Provided by: libbio-graphics-perl_2.40-2_all bug


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


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


       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.

       The following options are standard among all Glyphs.  See Bio::Graphics::Glyph for a full

         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                black

         -label        Whether to draw a label        0 (false)

         -description  Whether to draw a description  0 (false)

         -strand_arrow Whether to indicate            0 (false)

         -hilite       Highlight color                undef (no color)

       In addition, the cds 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

         -translation Number of lines of reading      3frame
                      frames to show. One of
                      "3frame", or "6frame".
                      For 6frame, specify a height
                      of at least 30 pixels.

         -sixframe   Draw a six-frame staff           0 (false; usually draws 3 frame)
                     This value overrides
                     -translation, which essentially
                     does the same thing.

                     Don't draw the reading frame 0   false
                     unless it is a feature

         -sub_part   For objects with multiple        undef
                     subpart types, defines which
                     is the CDS part.

         -codontable   Codon table to use             1 (see Bio::Tools::CodonTable)

         -phase_style  The way phase is to be
                       interpreted. One of            "012"
                       "012" or "021"
         -ignore_empty_phase                          false
                     Only draw features that have
                     their phase defined.

         -cds_only   Only draw features of type       false

       This glyph is more sensitive to the underlying data model than usual, so there are a few
       additional options to use to help adapt the glyph to different environments.

       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.

       The -phase_style controls how the value returned by the phase() or frame() methods is to
       be interpreted. The official interpretation is that the phase value indicates the offset
       into the feature at which the reading frame starts -- e.g. a phase of "2" means the
       reading frame starts after skipping two bases from the beginning of the feature.  However,
       many GFF2 format feature files interpret this field to mean the position reading frame of
       the first base of the feature -- e.g. a phase of "2" means that the reading frame starts
       after skipping just one base from the beginning of the feature. Specify "012" to interpret
       the phase field in the correct way, and "021" to interpret the phase field in the legacy
       way. The default is "012."

       Here is how the option names were chosen:

           * * *                  Base the reading frame starts on
           A B C A B C A B C...
           0 1 2                  PHASE REPRESENTED CORRECTLY
           0 2 1                  PHASE REPRESENTED IN THE LEGACY WAY

       Set the -ignore_empty_phase option to true if you wish to skip subfeatures that do not
       have a defined phase() or frame(). This is useful if you are rendering exons that have
       both translated and untranslated parts, and you wish to skip the untranslated parts.

       Set the -cds_only option to true if you wish to draw the glyph only for subfeatures of
       type 'CDS'. This is recommended.


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

        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.


       Please report them.


       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


       Lincoln Stein <>

       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.