Toolbar

Summary

Bio::Graphics::Glyph::transcript2 - The "transcript2" glyph

Package variables

Included modules

Inherit

Bio::Graphics::Glyph::transcript

Synopsis

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

Description

This glyph is used for drawing transcripts. It is like "transcript"
except that if there is sufficient room the terminal exon is shaped
like an arrow in order to indicate the direction of transcription. If
there isn't enough room, a small arrow is drawn. 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
  ------         -----------                  -------

  -arrow_length  Length of the directional   8
                 arrow.

Methods

Methods description

None available.

Methods code

sub bump {

  my $self = shift;
  return $self->SUPER::bump(@_) if $self->all_callbacks;
  return 0;  # never allow our components to bump
}

1;


__END__

}

sub draw_component {

  my $self = shift;
  return unless $self->level > 0;

  my $gd = shift;
  my ($left,$top) = @_;
  my @rect = $self->bounds(@_);

  my $width = abs($rect[2] - $rect[0]);
  my $filled = defined($self->{partno}) && $width >= MIN_WIDTH_FOR_ARROW;

  if ($filled) {
    my $f      = $self->feature;
    my $strand = $f->strand;
    my ($first,$last)  = ($self->{partno} == 0 , $self->{partno} == $self->{total_parts}-1);
    ($first,$last)     = ($last,$first) if $self->{flip};

    if ($strand < 0 && $first) { # first exon, minus strand transcript
      $self->filled_arrow($gd,-1,@rect);
    } elsif ($strand >= 0 && $last) { # last exon, plus strand
      $self->filled_arrow($gd,+1,@rect);
    } else {
      $self->SUPER::draw_component($gd,@_);
    }
  }

  else {
    $self->SUPER::draw_component($gd,@_);
  }

}

sub draw_connectors {

  my $self = shift;
  my ($gd,$dx,$dy) = @_;

  my $part;
  my $strand = $self->feature->strand;
  $strand   *= -1 if $self->{flip};  #sigh
  if (my @parts  = $self->parts) {
    $part   = $strand >= 0 ? $parts[-1] : $parts[0];
  } else {
    # no parts -- so draw an intron spanning whole thing
    my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
    $self->_connector($gd,$dx,$dy,$x1,$y1,$x1,$y2,$x2,$y1,$x2,$y2);
    $part = $self;
  }
  my @rect   = $part->bounds();
  my $width  = abs($rect[2] - $rect[0]);
  my $filled = $width >= MIN_WIDTH_FOR_ARROW;

  if ($filled) {
    $self->Bio::Graphics::Glyph::generic::draw_connectors(@_);
  } else {
    $self->SUPER::draw_connectors(@_);
  }

}

sub pad_left {

  my $self = shift;
  my $pad = $self->Bio::Graphics::Glyph::generic::pad_left;
  return $pad unless ($self->feature->strand||0) < 0;  #uninitialized var warning
  my $first = ($self->parts)[0] || $self;
  my @rect  = $first->bounds();
  my $width = abs($rect[2] - $rect[0]);
  return $self->SUPER::pad_left if $width < MIN_WIDTH_FOR_ARROW;
  return $pad;

}

sub pad_right {

  my $self = shift;
  my $pad = $self->Bio::Graphics::Glyph::generic::pad_right;
  return $pad if $self->{level} > 0;
  my $last = ($self->parts)[-1] || $self;
  my @rect  = $last->bounds();
  my $width = abs($rect[2] - $rect[0]);
  return $self->SUPER::pad_right if $width < MIN_WIDTH_FOR_ARROW;
  return $pad

}

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.