NAME

       Bio::Graphics::Glyph::gene - A GFF3-compatible gene glyph

SYNOPSIS

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

DESCRIPTION

       This glyph is used for drawing genes that may have alternatively-spliced transcripts. The
       various isoforms are stacked on top of each other and given a single label and description
       that apply to the entire stack. Each individual transcript's name is optionally printed to
       the left of the transcript glyph.

       Transcripts (splice isoforms) are drawn using the processed_transcript glyph.  CDS
       features are 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.

       This glyph is designed to work properly with GFF3-style three-tier genes, in which the top
       level feature has the Sequence Ontology type of "gene", the second level feature(s) have
       the SO type "mRNA", and the third level feature(s) have the SO type "CDS",
       "five_prime_utr" and "three_prime_utr."  Subparts named "UTR" are also honored.  The
       feature can contain other subparts as well (e.g. exon, intron, translation), but they are
       currently ignored unless the option sub_part is supplied.  If the sub_part option is used
       that feature type will be used and CDS and UTR features will be excluded.  This could be
       used for specifying that exons be used instead, for example.

       This glyph is a subclass of processed_transcript, and recognizes the same options.

   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 gene glyph recognizes the following glyph-specific options:

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

         -label_transcripts                           undef (false)
                        Flag. If true, then the
                        display name of each
                        transcript will be drawn
                        to the left of the transcript
                        glyph.

         -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.

BUGS

       The SO terms are hard-coded. They should be more flexible and should recognize ISA
       relationships.

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.