Summary

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

Package variables

Included modules

Inherit

Bio::Graphics::Glyph::segments

Synopsis

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

Description

This glyph is used for drawing transcripts. It is essentially a
"segments" glyph in which the connecting segments are hats. The
direction of the transcript is indicated by an arrow attached to the
end of the glyph. 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)

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

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

  -arrow_length  Length of the directional   8
                 arrow.

Methods

Methods description

None available.

Methods code

sub pad_left {

  my $self = shift;
  my $pad  = $self->SUPER::pad_left;
  return $pad if $self->{level} > 0;
  my $strand = $self->feature->strand;
  return $pad unless defined $strand && $strand < 0;
  return $self->arrow_length > $pad ? $self->arrow_length : $pad;

}

sub pad_right {

  my $self = shift;
  my $pad  = $self->SUPER::pad_right;
  return $pad if $self->{level} > 0;
  my $strand = $self->feature->strand;
  return $pad unless defined($strand) && $strand > 0;
  return $self->arrow_length > $pad ? $self->arrow_length : $pad;

}

sub draw_component {

  my $self = shift;
  return unless $self->level > 0;
  $self->SUPER::draw_component(@_);

}

sub draw_connectors {

  my $self = shift;
  my $gd = shift;
  my ($left,$top) = @_;
  $self->SUPER::draw_connectors($gd,$left,$top);
  my @parts = $self->parts;

  # H'mmm.  No parts.  Must be in an intron, so draw intron
  # spanning entire range
  if (!@parts) {
    my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
    $self->_connector($gd,$left,$top,$x1,$y1,$x1,$y2,$x2,$y1,$x2,$y2);
    @parts = $self;
  }

  if ($self->feature->strand >= 0) {
    my($x1,$y1,$x2,$y2) = $parts[-1]->bounds(@_);
    my $center = ($y2+$y1)/2;
    $self->arrow($gd,$x2,$x2+$self->arrow_length,$center);
  } else {
    my($x1,$y1,$x2,$y2) = $parts[0]->bounds(@_);
    my $center = ($y2+$y1)/2;
    $self->arrow($gd,$x1,$x1 - $self->arrow_length,$center);
  }

}

sub arrow_length {

  my $self = shift;
  return $self->option('arrow_length') || 8;

}

sub connector {

  my $self = shift;
  return $self->SUPER::connector(@_) if $self->all_callbacks;
  return 'hat';

}

General documentation

Please report them.

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

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.