processed_transcript documentation.

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

No package variables defined.

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

  -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.

sub is_utr {

  my $self = shift;
  return $self->feature->primary_tag =~ /UTR|untranslated_region/i;

}

sub thin_utr {

  my $self = shift;
  $self->option('thin_utr');

}

sub utr_color {

  my $self = shift;
  return $self->color('utr_color') if $self->option('utr_color');
  return $self->factory->translate_color(DEFAULT_UTR_COLOR);

}

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;

}

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);

}

sub bgcolor {

  my $self = shift;
  return $self->SUPER::bgcolor unless $self->is_utr;
  return $self->utr_color;

}

sub connector {

  my $self = shift;
  return 'quill' if $self->option('decorate_introns');
  return $self->SUPER::connector(@_);

}

General documentation

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.

is_utr	No description	Code
thin_utr	No description	Code
utr_color	No description	Code
height	No description	Code
pad_top	No description	Code
bgcolor	No description	Code
connector	No description	Code