| line |
true |
false |
branch |
|
375
|
0 |
1 |
if exists $args{-'map_coords'} and ref $args{-'map_coords'} eq 'CODE'
|
|
378
|
0 |
1 |
if exists $args{-'smart_features'}
|
|
379
|
1 |
0 |
if exists $args{-'safe'}
|
|
380
|
0 |
1 |
if $args{-'safe_world'}
|
|
381
|
0 |
1 |
if $args{-'allow_whitespace'}
|
|
388
|
1 |
0 |
if (my $file = $args{-'file'}) { }
|
|
|
0 |
0 |
elsif (my $text = $args{-'text'}) { }
|
|
390
|
0 |
1 |
if (defined fileno $file) { }
|
|
|
0 |
1 |
elsif ($file eq '-') { }
|
|
421
|
0 |
0 |
unless ($has_libs = defined &nfreeze)
|
|
427
|
0 |
0 |
unless $has_libs
|
|
433
|
0 |
0 |
unless my $file = $has_libs && $args{-'file'}
|
|
436
|
0 |
0 |
if (-e $cachefile and (stat _)[9] >= $self->file_mtime($args{-'file'})) { }
|
|
439
|
0 |
0 |
if $parsed_file->safe
|
|
446
|
0 |
0 |
if $@
|
|
482
|
0 |
0 |
unless my $m = (stat $f)[9]
|
|
483
|
0 |
0 |
if $mtime < $m
|
|
484
|
0 |
0 |
unless open my $fh, '<', $file
|
|
490
|
0 |
0 |
if (/^\#exec/)
|
|
493
|
0 |
0 |
if (/^\#include\s+(.+)/i)
|
|
496
|
0 |
0 |
if $mtime < $m
|
|
511
|
0 |
0 |
unless open my $fh, '<', $file
|
|
517
|
0 |
0 |
if (/^\#include\s+(.+)/i)
|
|
520
|
0 |
0 |
@files ? :
|
|
590
|
0 |
0 |
unless ($panel and UNIVERSAL::isa($panel, 'Bio::Graphics::Panel'))
|
|
617
|
0 |
0 |
if ($options and ref $options eq 'HASH') { }
|
|
621
|
0 |
0 |
if ($options == 1) { }
|
|
|
0 |
0 |
elsif ($options == 2) { }
|
|
|
0 |
0 |
elsif ($options == 3) { }
|
|
|
0 |
0 |
elsif ($options == 4) { }
|
|
|
0 |
0 |
elsif ($options == 5) { }
|
|
638
|
0 |
0 |
unless @types
|
|
640
|
0 |
0 |
if defined $selector and not &$selector($self, $label)
|
|
642
|
0 |
0 |
!$range ? :
|
|
648
|
0 |
0 |
unless @features
|
|
651
|
0 |
0 |
if $_->has_tag('_ff_group')
|
|
655
|
0 |
0 |
if defined $max_bump
|
|
656
|
0 |
0 |
if defined $max_label
|
|
658
|
0 |
0 |
$override_options ? :
|
|
672
|
0 |
0 |
if (defined $position_to_insert) { }
|
|
678
|
0 |
0 |
wantarray ? :
|
|
684
|
0 |
1 |
unless defined fileno $file
|
|
685
|
0 |
1 |
unless my(@stat) = stat $file
|
|
686
|
0 |
1 |
if ($$self{'stat'} and @{$$self{'stat'};}) { }
|
|
688
|
0 |
0 |
if $stat[$_] > $$self{'stat'}[$_]
|
|
717
|
0 |
0 |
if @_
|
|
736
|
0 |
0 |
if @_
|
|
757
|
0 |
1 |
unless my $fh = 'IO::File'->new($f)
|
|
773
|
0 |
4 |
unless $self->parse_line($_)
|
|
793
|
0 |
5 |
if (/^#include\s+(.+)/i)
|
|
796
|
0 |
0 |
if $$self{'includes'}{$include_file}++
|
|
802
|
0 |
5 |
if (/^#exec\s+(.+)/i)
