Bio::Graphics::Glyph processed_transcript
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Summary
Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph
Package variables
No package variables defined.
Included modules
Bio::Graphics::Glyph::transcript2
Inherit
Bio::Graphics::Glyph::transcript2
Synopsis
  See Bio::Graphics::Panel and 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." 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
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.
Methods
bgcolor
No description
Code
connector
No description
Code
height
No description
Code
is_utr
No description
Code
pad_top
No description
Code
thin_utr
No description
Code
utr_color
No description
Code
Methods description
None available.
Methods code
bgcolordescriptionprevnextTop
sub bgcolor {
  my $self = shift;
  return $self->SUPER::bgcolor unless $self->is_utr;
  return $self->utr_color;
}
connectordescriptionprevnextTop
sub connector {
  my $self = shift;
  return 'quill' if $self->option('decorate_introns');
  return $self->SUPER::connector(@_);
}


1;


__END__
}
heightdescriptionprevnextTop
sub height {
  my $self = shift;
  my $height    = $self->SUPER::height;
  return $height unless $self->thin_utr;
  return $self->is_utr ? int($height/1.5+0.5) : $height;
}
is_utrdescriptionprevnextTop
sub is_utr {
  my $self = shift;
  return $self->feature->primary_tag =~ /UTR|untranslated_region/i;
}
pad_topdescriptionprevnextTop
sub pad_top {
  my $self = shift;
  my $pad_top = $self->SUPER::pad_top;
  return $pad_top unless $self->thin_utr && $self->is_utr;
  return $pad_top + int(0.167*$self->SUPER::height + 0.5);
}
thin_utrdescriptionprevnextTop
sub thin_utr {
  my $self = shift;
  $self->option('thin_utr');
}
utr_colordescriptionprevnextTop
sub utr_color {
  my $self = shift;
  return $self->color('utr_color') if $self->option('utr_color');
  return $self->factory->translate_color(DEFAULT_UTR_COLOR);
}
General documentation
BUGSTop
Please report them.
SEE ALSOTop
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
AUTHORTop
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.