NAME¶
Bio::Graphics::Glyph::fixedwidth - A base class fixed width glyphs
SYNOPSIS¶
use Bio::Graphics;
use Bio::Seq;
use Bio::SeqFeature::Generic;
my $bsg = 'Bio::SeqFeature::Generic';
my $seq = Bio::Seq->new(-length=>1000);
my $whole = $bsg->new(-display_name => 'Clone82',
-start => 1,
-end => $seq->length);
my $f1 = $bsg->new(-start => 100,
-end => 300,
-display_name => 'feature 1',
);
my $f2 = $bsg->new(-start => 500,
-end => 800,
-display_name => 'feature 2',
);
my $panel = Bio::Graphics::Panel->new(-length => $seq->length,
-width => 800,
-key_style => 'between',
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track($whole,
-glyph => 'arrow',
-double => 1,
-tick => 2,
-label => 1,
);
$panel->add_track([$f1,$f2],
-glyph => 'fixedwidth',
-label => 1,
-fixed_height => 20,
-fixed_width => 20,
-key => 'fixed width');
binmode STDOUT;
print $panel->png;
DESCRIPTION¶
This glyph is a base class for glyphs that wish to draw a fixed width content,
such as an icon, image, scatterplot, and it would be inappropriate for the
content to be stretched to match the start and end point of the associated
feature. Instead the glyph draws a simple box spanning the feature's start:end
region, two diagonal connecting lines, and then a fixed width rectangle
beneath the box.
This glyph does nothing very interesting itself. It is intended that subclasses
should override the
draw_contents() method to draw something
interesting. See "Subclassing" for a simple example.
OPTIONS¶
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)
-hilite Highlight color undef (no color)
The following additional options are available to the "fixedwidth"
glyph:
Option Description Default
------ ----------- -------
-fixed_width Width of the content 0
-fixed_height Height of the content Same as -height
-fixed_gap Vertical gap between the box 8
that shows the extent of the
feature and the fixed-width
content.
If -fixed_gap is less than 8
then the diagonal connecting
lines are not drawn.
EXAMPLE SUBCLASS¶
To draw something interesting in the fixed rectangle, override the draw_contents
method. It takes four arguments consisting of the GD object, and the left,
top, right and bottom coordinates of the fixed rectangle. Example:
package Bio::Graphics::Glyph::fixedexample;
use strict;
use base 'Bio::Graphics::Glyph::fixedwidth';
sub draw_contents {
my $self = shift;
my ($gd,$left,$top,$right,$bottom) = @_;
$self->unfilled_box($gd,$left,$top,$right,$bottom);
$gd->line($left,$top,$right,$bottom,$self->fgcolor);
$gd->line($left,$bottom,$right,$top,$self->fgcolor);
}
1;
This will draw the outline of the fixed rectangle. The rectangle will contain
two diagonal lines. Not very interesting, but an example, nonetheless.
See the stackedplot glyph for a more interesting subclass.
BUGS AND LIMITATIONS¶
This glyph should used as the base for the image glyph, but isn't. This will be
fixed.
SEE ALSO¶
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow,
Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna,
Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line,
Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2,
Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR¶
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2007 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.