Raw content of Bio::Graphics::Glyph::dna
<![CDATA[package Bio::Graphics::Glyph::dna;
use strict;
use Bio::Graphics::Glyph::generic;
use vars '@ISA';
@ISA = qw(Bio::Graphics::Glyph::generic);
my %complement = (g=>'c',a=>'t',t=>'a',c=>'g',n=>'n',
G=>'C',A=>'T',T=>'A',C=>'G',N=>'N');
# turn off description
sub description { 0 }
# turn off label
# sub label { 1 }
sub height {
my $self = shift;
my $font = $self->font;
return $self->dna_fits ? 2*$font->height
: $self->do_gc ? $self->SUPER::height
: 0;
}
sub do_gc {
my $self = shift;
my $do_gc = $self->option('do_gc');
return if defined($do_gc) && !$do_gc;
return 1;
}
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'); # to catch Bio::PrimarySeqI objects
$dna or return;
# workaround for my misreading of interface -- LS
$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; # avoid div by zero
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;
}
}
sub make_key_feature {
my $self = shift;
my @gatc = qw(g a t c);
my $offset = $self->panel->offset;
my $scale = 1/$self->scale; # base pairs/pixel
my $start = $offset+1;
my $stop = $offset+100*$scale;
my $feature =
Bio::Graphics::Feature->new(-start=> $start,
-stop => $stop,
-seq => join('',map{$gatc[rand 4]} (1..500)),
-name => $self->option('key'),
-strand => '+1',
);
$feature;
}
1;
__END__
=head1 NAME
Bio::Graphics::Glyph::dna - The "dna" glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
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.
=head2 OPTIONS
The following options are standard among all Glyphs. See
L<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
=head1 BUGS
Please report them.
=head1 SEE ALSO
L<Bio::Graphics::Panel>,
L<Bio::Graphics::Glyph>,
L<Bio::Graphics::Glyph::arrow>,
L<Bio::Graphics::Glyph::cds>,
L<Bio::Graphics::Glyph::crossbox>,
L<Bio::Graphics::Glyph::diamond>,
L<Bio::Graphics::Glyph::dna>,
L<Bio::Graphics::Glyph::dot>,
L<Bio::Graphics::Glyph::ellipse>,
L<Bio::Graphics::Glyph::extending_arrow>,
L<Bio::Graphics::Glyph::generic>,
L<Bio::Graphics::Glyph::graded_segments>,
L<Bio::Graphics::Glyph::heterogeneous_segments>,
L<Bio::Graphics::Glyph::line>,
L<Bio::Graphics::Glyph::pinsertion>,
L<Bio::Graphics::Glyph::primers>,
L<Bio::Graphics::Glyph::rndrect>,
L<Bio::Graphics::Glyph::segments>,
L<Bio::Graphics::Glyph::ruler_arrow>,
L<Bio::Graphics::Glyph::toomany>,
L<Bio::Graphics::Glyph::transcript>,
L<Bio::Graphics::Glyph::transcript2>,
L<Bio::Graphics::Glyph::translation>,
L<Bio::Graphics::Glyph::triangle>,
L<Bio::DB::GFF>,
L<Bio::SeqI>,
L<Bio::SeqFeatureI>,
L<Bio::Das>,
L<GD>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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.
=cut
]]>