|
|
804
|
0 |
0 |
unless open my $fh, '-|'
|
|
809
|
0 |
5 |
if $line =~ /^\s*\#[^\#]?$/
|
|
817
|
1 |
4 |
if ($new_state ne $old_state)
|
|
822
|
4 |
1 |
if ($new_state eq 'config') { }
|
|
|
1 |
0 |
elsif ($new_state eq 'data') { }
|
|
836
|
0 |
5 |
if ($current_state eq 'data') { }
|
|
|
5 |
0 |
elsif ($current_state eq 'config') { }
|
|
837
|
0 |
0 |
if $line =~ /^\s*\[([^\]]+)\]/
|
|
841
|
0 |
5 |
if $line =~ /^\#\#(\w+)/
|
|
842
|
1 |
4 |
if $line =~ /^reference\s*=/
|
|
844
|
0 |
4 |
if $line =~ /^\s*$/
|
|
845
|
1 |
3 |
if $line =~ /^\[(.+)\]/
|
|
846
|
3 |
0 |
if $line =~ /^[\w:\s]+=/ and $$self{'current_config'}
|
|
848
|
0 |
0 |
if $line =~ /^\s+(.+)/ and $$self{'current_tag'}
|
|
850
|
0 |
0 |
if $line =~ /^\#/
|
|
861
|
4 |
0 |
unless /\#[0-9a-f]{6,8}\s*$/i or /\w+\#\w+/ or /\w+\"*\s*\#\d+$/
|
|
863
|
0 |
4 |
if (/^\s+(.+)/ and $$self{'current_tag'}) { }
|
|
|
1 |
3 |
elsif (/^\[(.+)\]/) { }
|
|
|
3 |
0 |
elsif (/^([\w: -]+?)\s*=\s*(.*)/) { }
|
|
|
0 |
0 |
elsif (/^$/) { }
|
|
868
|
0 |
0 |
if $$self{'config'}{$cc}{$$self{'current_tag'}} =~ /^sub\s*\{/
|
|
875
|
1 |
0 |
$label =~ /^(general|default)$/i ? :
|
|
876
|
0 |
1 |
unless $cc eq 'general'
|
|
884
|
3 |
0 |
defined $2 ? :
|
|
903
|
0 |
0 |
unless $$self{'loader'} ||= $self->_make_loader($line)
|
|
915
|
0 |
0 |
if (/^\#\#gff-version\s+([23])/) { }
|
|
|
0 |
0 |
elsif (/^reference\s*=.+/) { }
|
|
923
|
0 |
0 |
if /^\s+/ and length $tokens[0]
|
|
925
|
0 |
0 |
if (@tokens >= 8 and $tokens[3] =~ /^-?\d+$/ and $tokens[4] =~ /^-?\d+$/) { }
|
|
932
|
0 |
0 |
unless $type->can('new')
|
|
938
|
0 |
0 |
if $self->allow_whitespace
|
|
941
|
0 |
0 |
if $loader
|
|
965
|
0 |
0 |
if @_
|
|
987
|
0 |
0 |
if $self->smart_features
|
|
988
|
0 |
0 |
if defined $type
|
|
1016
|
0 |
0 |
$type =~ /^(general|default)$/i ? :
|
|
1017
|
0 |
0 |
unless $cc eq 'general' or $$self{'config'}{$cc}
|
|
1018
|
0 |
0 |
if (defined $type_configuration)
|
|
1044
|
0 |
0 |
unless @_ == 3
|
|
1047
|
0 |
0 |
if (not $$self{'config'}{$type}) { }
|
|
1092
|
0 |
0 |
if (@_ > 2) { }
|
|
|
0 |
0 |
elsif (@_ <= 1) { }
|
|
|
0 |
0 |
elsif ($self->safe) { }
|
|
|
0 |
0 |
elsif ($self->safe_world) { }
|
|
1109
|
0 |
0 |
if $$self{'code_check'}++
|
|
1128
|
0 |
0 |
if defined $value
|
|
1140
|
0 |
0 |
unless my $config = $$self{'config'}
|
|
1141
|
0 |
0 |
unless @_
|
|
1142
|
0 |
0 |
if @_ == 1
|
|
1143
|
0 |
0 |
if @_ == 2 and defined $_[0] and exists $$config{$_[0]}
|
|
