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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Graphics::Glyph::gene \- A GFF3\-compatible gene glyph .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& See L and L. .Ve .SH "DESCRIPTION" .IX Header "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. .PP Transcripts (splice isoforms) are drawn using the processed_transcript glyph. \s-1CDS\s0 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 \s-1CDS\s0 by setting the \&\*(L"thin_utr\*(R" option. .PP 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 \*(L"gene\*(R", the second level feature(s) have the \s-1SO\s0 type \*(L"mRNA\*(R", and the third level feature(s) have the \s-1SO\s0 type \*(L"\s-1CDS\*(R",\s0 \*(L"five_prime_utr\*(R" and \*(L"three_prime_utr.\*(R" Subparts named \*(L"\s-1UTR\*(R"\s0 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 \s-1CDS\s0 and \s-1UTR\s0 features will be excluded. This could be used for specifying that exons be used instead, for example. .PP This glyph is a subclass of processed_transcript, and recognizes the same options. .SS "\s-1OPTIONS\s0" .IX Subsection "OPTIONS" The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. .PP .Vb 2 \& 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) .Ve .PP In addition, the gene glyph recognizes the following glyph-specific options: .PP .Vb 2 \& 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. .Ve .SH "BUGS" .IX Header "BUGS" The \s-1SO\s0 terms are hard-coded. They should be more flexible and should recognize \s-1ISA\s0 relationships. .SH "SEE ALSO" .IX Header "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, \&\s-1GD\s0 .SH "AUTHOR" .IX Header "AUTHOR" Lincoln Stein .PP Copyright (c) 2001 Cold Spring Harbor Laboratory .PP This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See \s-1DISCLAIMER\s0.txt for disclaimers of warranty.