| line |
true |
false |
branch |
|
376
|
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 &Bio::Graphics::FeatureFile::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) |
|
797
|
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 =~ /^\[(.+)\]/ |
|
847
|
3 |
0 |
if $line =~ /^[\w:\s]+=/ and $self->{'current_config'} |
|
849
|
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 (/^$/) { } |
|
869
|
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 @_ |