This glyph was designed to show a segment that goes beyond the panel.
Dashed line indicates the end goes beyond the panel and arrow
indicates the direction.
Also see the anchored_arrw and arrow glyphs.
The following options are standard among all Glyphs. See
Bio::Graphics::Glyph for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
In addition to the generic options, this glyph recognizes:
Option Name Description Default
----------- ----------- -------
dashline_length length of drawn dash line 20
None available.
sub box
{ my $self = shift;
my ($x1, $y1, $x2, $y2) = ($self->left, $self->top, $self->right, $self->bottom);
$x1 = $self->panel->left if $x1 < $self->panel->left;
my $start = $self->feature->start;
my $stop = $start + $self->feature->length;
my $p_seg_start = $self->panel->offset;
my $pl = $self->panel->pad_left;
if ($start < $p_seg_start && $x1 eq $self->panel->left) {
$x1 -= $self->panel->pad_left;
my $map_x1 = $pl - $self->scale * ($p_seg_start - $start);
if ($map_x1 > $x1){
$x1 = $map_x1;
}
}
if ($stop > $p_seg_start + $self->panel->length) {
$x2 += $self->panel->pad_right;
my $map_x2 = $pl + $self->scale * ($stop - $p_seg_start);
if ($map_x2 <= $x2) {
$x2 = $map_x2;
}
}
return ($x1, $y1, $x2, $y2); } | sub draw_label
{ my $self = shift;
my ($gd,$left,$top,$partno,$total_parts) = @_;
my $label = $self->label or return;
my ($x1,$y1,$x2,$y2) = $self->bounds($left, $top);
$x1 = $self->panel->left if $x1 < $self->panel->left;
my $extended_x1 = $self->extended_left($x1, $left);
if ($extended_x1 < $x1) {
$x1 -= $self->panel->pad_left;
if ($extended_x1 > $x1) {
$x1 = $extended_x1;
}
}
my $font = $self->option('labelfont') || $self->font;
$gd->string($font,
$x1,
$self->top + $top,
$label,
$self->fontcolor);} | sub draw
{ my $self = shift;
my $gd = shift;
my ($dx,$dy) = @_;
my ($x1,$y1,$x2,$y2) = $self->bounds(@_);
my $fg = $self->set_pen;
my $a2 = ($self->height)/2;
my $center = $y1+$a2;
$x1 = $self->panel->left if $x1 < $self->panel->left;
$x2 = $self->panel->right if $x2 > $self->panel->right;
my ($sw,$ne,$base_w,$base_e) = $self->arrowheads;
my $dash_len = $self->dashline_length;
my ($line_x1, $line_x2) = ($x1, $x2);
my $extended_x1 = $self->extended_left($x1, $dx);
if ($extended_x1 < $x1) {
$x1 -= $self->panel->pad_left;
if ($extended_x1 > $x1) {
$x1 = $extended_x1;
$line_x1 = $x1;
} else {
my $dash_x2 = $x1 + $dash_len;
$dash_x2 += $a2 if $sw;
$dash_x2 = $line_x2 if ($dash_x2 > $x2);
$gd->dashedLine($x1,$center,$dash_x2,$center,$fg);
$line_x1 = $dash_x2;
}
}
my $extending_x2 = $self->extended_right($x2, $dx);
if ($extending_x2 > $x2) {
$x2 += $self->panel->pad_right - $a2;
if ($extending_x2 <= $x2) {
$x2 = $extending_x2;
$line_x2 = $x2;
} else {
my $dash_x1 = $x2 - $dash_len;
$dash_x1 -= $a2 if $ne;
$dash_x1 = $x1 if ($dash_x1 < $x1);
$gd->dashedLine($dash_x1,$center,$x2,$center,$fg);
$line_x2 = $dash_x1;
}
}
$gd->line($line_x1,$center,$line_x2,$center,$fg);
$self->arrowhead($gd,$x1,$center,$a2,-1) if $sw;
$self->arrowhead($gd,$x2,$center,$a2,+1) if $ne;
$gd->line($x2,$center-$a2,$x2,$center+$a2,$fg) if $base_e;
$gd->line($x1,$center-$a2,$x1,$center+$a2,$fg) if $base_w;
if ($self->option('tick')) {
my $font = $self->font;
my $width = $font->width;
my $font_color = $self->fontcolor;
my $height = $self->height;
my $relative = $self->option('relative_coords');
my $start = $relative ? 1 : $self->feature->start;
my $stop = $start + $self->feature->length - 1;
my $offset = $relative ? $self->feature->start-1 : 0;
my $reversed = $self->feature->strand < 0;
my $units = $self->option('units') || '';
my $divisor = $UNITS{$units} || 1 if $units;
my ($major_ticks,$minor_ticks) = $self->panel->ticks($start,$stop,$font,$divisor);
my $scale = $self->option('scale');
my $left = $sw ? $x1+$height : $x1;
my $right = $ne ? $x2-$height : $x2;
my $format = ($major_ticks->[1]-$major_ticks->[0])/($divisor||1) < 1 ? "%.1f$units" : "%d$units";
for my $i (@$major_ticks) {
my $tickpos = $dx + ($reversed ? $self->map_pt($stop - $i + $offset)
: $self->map_pt($i + $offset));
next if $tickpos < $left or $tickpos > $right;
$gd->line($tickpos,$center-$a2,$tickpos,$center+$a2,$fg);
my $label = $scale ? $i / $scale : $i;
if ($units) {
my $scaled = $label/$divisor;
$label = sprintf($format,$scaled);
}
my $middle = $tickpos - (length($label) * $width)/2;
$gd->string($font,$middle,$center+$a2-1,$label,$font_color);
}
if ($self->option('tick') >= 2) {
my $a4 = $self->height/4;
for my $i (@$minor_ticks) {
my $tickpos = $dx + ($reversed ? $self->map_pt($stop - $i + $offset)
: $self->map_pt($i + $offset));
next if $tickpos < $left or $tickpos > $right;
$gd->line($tickpos,$center-$a4,$tickpos,$center+$a4,$fg);
}
}
}
$self->draw_label($gd,$dx,$dy) if $self->option('label');
$self->draw_description($gd,$dx,$dy) if $self->option('description'); } | sub arrowheads
{ my $self = shift;
my ($ne,$sw,$base_e,$base_w);
if ($self->option('double')) {
$ne = $sw = 1;
} else {
$ne = $self->option('northeast') || $self->option('east');
$sw = $self->option('southwest') || $self->option('west');
}
unless (defined($ne) || defined($sw)) {
$ne = 1 if $self->feature->strand > 0;
$sw = 1 if $self->feature->strand < 0;
}
return ($sw,$ne,0,0) unless $self->option('base');
return ($sw,$ne,!$sw,!$ne);} | Please report them.