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)