Bio::Graphics::Glyph::translation - The "6-frame translation" glyph

       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.

perl v5.30.0                                       2019-11-25             Bio::Graphics::Glyph::translation(3pm)

       Please report them.

       This glyph draws the conceptual translation of DNA sequences.  At high magnifications, it simply draws
       lines indicating open reading frames.  At low magnifications, it draws a conceptual protein translation.
       Options can be used to set 1-frame, 3-frame or 6-frame translations.

   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
         ------        -----------                 -------

         -translation  Type of translation to      1frame
                       perform.  One of "1frame",
                       "3frame", or "6frame"

         -strand       Forward (+1) or reverse (-1) +1
                       translation.

         -frame0       Color for the first frame    fgcolor

         -frame1       Color for the second frame   fgcolor

         -frame2       Color for the third frame    fgcolor

         -gridcolor    Color for the horizontal     lightgrey
                       lines of the reading frames

         -start_codons Draw little arrowheads       0 (false)
                       indicating start codons

         -stop_codons  Draw little vertical ticks   1 (true)
                       indicating stop codons

         -arrow_height Height of the start codon    1
                       arrowheads

         -show_sequence Show the amino acid sequence 1 (true)
                       if there's room.

         -triletter_code Show the 3-letter amino acid 0 (false)
                       code if there's room

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

       Bio::Graphics::Glyph::translation - The "6-frame translation" glyph

       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

       This produces a nice gbrowse display in which the DNA/GC Content glyph is sandwiched between the forward
       and reverse three-frame translations.  The frames are color-coordinated with the example configuration
       for the "cds" glyph.

        [TranslationF]
        glyph        = translation
        global feature = 1
        frame0       = cadetblue
        frame1       = blue
        frame2       = darkblue
        height       = 20
        fgcolor      = purple
        strand       = +1
        translation  = 3frame
        key          = 3-frame translation (forward)

        [DNA/GC Content]
        glyph        = dna
        global feature = 1
        height       = 40
        do_gc        = 1
        fgcolor      = red
        axis_color   = blue

        [TranslationR]
        glyph        = translation
        global feature = 1
        frame0       = darkred
        frame1       = red
        frame2       = crimson
        height       = 20
        fgcolor      = blue
        strand       = -1
        translation  = 3frame
        key          = 3-frame translation (reverse)

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