Bio::Graphics::Glyph transcript
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Summary
Bio::Graphics::Glyph::transcript - The "transcript" glyph
Package variables
No package variables defined.
Included modules
Bio::Graphics::Glyph::segments
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
arrow_length
No description
Code
connector
No description
Code
draw_component
No description
Code
draw_connectors
No description
Code
pad_left
No description
Code
pad_right
No description
Code
Methods description
None available.
Methods code
arrow_lengthdescriptionprevnextTop
sub arrow_length {
  my $self = shift;
  return $self->option('arrow_length') || 8;
}

# override option() for force the "hat" type of connector
}
connectordescriptionprevnextTop
sub connector {
  my $self = shift;
  return $self->SUPER::connector(@_) if $self->all_callbacks;
  return ($self->option('connector') || 'hat');
}


1;

__END__
}
draw_componentdescriptionprevnextTop
sub draw_component {
  my $self = shift;
  return unless $self->level > 0;
  $self->SUPER::draw_component(@_);
}
draw_connectorsdescriptionprevnextTop
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; } # flip argument makes this confusing
# certainly there's a simpler way to express this idea
my $strand = $self->feature->strand; my ($first,$last) = ($parts[0],$parts[-1]); ($first,$last) = ($last,$first) if exists $self->{flip}; if ($strand >= 0) { my($x1,$y1,$x2,$y2) = $last->bounds(@_); my $center = ($y2+$y1)/2;
$self->{flip} ? $self->arrow($gd,$x1,$x1-$self->arrow_length,$center) : $self->arrow($gd,$x2,$x2+$self->arrow_length,$center); } else { my($x1,$y1,$x2,$y2) = $first->bounds(@_); my $center = ($y2+$y1)/2;
$self->{flip } ? $self->arrow($gd,$x2,$x2+$self->arrow_length,$center) : $self->arrow($gd,$x1,$x1 - $self->arrow_length,$center); }
}
pad_leftdescriptionprevnextTop
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;
}
pad_rightdescriptionprevnextTop
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;
}
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.