Bio-Graphics-Glyph-decorated_gene
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}
sub add_tracks
{
my $panel = shift;
# ruler
can_ok($panel, qw(add_track));
$panel->add_track(
Bio::Graphics::Feature->new(-start => $gene_minus->start-100, -end => $gene_minus->end),
-glyph => 'arrow',
-bump => 0,
-double => 1,
-tick => 2
);
ok(1, 'ruler made');
$panel->add_track
(
$gene_minus,
-glyph => 'decorated_gene',
-label_transcripts => 1,
-description => 1,
-label => 1,
-height => 12,
-decoration_image_map => 1,
-box_subparts => 2,
-decoration_visible => 1,
-decoration_color => sub {
my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_;
return 'black' if ($glyph->active_decoration->name eq "TM");
return 'yellow' if ($glyph->active_decoration->type eq "SignalP4")
},
-additional_decorations => sub {
my $feature = shift;
my ($id) = $feature->get_tag_values('load_id');
my %add_h = ( "rna_PFA0680c-1" => "test:callback:100:130:0" );
return $add_h{$id};
},
-decoration_position => sub {
my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_;
return '12' if ($glyph->active_decoration->name eq "VTS");
return '-10'if ($glyph->active_decoration->name eq "TM");
return '1';
}
);
ok(1, 'track1 added');
my ($gene2) = $store->features(-name => 'test1');
$panel->add_track
(
$gene2,
-glyph => 'decorated_gene',
-description => sub { "Gene label and description do not bump with extended decoration boundaries" },
-label => 1,
-label_position => 'top',
-height => 12,
-decoration_visible => 1,
-decoration_border => "dashed",
-decoration_color => "transparent",
-decoration_label_position => "above",
-decoration_label => 1,
-decoration_border_color => "blue",
-decoration_height => sub {
my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_;
return '24' if ($glyph->active_decoration->name eq "very interesting region");
return '10';}
);
ok(1, 'track2 added');
$panel->add_track
(
$gene2,
-glyph => 'decorated_gene',
-description => sub { "Gene label and description do not bump with extended decoration boundaries" },
-label => 1,
-label_position => 'below',
-height => 12,
-decoration_visible => sub {
my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_;
return '0' if ($glyph->active_decoration->name eq "very interesting region");
return '1';},
-decoration_border => "dashed",
-decoration_color => "yellow",
-decoration_label_position => 'below',
-decoration_label => 1,
-decoration_level => 'mRNA',
-decoration_border_color => "blue",
-decoration_height => 12,
-decoration_position => sub {
my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_;
return '12' if ($glyph->active_decoration->name eq "SP");
return '12';}
);
ok(1, 'track3 added');
$panel->add_track
(
$gene2,
-glyph => 'decorated_gene',
-description => sub { "Gene label and description do not bump with extended decoration boundaries" },
-label => 1,
-label_position => 'below',
-height => 12,
-decoration_visible => sub {
my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_;
return '0' if ($glyph->active_decoration->name eq "very interesting region" || $glyph->active_decoration->name eq "SP");
return '1';},
-decoration_border => "dashed",
-decoration_color => "yellow",
-decoration_label_position => 'below',
-decoration_label => 1,
-decoration_border_color => "blue",
-decoration_height => 12,
-additional_decorations => 'TMHMM:TM:25:45:24',
-decoration_level => 'mRNA',
-decoration_position => sub {
my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_;
return '12' if ($glyph->active_decoration->name eq "TM");
( run in 1.518 second using v1.01-cache-2.11-cpan-7fcb06a456a )