NAME

       Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph

SYNOPSIS

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

DESCRIPTION

       This glyph is used for drawing processed transcripts that have both CDS and UTR segments.
       The CDS is drawn in the background color, and the UTRs are drawn in an alternate color
       selected by the utr_color option.  In addition, you can make the UTRs thinner than the CDS
       by setting the "thin_utr" option.

       For this glyph to produce the desired results, you should pass it a compound
       Bio::SeqFeature that has subfeatures of primary_tag "CDS" and "UTR".  In fact, you may
       give it more specific types of UTR, including 5'-UTR, 3'-UTR, or the Sequence Ontology
       terms "untranslated_region," "five_prime_untranslated_region," and
       "three_prime_untranslated_region."

   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                 undef (false)

         -connector_color
                       Connector color                black

         -label        Whether to draw a label        undef (false)

         -description  Whether to draw a description  undef (false)

         -strand_arrow Whether to indicate            undef (false)
                        strandedness

         -hilite       Highlight color                undef (no color)

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

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

         -thin_utr      Flag.  If true, UTRs will      undef (false)
                        be drawn at 2/3 of the
                        height of CDS segments.

         -utr_color     Color of UTR segments.         Gray #D0D0D0

         -decorate_introns
                        Draw strand with little arrows undef (false)
                        on the intron.

         -adjust_exons  Fix exons so that they don't   undef (false)
                        overlap UTRs

         -implied_utrs  Whether UTRs should be implied undef (false)
                        from exons and CDS features

         -one_cds       Some databases (e.g. FlyBase) represent their
                        transcripts as having a single CDS that is
                        broken up into multiple parts. Set this to
                        true to display this type of feature.

       The -adjust_exons option is needed to handle features in which the exons (SO type "exon")
       overlaps with the UTRs (SO types "five_prime_UTR" and "three_prime_UTR").  The exon parts
       of the glyph will be clipped so that it doesn't overlap with the UTR parts.

       The -implied_utrs option is needed if there are no explicit UTR features.  In this case,
       UTRs are derived by subtracting the positions of "CDS" subfeatures from the positions of
       "exon" subfeatures.  -implied_utrs implies the -adjust_exons option.

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 v5.18.1                                2013-1Bio::Graphics::Glyph::processed_transcript(3pm)