| line |
!l |
l&&!r |
l&&r |
condition |
|
375
|
1 |
0 |
0 |
exists $args{-'map_coords'} and ref $args{-'map_coords'} eq 'CODE'
|
|
433
|
0 |
0 |
0 |
$has_libs && $args{-'file'}
|
|
436
|
0 |
0 |
0 |
-e $cachefile and (stat _)[9] >= $self->file_mtime($args{-'file'})
|
|
590
|
0 |
0 |
0 |
$panel and UNIVERSAL::isa($panel, 'Bio::Graphics::Panel')
|
|
617
|
0 |
0 |
0 |
$options and ref $options eq 'HASH'
|
|
640
|
0 |
0 |
0 |
defined $selector and not &$selector($self, $label)
|
|
686
|
0 |
1 |
0 |
$$self{'stat'} and @{$$self{'stat'};}
|
|
701
|
0 |
0 |
0 |
$feat->start <= $max && $feat->end >= $min
|
|
846
|
0 |
0 |
3 |
$line =~ /^[\w:\s]+=/ and $$self{'current_config'}
|
|
848
|
0 |
0 |
0 |
$line =~ /^\s+(.+)/ and $$self{'current_tag'}
|
|
863
|
4 |
0 |
0 |
/^\s+(.+)/ and $$self{'current_tag'}
|
|
923
|
0 |
0 |
0 |
/^\s+/ and length $tokens[0]
|
|
925
|
0 |
0 |
0 |
@tokens >= 8 and $tokens[3] =~ /^-?\d+$/
|
|
|
0 |
0 |
0 |
@tokens >= 8 and $tokens[3] =~ /^-?\d+$/ and $tokens[4] =~ /^-?\d+$/
|
|
1143
|
0 |
0 |
0 |
@_ == 2 and defined $_[0]
|
|
|
0 |
0 |
0 |
@_ == 2 and defined $_[0] and exists $$config{$_[0]}
|
|
1225
|
0 |
0 |
0 |
$setting =~ /^sub\s*(\(\$\$\))*\s*\{/ and my $context = $$self{'safe_context'}
|
|
1285
|
0 |
0 |
0 |
$$self{'safe'} and not $d
|
|
1306
|
0 |
0 |
0 |
$safe and not $$self{'safe_content'}
|
|
1456
|
0 |
0 |
0 |
$Bio::Root::Version::VERSION >= 1.0069 and $Bio::Root::Version::VERSION <= 1.006901
|
|
1515
|
0 |
0 |
0 |
$_[0] && $_[0] =~ /^-/
|
|
1518
|
0 |
0 |
0 |
$types and not ref $types
|
|
1519
|
0 |
0 |
0 |
$types && @$types
|
|
1704
|
0 |
0 |
0 |
defined $$self{'min'} and defined $$self{'max'}
|
|
1817
|
0 |
0 |
0 |
defined $start and defined $stop
|
|
1823
|
0 |
0 |
0 |
$options and ref $options eq 'HASH'
|
|
1904
|
0 |
0 |
0 |
ref $linkrule and ref $linkrule eq 'CODE'
|
|
1969
|
0 |
0 |
0 |
$feature->can('target') and my $target = $feature->target
|
| line |
l |
!l |
condition |
|
620
|
0 |
0 |
$options ||= 0
|
|
637
|
0 |
0 |
$self->setting($label, 'feature') || ''
|
|
865
|
0 |
0 |
$$self{'current_config'} ||= 'general'
|
|
883
|
3 |
0 |
$$self{'current_config'} ||= 'general'
|
|
1806
|
0 |
0 |
$self->setting('general', 'pixels') || $self->setting('general', 'width') || 600
|
|
1902
|
0 |
0 |
$panel ||= 'Bio::Graphics::Panel'
|
|
1914
|
0 |
0 |
$linkrule ||= ''
|
|
1933
|
0 |
0 |
($n = $seq_id) && "$n" || ''
|
|
|
0 |
0 |
