Bio::Graphics::Glyph::fixedwidth - A base class fixed width glyphs

- NAME
- SYNOPSIS
- DESCRIPTION

- OPTIONS
- EXAMPLE SUBCLASS

- BUGS AND LIMITATIONS
- SEE ALSO
- AUTHOR

# NAME

Bio::Graphics::Glyph::fixedwidth - A base class fixed width glyphs

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# 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;

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# 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 the Bio::Graphics::Glyph manpage 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.

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# BUGS AND LIMITATIONS

This glyph should used as the base for the image glyph, but isn't. This will be fixed.

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# SEE ALSO

the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Glyph::arrow manpage, the Bio::Graphics::Glyph::cds manpage, the Bio::Graphics::Glyph::crossbox manpage, the Bio::Graphics::Glyph::diamond manpage, the Bio::Graphics::Glyph::dna manpage, the Bio::Graphics::Glyph::dot manpage, the Bio::Graphics::Glyph::ellipse manpage, the Bio::Graphics::Glyph::extending_arrow manpage, the Bio::Graphics::Glyph::generic manpage, the Bio::Graphics::Glyph::graded_segments manpage, the Bio::Graphics::Glyph::heterogeneous_segments manpage, the Bio::Graphics::Glyph::line manpage, the Bio::Graphics::Glyph::pinsertion manpage, the Bio::Graphics::Glyph::primers manpage, the Bio::Graphics::Glyph::rndrect manpage, the Bio::Graphics::Glyph::segments manpage, the Bio::Graphics::Glyph::ruler_arrow manpage, the Bio::Graphics::Glyph::toomany manpage, the Bio::Graphics::Glyph::transcript manpage, the Bio::Graphics::Glyph::transcript2 manpage, the Bio::Graphics::Glyph::translation manpage, the Bio::Graphics::Glyph::triangle manpage, the Bio::DB::GFF manpage, the Bio::SeqI manpage, the Bio::SeqFeatureI manpage, the Bio::Das manpage, GD

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# 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.

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Bio::Graphics::Glyph::fixedwidth - A base class fixed width glyphs