package Bio::Graphics::Glyph::alignment;

use strict;

use base qw(Bio::Graphics::Glyph::graded_segments);

sub my_description {
    return <<END;
This glyph is a synonym for the "graded_segments" glyph, and is used for
drawing features that consist of discontinuous segments.  The
color intensity of each segment is proportional to the score.
END
}
sub my_options {
    return {
	max_score => [
	    'integer',
	    undef,
	    "Maximum value of the feature's \"score\" attribute."],
	min_score => [
	    'integer',
	    undef,
	    "Minimum value of the feature's \"score\" attribute."],
	vary_fg => [
	    'boolean',
	    undef,
	    "Vary the foreground color as well as the background."],
	merge_parts => [
	    'boolean',
	    undef,
	    "At low magnifications, smooth small gaps to improve the visual display.",
	    "See this glyph's manual page for the gory details."],
	max_gap => [
	    'integer',
	    undef,
	    'Do not merge across gaps that exceed this threshold.'],
    }
}

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

  -hilite       Highlight color                undef (no color)

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