1144
|
0 |
0 |
if @_ > 2
|
|
1166
|
0 |
0 |
unless $self->safe
|
|
1170
|
0 |
0 |
unless defined $setting
|
|
1171
|
0 |
0 |
if ref $setting eq 'CODE'
|
|
1172
|
0 |
0 |
if ($setting =~ /^\\&([:\w]+)/) { }
|
|
|
0 |
0 |
elsif ($setting =~ /^sub\s*(\(\$\$\))*\s*\{/) { }
|
|
1175
|
0 |
0 |
$subroutine_name =~ /::/ ? :
|
|
1179
|
0 |
0 |
if $@
|
|
1187
|
0 |
0 |
if $@
|
|
1222
|
0 |
0 |
unless defined $setting
|
|
1223
|
0 |
0 |
if ref $setting eq 'CODE'
|
|
1225
|
0 |
0 |
if ($setting =~ /^sub\s*(\(\$\$\))*\s*\{/ and my $context = $$self{'safe_context'}) { }
|
|
1243
|
0 |
0 |
if $@
|
|
1244
|
0 |
0 |
unless ($success)
|
|
1252
|
0 |
0 |
if ($_[-1]->isa('Bio::Graphics::Glyph'))
|
|
1257
|
0 |
0 |
$prototype ? :
|
|
1284
|
0 |
0 |
if @_
|
|
1285
|
0 |
0 |
if $$self{'safe'} and not $d
|
|
1306
|
0 |
0 |
if ($safe and not $$self{'safe_content'})
|
|
1309
|
0 |
0 |
unless ('Safe::World'->can('new'))
|
|
1314
|
0 |
0 |
unless ($$self{'safe_lib'})
|
|
1315
|
0 |
0 |
unless $$self{'safe_lib'} = 'Safe::World'->new('sharepack', ['Bio::DB::SeqFeature', 'Bio::Graphics::Feature', 'Bio::SeqFeature::Lite', 'Bio::Graphics::Glyph'])
|
|
1321
|
0 |
0 |
unless $$self{'safe_lib'}->eval("use Bio::DB::SeqFeature;\nuse Bio::Graphics::Feature;\nuse Bio::SeqFeature::Lite;\nuse Bio::Graphics::Glyph; \n1;\n")
|
|
1330
|
0 |
0 |
unless $$self{'safe_context'} = 'Safe::World'->new('root', $self->base2package)
|
|
1380
|
0 |
0 |
unless my $config = $$self{'config'}
|
|
1382
|
0 |
0 |
unless ($hashref)
|
|
1384
|
0 |
0 |
unless $hashref = $$config{$type}
|
|
1406
|
0 |
0 |
unless my $config = $$self{'config'}
|
|
1407
|
0 |
0 |
unless my $hashref = $$config{$type}
|
|
1428
|
0 |
0 |
unless my $types = $$self{'types'}
|
|
1456
|
0 |
0 |
if ($Bio::Root::Version::VERSION >= 1.0069 and $Bio::Root::Version::VERSION <= 1.006901)
|
|
1462
|
0 |
0 |
unless 'Bio::DB::GFF::Typename'->can('new')
|
|
1515
|
0 |
0 |
defined($_[0] && $_[0] =~ /^-/) ? :
|
|
1518
|
0 |
0 |
if $types and not ref $types
|
|
1519
|
0 |
0 |
$types && @$types ? :
|
|
1521
|
0 |
0 |
if $seq_id
|
|
1522
|
0 |
0 |
if defined $start
|
|
1523
|
0 |
0 |
if defined $end
|
|
1527
|
0 |
0 |
if ($iterator) { }
|
|
1531
|
0 |
0 |
wantarray ? :
|
|
1553
|
0 |
0 |
if $_[0] =~ /^\+/ or $_[0] > 0
|
|
1554
|
0 |
0 |
if $_[0] =~ /^\-/ or $_[0] < 0
|
|
1580
|
0 |
0 |
$_[0] =~ /^-/ ? :
|
|
1611
|
0 |
0 |
if defined $name
|
|
1612
|
0 |
0 |
if defined $ref
|
|
1613
|
0 |
0 |
if defined $start
