Summary

Bio::Graphics::Glyph::wormbase_transcript - The "wormbase_transcript" glyph

Package variables

Included modules

Inherit

Bio::Graphics::Glyph::transcript2

Synopsis

  See Bio::Graphics::Panel and Bio::Graphics::Glyph.

Description

This glyph is used for drawing transcripts. It is like "transcript2"
except that if the underlying feature is an Ace::Sequence object, the
description is derived from some wormbase-specific fields, including
info(), brief_identification() and locus(). Otherwise, the
description is obtained from the notes() field.
In addition, this glyph can show different bgcolors depending on the
direction of transcription. 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                 0 (false)

  -connector_color
                Connector color                black

  -label        Whether to draw a label	       0 (false)

  -description  Whether to draw a description  0 (false)

  -strand_arrow Whether to indicate            0 (false)
                 strandedness

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

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

  -forwardcolor  Bgcolor for forward          Same as -bgcolor.
                    transcripts

  -reversecolor  Bgcolor for reverse          Same as -bgcolor.
                    transcripts

Methods

Methods description

None available.

Methods code

sub bgcolor {

  my $self = shift;
  my $feature = $self->feature;
  if ($feature->strand >= 0) {
    return $self->color('forwardcolor');
  } else {
    return $self->color('reversecolor');
  }

}

sub get_description {

  my $self    = shift;
  my $feature = shift;

  # fetch modularity-breaking acedb sequence object information
  # for backward compatibility with wormbase requirements
  if ($feature->isa('Ace::Sequence::Transcript')) {
    return eval {
      my $t       = $feature->info;
      my $id      = $t->Brief_identification;
      my $comment = $t->Locus;
      $comment   .= $comment ? " ($id)" : $id if $id;
      $comment;
    };
  } else {
    return join '; ',eval { $feature->notes };
  }

}

General documentation

Please report them.

Bio::Graphics::Panel,
Bio::Graphics::Track,
Bio::Graphics::Glyph::transcript2,
Bio::Graphics::Glyph::anchored_arrow,
Bio::Graphics::Glyph::arrow,
Bio::Graphics::Glyph::box,
Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript,

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.