Bio::Graphics::Glyph::dna(3pm)				User Contributed Perl Documentation			    Bio::Graphics::Glyph::dna(3pm)

NAME

       Bio::Graphics::Glyph::dna - The "dna" glyph

SYNOPSIS

	 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

       This glyph draws DNA sequences.	At high magnifications, this glyph will draw the actual base pairs of the sequence (both strands).  At low
       magnifications, the glyph will plot the GC content.  By default, the GC calculation will use non-overlapping bins, but this can be changed
       by specifying the gc_window option, in which case, a sliding window calculation will be used.

       For this glyph to work, the feature must return a Bio::PrimarySeq DNA object in response to the seq() method. For example, you can use a
       Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq like this:

	 my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
	 my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end => 800 );
	 $feature->attach_seq($dna);
	 $panel->add_track( $feature, -glyph => 'dna' );

       A Bio::Graphics::Feature object may also be used.

   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)

       In addition to the common options, the following glyph-specific options are recognized:

	 Option      Description	       Default
	 ------      -----------	       -------

	 -do_gc      Whether to draw the GC	 true
		     graph at low mags

	 -gc_window  Size of the sliding window  E<lt>noneE<gt>
		     to use in the GC content
		     calculation.  If this is
		     not defined, non-
		     overlapping bins will be
		     used. If this is set to
		     "auto", then the glyph will
		     choose a window equal to
		     1% of the interval.

	 -gc_bins    Fixed number of intervals	 100
		     to sample across the
		     panel.

	 -axis_color Color of the vertical axes  fgcolor
		     in the GC content graph

	 -strand      Show both forward and	 auto
		     reverse strand, one of
		     "forward", "reverse",
		     "both" or "auto".
		     In "auto" mode,
		     +1 strand features will
		     show the plus strand
		     -1 strand features will
		     show the reverse complement
		     and strandless features will
		     show both

       NOTE: -gc_window=>'auto' gives nice results and is recommended for drawing GC content. The GC content axes draw slightly outside the panel,
       so you may wish to add some extra padding on the right and left.

BUGS

       Please report them.

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>.

       Sliding window GC calculation added by Peter Ashton <pda@sanger.ac.uk>.

       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.

perl v5.14.2							    2012-02-20					    Bio::Graphics::Glyph::dna(3pm)