Provided by: libbio-graphics-perl_2.40-3_all bug

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.