Bio::Graphics::Glyph::dna man page on Pidora

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Bio::Graphics::Glyph::User3Contributed Perl DocumeBio::Graphics::Glyph::dna(3)

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 v5.14.1			  2011-07-22	  Bio::Graphics::Glyph::dna(3)
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