|
|
1614
|
0 |
0 |
if defined $end
|
|
1666
|
0 |
0 |
unless my $refs = $$self{'refs'}
|
|
1704
|
0 |
0 |
if defined $$self{'min'} and defined $$self{'max'}
|
|
1707
|
0 |
0 |
if (my $bases = $self->setting('general', 'bases'))
|
|
1711
|
0 |
0 |
unless (defined $min)
|
|
1715
|
0 |
0 |
if not defined $min or $min > $f->start
|
|
1716
|
0 |
0 |
if not defined $max or $max < $f->start
|
|
1737
|
0 |
0 |
if ($s->safe) { }
|
|
|
0 |
0 |
elsif ($s->safe_world) { }
|
|
1744
|
0 |
0 |
if $$s{'loader'}
|
|
1770
|
0 |
0 |
if $self->_setting($s, $o) =~ /\Asub\s*{/
|
|
1779
|
0 |
0 |
unless my $init_code = $self->_setting('general', 'init_code')
|
|
1782
|
0 |
0 |
if $@
|
|
1787
|
0 |
0 |
if exists $$self{'base2package'}
|
|
1803
|
0 |
0 |
unless 'Bio::Graphics::Panel'->can('new')
|
|
1813
|
0 |
0 |
if (my $bases = $self->setting('general', 'bases'))
|
|
1817
|
0 |
0 |
unless (defined $start and defined $stop)
|
|
1818
|
0 |
0 |
unless defined $start
|
|
1819
|
0 |
0 |
unless defined $stop
|
|
1823
|
0 |
0 |
if $options and ref $options eq 'HASH'
|
|
1854
|
0 |
0 |
if @_
|
|
1876
|
0 |
0 |
$feature->can('type') ? :
|
|
1878
|
0 |
0 |
unless $type
|
|
1881
|
0 |
0 |
unless @labels
|
|
1882
|
0 |
0 |
unless @labels
|
|
1883
|
0 |
0 |
wantarray ? :
|
|
1904
|
0 |
0 |
if (ref $linkrule and ref $linkrule eq 'CODE')
|
|
1906
|
0 |
0 |
if $@
|
|
1910
|
0 |
0 |
unless defined &CGI::escape
|
|
1911
|
0 |
0 |
$dont_escape ? :
|
|
1915
|
0 |
0 |
$feature->can('seq_id') ? :
|
|
1933
|
0 |
0 |
$1 eq 'id' ? :
|
|
|
0 |
0 |
$1 eq 'description' ? :
|
|
|
0 |
0 |
$1 eq 'length' ? :
|
|
|
0 |
0 |
$1 eq 'segend' ? :
|
|
|
0 |
0 |
$1 eq 'segstart' ? :
|
|
|
0 |
0 |
$1 eq 'stop' ? :
|
|
|
0 |
0 |
$1 eq 'end' ? :
|
|
|
0 |
0 |
$1 eq 'start' ? :
|
|
|
0 |
0 |
$1 =~ /seq_?id/ ? :
|
|
|
0 |
0 |
$1 eq 'source' ? :
|
|
|
0 |
0 |
$1 eq 'method' ? :
|
|
|
0 |
0 |
$1 eq 'type' ? :
|
|
|
0 |
0 |
$1 eq 'class' ? :
|
|
|
0 |
0 |
$1 eq 'name' ? :
|
|
|
0 |
0 |
$1 eq 'ref' ? :
|
|
1946
|
0 |
0 |
unless ($linkrule)
|
|
1962
|
0 |
0 |
unless $linkrule
|
|
1967
|
0 |
0 |
$feature->can('seq_id') ? :
|
|
1969
|
0 |
0 |
if ($feature->can('target') and my $target = $feature->target) { }
|
|
1970
|
0 |
0 |
defined $seqid ? :
|
|
1977
|
0 |
0 |
$feature->can('display_name') ? :
|
|
|
0 |
0 |
defined $seqid ? :
|
|
1985
|
0 |
0 |
if $@
|
|
1995
|
0 |
0 |
wantarray ? :
|
|
2000
|
0 |
0 |
unless my $config = $$self{'config'}
|
|
2046
|
0 |
0 |
if @_
|