($n = $feature->display_name) && "$n" || ''
|
|
|
0 |
0 |
eval {
do {
$feature->class
}
} || ''
|
|
|
0 |
0 |
eval {
do {
$feature->method
}
} || $feature->primary_tag || ''
|
|
|
0 |
0 |
eval {
do {
$feature->method
}
} || $feature->primary_tag || ''
|
|
|
0 |
0 |
eval {
do {
$feature->source
}
} || $feature->source_tag || ''
|
|
|
0 |
0 |
eval {
do {
$feature->seq_id
}
} || eval {
do {
$feature->location->seq_id
}
} || ''
|
|
|
0 |
0 |
$feature->start || ''
|
|
|
0 |
0 |
$feature->end || ''
|
|
|
0 |
0 |
$feature->end || ''
|
|
|
0 |
0 |
$panel->start || ''
|
|
|
0 |
0 |
$panel->end || ''
|
|
|
0 |
0 |
$feature->length || 0
|
|
|
0 |
0 |
eval {
do {
join '', $feature->notes
}
} || ''
|
|
|
0 |
0 |
eval {
do {
$feature->feature_id
}
} || eval {
do {
$feature->primary_id
}
} || ''
|
|
1977
|
0 |
0 |
$feature->start || '?'
|
|
|
0 |
0 |
$feature->end || '?'
|
|
2004
|
0 |
0 |
$feature || ''
|
|
2027
|
0 |
0 |
shift() || 'general'
|
| line |
l |
!l&&r |
!l&&!r |
condition |
|
601
|
0 |
0 |
0 |
$self->setting($_, 'feature') || $_
|
|
606
|
0 |
0 |
0 |
exists $lc_types{lc $_} || exists $lc_types{lc $_->method}
|
|
660
|
0 |
0 |
0 |
$features[0]->type || $label
|
|
861
|
0 |
0 |
4 |
/\#[0-9a-f]{6,8}\s*$/i or /\w+\#\w+/
|
|
|
0 |
0 |
4 |
/\#[0-9a-f]{6,8}\s*$/i or /\w+\#\w+/ or /\w+\"*\s*\#\d+$/
|
|
903
|
0 |
0 |
1 |
$$self{'loader'} ||= $self->_make_loader($line)
|
|
947
|
0 |
0 |
1 |
$$self{'db'} ||= 'Bio::DB::SeqFeature::Store'->new(-'adaptor', 'memory', -'write', 1)
|
|
1017
|
0 |
0 |
0 |
$cc eq 'general' or $$self{'config'}{$cc}
|
|
1553
|
0 |
0 |
0 |
$_[0] =~ /^\+/ or $_[0] > 0
|
|
1554
|
0 |
0 |
0 |
$_[0] =~ /^\-/ or $_[0] < 0
|
|
1715
|
0 |
0 |
0 |
not defined $min or $min > $f->start
|
|
1716
|
0 |
0 |
0 |
not defined $max or $max < $f->start
|
|
1794
|
0 |
0 |
0 |
$$self{'gff'} ||= 'Bio::DB::GFF'->new(-'adaptor', 'memory')
|
|
1853
|
0 |
0 |
0 |
$$self{'m_time'} || $$self{'stat'}[9]
|
|
1916
|
0 |
0 |
0 |
$seq_id ||= $feature->seq_id
|
|
1948
|
0 |
0 |
0 |
$linkrule ||= $self->setting($label, 'link')
|
|
1949
|
0 |
0 |
0 |
$linkrule ||= $self->setting('general', 'link')
|
|
1961
|
0 |
0 |
0 |
$linkrule ||= $self->setting('general', 'title')
|
|
1966
|
0 |
0 |
0 |
eval {
do {
$feature->method
}
} || $feature->primary_tag
|
|
1993
|
0 |
0 |
0 |
$$self{'_type2label'} ||= $self->invert_types
|
|
2003
|
0 |
0 |
0 |
$$config{$label}{'feature'} || $label
|