This glyph draws DNA sequences. At high magnifications, this glyph
will draw the actual base pairs of the sequence (both strands). At
low magnifications, the glyph will plot the GC content.
For this glyph to work, the feature must return a DNA sequence string
in response to the dna() method.
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 common options, the following glyph-specific
options are recognized:
Option Description Default
------ ----------- -------
-do_gc Whether to draw the GC true
graph at low mags
-gc_bins Fixed number of intervals 100
to sample across the
panel.
-axis_color Color of the vertical axes fgcolor
in the GC content graph
-strand Show both forward and auto
reverse strand, one of
"forward", "reverse",
"both" or "auto".
In "auto" mode,
+1 strand features will
show the plus strand
-1 strand features will
show the reverse complement
and strandless features will
show both
None available.
sub draw_component
{ my $self = shift;
my $gd = shift;
my ($x1,$y1,$x2,$y2) = $self->bounds(@_);
my $dna = eval { $self->feature->seq };
$dna = $dna->seq if ref($dna) and $dna->can('seq');
$dna or return;
$dna = $dna->seq if ref($dna) && $dna->can('seq');
if ($self->dna_fits) {
$self->draw_dna($gd,$dna,$x1,$y1,$x2,$y2);
} elsif ($self->do_gc) {
$self->draw_gc_content($gd,$dna,$x1,$y1,$x2,$y2);
}} | sub draw_dna
{ my $self = shift;
my ($gd,$dna,$x1,$y1,$x2,$y2) = @_;
my $pixels_per_base = $self->scale;
my $feature = $self->feature;
my $strand = $feature->strand;
$strand *= -1 if $self->{flip};
my @bases = split '',$strand >= 0 ? $dna : $self->reversec($dna);
my $color = $self->fgcolor;
my $font = $self->font;
my $lineheight = $font->height;
$y1 -= $lineheight/2 - 3;
my $strands = $self->option('strand') || 'auto';
my ($forward,$reverse);
if ($strands eq 'auto') {
$forward = $feature->strand >= 0;
$reverse = $feature->strand <= 0;
} elsif ($strands eq 'both') {
$forward = $reverse = 1;
} elsif ($strands eq 'reverse') {
$reverse = 1;
} else {
$forward = 1;
}
my $start = $self->map_no_trunc($feature->start);
my $end = $self->map_no_trunc($feature->end);
my $offset = int(($x1-$start-1)/$pixels_per_base);
for (my $i=$offset;$i<@bases;$i++) {
my $x = $start + $i * $pixels_per_base;
next if $x+1 < $x1;
last if $x > $x2;
$gd->char($font,$x+1,$y1,$bases[$i],$color) if $forward;
$gd->char($font,$x+1,$y1+($forward ? $lineheight:0),$complement{$bases[$i]}||$bases[$i],$color) if $reverse;
}} | sub draw_gc_content
{ my $self = shift;
my $gd = shift;
my $dna = shift;
my ($x1,$y1,$x2,$y2) = @_;
my $bin_size = length($dna) / ($self->option('gc_bins') || 100);
$bin_size = 100 if $bin_size < 100;
my @bins;
for (my $i = 0; $i < length($dna) - $bin_size; $i+= $bin_size) {
my $subseq = substr($dna,$i,$bin_size);
my $gc = $subseq =~ tr/gcGC/gcGC/;
my $content = $gc/$bin_size;
push @bins,$content;
}
push @bins,0.5 unless @bins;
my $bin_width = ($x2-$x1)/@bins;
my $bin_height = $y2-$y1;
my $fgcolor = $self->fgcolor;
my $bgcolor = $self->factory->translate_color($self->panel->gridcolor);
my $axiscolor = $self->color('axis_color') || $fgcolor;
$gd->line($x1, $y1, $x1, $y2, $axiscolor);
$gd->line($x2-2,$y1, $x2-2,$y2, $axiscolor);
$gd->line($x1, $y1, $x1+3,$y1, $axiscolor);
$gd->line($x1, $y2, $x1+3,$y2, $axiscolor);
$gd->line($x1, ($y2+$y1)/2,$x1+3,($y2+$y1)/2,$axiscolor);
$gd->line($x2-4,$y1, $x2-1, $y1, $axiscolor);
$gd->line($x2-4,$y2, $x2-1, $y2, $axiscolor);
$gd->line($x2-4,($y2+$y1)/2,$x2-1,($y2+$y1)/2,$axiscolor);
$gd->line($x1+5,$y2, $x2-5,$y2, $bgcolor);
$gd->line($x1+5,($y2+$y1)/2,$x2-5,($y2+$y1)/2,$bgcolor);
$gd->line($x1+5,$y1, $x2-5,$y1, $bgcolor);
$gd->string($self->font,$x1+5,$y1,'% gc',$axiscolor) if $bin_height > $self->font->height*2;
for (my $i = 0; $i < @bins; $i++) {
my $bin_start = $x1+$i*$bin_width;
my $bin_stop = $bin_start + $bin_width;
my $y = $y2 - ($bin_height*$bins[$i]);
$gd->line($bin_start,$y,$bin_stop,$y,$fgcolor);
$gd->line($bin_stop,$y,$bin_stop,$y2 - ($bin_height*$bins[$i+1]),$fgcolor)
if $i < @bins-1;
}} | Please report them.
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.