NAME

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

SYNOPSIS

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

DESCRIPTION

This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the frame in which the translation occurs. At low magnifications, draws the amino acid sequence of the resulting protein. Amino acids that are created by a splice are optionally shown in a distinctive color.

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)

  -strand_arrow Whether to indicate            0 (false)
                 strandedness

In addition, the alignment glyph recognizes the following glyph-specific options:

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

  -frame0f    Color for first (+) frame    background color

  -frame1f    Color for second (+) frame   background color

  -frame2f    Color for third (+) frame    background color

  -frame0r    Color for first (-) frame    background color

  -frame1r    Color for second (-) frame   background color

  -frame2r    Color for third (-) frame    background color

  -gridcolor  Color for the "staff"        lightslategray

  -sixframe   Draw a six-frame staff       0 (false; usually draws 3 frame)

  -require_subparts
              Don't draw the reading frame 0 (false)
              unless it is a feature
              subpart.

The -require_subparts option is suggested when rendering spliced transcripts which contain multiple CDS subparts. Otherwise, the glyph will hickup when zoomed way down onto an intron between two CDSs (a phantom reading frame will appear). For unspliced sequences, do *not* use -require_subparts.

SUGGESTED STANZA FOR GENOME BROWSER

Using the "coding" aggregator, this produces a nice gbrowse display.

 [CDS]
 feature      = coding
 glyph        = cds
 frame0f      = cadetblue
 frame1f      = blue
 frame2f      = darkblue
 frame0r      = darkred
 frame1r      = red
 frame2r      = crimson
 description  = 0
 height       = 13
 label        = CDS frame
 key          = CDS
 citation     = This track shows CDS reading frames.

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>

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.