Bio::Graphics::Glyph::translation(3pm)			User Contributed Perl Documentation		    Bio::Graphics::Glyph::translation(3pm)

NAME

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

SYNOPSIS

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

DESCRIPTION

       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)

SUGGESTED STANZA FOR GENOME BROWSER

       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)

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.

perl v5.14.2							    2012-02-20				    Bio::Graphics::Glyph::translation(3pm)