARRAY') { }
|
|
|
0 |
0 |
elsif (ref $type eq 'HASH') { }
|
|
1422
|
0 |
0 |
if ($self->organism_id and $operation eq 'by_alias') { }
|
|
|
0 |
0 |
elsif ($self->organism_id) { }
|
|
1423
|
0 |
0 |
$self->use_all_feature_names ? :
|
|
1431
|
0 |
0 |
if ($operation eq 'by_alias') { }
|
|
1432
|
0 |
0 |
if ($self->use_all_feature_names) { }
|
|
1434
|
0 |
0 |
$from_part ? :
|
|
1441
|
0 |
0 |
if ($self->fulltext) { }
|
|
|
0 |
0 |
elsif ($wildcard) { }
|
|
1451
|
0 |
0 |
$where_part ? :
|
|
1458
|
0 |
0 |
$from_part ? :
|
|
1464
|
0 |
0 |
if ($self->fulltext) { }
|
|
|
0 |
0 |
elsif ($wildcard) { }
|
|
1478
|
0 |
0 |
$where_part ? :
|
|
1490
|
0 |
0 |
if ($self->fulltext) { }
|
|
|
0 |
0 |
elsif ($wildcard) { }
|
|
1501
|
0 |
0 |
$where_part ? :
|
|
1517
|
0 |
0 |
if ($wildcard)
|
|
1527
|
0 |
0 |
unless $sth->execute(lc $name)
|
|
1573
|
0 |
0 |
unless $isth->execute($$feature_id_ref{'feature_id'}, $self->gff_source_db_id)
|
|
1576
|
0 |
0 |
if ($isth->rows == 0)
|
|
1583
|
0 |
0 |
unless $is_srcfeature_query->execute($$feature_id_ref{'feature_id'})
|
|
1589
|
0 |
0 |
if ($is_srcfeature_query->rows == 1) { }
|
|
1594
|
0 |
0 |
if $base_start
|
|
1595
|
0 |
0 |
if $stop
|
|
1615
|
0 |
0 |
if $$hashref{'is_obsolete'} and not $self->allow_obsolete
|
|
1617
|
0 |
0 |
if ($self->refclass and $$hashref{'type_id'} == $self->refclass)
|
|
1630
|
0 |
0 |
if ($$hashref{'srcfeature_id'} != $old_srcfeature_id)
|
|
1631
|
0 |
0 |
unless $jsth->execute($$hashref{'srcfeature_id'})
|
|
1642
|
0 |
0 |
if ($$self{'recursivMapping'}) { }
|
|
1660
|
0 |
0 |
if ($recurs_sth->rows != 0) { }
|
|
1692
|
0 |
0 |
if ($class and $class eq 'CDS' and $self->inferCDS) { }
|
|
1700
|
0 |
0 |
ref $self->term2name('derives_from') eq 'ARRAY' ? :
|
|
1713
|
0 |
0 |
ref $self->term2name('part_of') eq 'ARRAY' ? :
|
|
1736
|
0 |
0 |
if $$exonref{'fmax'} < $poly_min
|
|
1737
|
0 |
0 |
if $$exonref{'fmin'} > $poly_max
|
|
1738
|
0 |
0 |
if $$exonref{'is_obsolete'} and not $self->allow_obsolete
|
|
1741
|
0 |
0 |
if ($$exonref{'fmin'} <= $poly_min and $$exonref{'fmax'} >= $poly_max) { }
|
|
1749
|
0 |
0 |
if ($$exonref{'fmax'} >= $poly_max and $$exonref{'fmin'} <= $poly_min) { }
|
|
1788
|
0 |
0 |
if $self->refclass == $$hashref{'type_id'}
|
|
1790
|
0 |
0 |
$srcf ? :
|
|
|
0 |
0 |
$srcf ? :
|
|
1855
|
0 |
0 |
unless 0 == index($name, '%')
|
|
1856
|
0 |
0 |
unless 0 == index(reverse($name), '%')
|
|
1864
|
0 |
0 |
if ($class)
|
|
1866
|
0 |
0 |
unless $type
|
|
1872
|
0 |
0 |
if $self->organism_id
|
|
1883
|
0 |
0 |
if ($self->fulltext) { }
|
|
1918
|
0 |
0 |
if $$self{'srcfeature_id'}{$id}
|
|
1940
|
0 |
0 |
if $$self{'gff_source_db_id'}
|
|
1967
|
0 |
0 |
if $$self{'source_dbxref'}{$source}
|
|
1996
|
0 |
0 |
unless defined $self->gff_source_db_id
|
|
2000
|
0 |
0 |
if (defined $$self{'dbxref_source'} and $dbxref and defined $$self{'dbxref_source'}{$dbxref})
|
|
2010
|
0 |
0 |
if ($sth->rows < 1)
|
|
2024
|
0 |
0 |
if (defined $$self{'dbxref_source'} and $dbxref and defined $$self{'dbxref_source'}{$dbxref}) { }
|
|
2028
|
0 |
0 |
if $dbxref
|
|
2049
|
0 |
0 |
if defined $$self{'source_dbxref_list'}
|
|
2168
|
0 |
0 |
if $self->organism_id
|
|
2171
|
0 |
0 |
unless $sth->execute($id)
|
|
2175
|
0 |
0 |
if (defined $tag) { }
|
|
2188
|
0 |
0 |
if scalar @array == 0
|
|
2192
|
0 |
0 |
if (not defined $tag or $tag eq 'translation')
|
|
2199
|
0 |
0 |
if ($self->name2term('polypeptide') and $type_id and $type_id == $self->name2term('polypeptide') or $self->name2term('protein') and $type_id and $type_id == $self->name2term('protein'))
|
|
2210
|
0 |
0 |
if ($aa)
|
|
2213
|
0 |
0 |
if ($tag) { }
|
|
2226
|
0 |
0 |
if wantarray
|
|
2228
|
0 |
0 |
if $tag
|
|
2260
|
0 |
0 |
unless ($$self{'reference_class'} or @_)
|
|
2264
|
0 |
0 |
if (@_)
|
|
2266
|
0 |
0 |
unless ($checkref)
|
|
2271
|
0 |
0 |
if @_
|
|
2279
|
0 |
0 |
if (@_)
|
|
2284
|
0 |
0 |
unless $sth->execute($type_id)
|
|
2312
|
0 |
0 |
if $$self{'chado_reference_class'}
|
|
2318
|
0 |
0 |
unless $sth->execute('MapReferenceType')
|
|
2323
|
0 |
0 |
if ($ref_cvtermid)
|
|
2326
|
0 |
0 |
unless $sth->execute($ref_cvtermid)
|
|
2328
|
0 |
0 |
if $$data{'name'}
|
|
2353
|
0 |
0 |
if @_
|
|
2422
|
0 |
0 |
unless @$self
|