Bio::Graphics::Glyph::primers - The "STS primers" glyph

Bio-Graphics documentation Contained in the Bio-Graphics distribution.

Index

Code Index:

NAME

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Bio::Graphics::Glyph::primers - The "STS primers" glyph

SYNOPSIS

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  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

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This glyph draws two arrows oriented towards each other and connected by a line of a contrasting color. The length of the arrows is immaterial, but the length of the glyph itself corresponds to the length of the scaled feature.

OPTIONS

In addition to the common options, the following glyph-specific options are recognized:

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

  -connect    Whether to connect the      true
              two arrowheads by a line.

  -connect_color  The color to use for the    bgcolor
              connecting line.

BUGS

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Please report them.

SEE ALSO

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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

AUTHOR

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Allen Day <day@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.

Bio-Graphics documentation Contained in the Bio-Graphics distribution. 
package Bio::Graphics::Glyph::primers;
#$Id: primers.pm,v 1.1 2008-12-08 23:18:43 lstein Exp $
# package to use for drawing something that looks like
# primer pairs.

use strict;
use base qw(Bio::Graphics::Glyph::generic);

use constant HEIGHT => 8;

# override draw method
sub draw_component {
  my $self = shift;
  my $gd = shift;
  my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
  my $height = $self->option('height') || $self->option('size') || HEIGHT;

  my $fg = $self->fgcolor;
  my $a2 = $height/2;
  my $center = $y1 + $a2;


  # just draw us as a solid line -- very simple
  if ($x2-$x1 < $height*2) {
    $gd->line($x1,$center,$x2,$center,$fg);
    return;
  }

  # otherwise draw two pairs of arrows
  # -->   <--
  my $trunc_left  = $x1 < $self->panel->left;
  my $trunc_right = $x2 > $self->panel->right;

  unless ($trunc_left) { 
    $gd->setThickness(2) if $height > 6;
    $gd->line($x1,$center,$x1 + $height,$center,$fg);
    $gd->line($x1 + $height,$center,$x1 + $height - $a2,$center-$a2,$fg);
    $gd->line($x1 + $height,$center,$x1 + $height - $a2,$center+$a2,$fg);
    $gd->setThickness(1);
  }

  unless ($trunc_right) {
    $gd->setThickness(2) if $height > 6;
    $gd->line($x2,$center,$x2 - $height,$center,$fg);
    $gd->line($x2 - $height,$center,$x2 - $height + $a2,$center+$a2,$fg);
    $gd->line($x2 - $height,$center,$x2 - $height + $a2,$center-$a2,$fg);
    $gd->setThickness(1);
  }

  # connect the dots if requested
  if ($self->connect) {
    my $c = $self->color('connect_color') || $self->bgcolor;
    $gd->line($x1 + ($trunc_left  ? 0 : $height + 2),$center,
	      $x2 - ($trunc_right ? 0 : $height + 2),$center,
	      $c);
  }

  # add a label if requested
  $self->draw_label($gd,@_)       if $self->option('label');
  $self->draw_description($gd,@_) if $self->option('description');

}

sub connect {
  my $self = shift;
  return $self->option('connect') if defined $self->option('connect');
  1;  # default
}

1;

__END__