Bio::Graphics::Glyph::fixedwidth(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::fixedwidth(3pm)
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.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::fixedwidth(3pm)