Raw content of Bio::Graphics::Glyph::alignment
<![CDATA[package Bio::Graphics::Glyph::alignment;
use strict;
use Bio::Graphics::Glyph::graded_segments;
use vars '@ISA';
@ISA = 'Bio::Graphics::Glyph::graded_segments';
1;
__END__
=head1 NAME
Bio::Graphics::Glyph::alignment - The "alignment" glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
This is identical to the "graded_segments" glyph, and is used for
drawing features that consist of discontinuous segments. The
color intensity of each segment is proportionate to the score.
=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)
-strand_arrow Whether to indicate 0 (false)
strandedness
In addition, the alignment glyph recognizes the following
glyph-specific options:
Option Description Default
------ ----------- -------
-max_score Maximum value of the Calculated
feature's "score" attribute
-min_score Minimum value of the Calculated
feature's "score" attribute
If max_score and min_score are not specified, then the glyph will
calculate the local maximum and minimum scores at run time.
=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
Allen Day E<lt>day@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
]]>