Bio::Graphics::Glyph::pinsertion - The "Drosophila P-element Insertion" glyph

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

Index

Code Index:

NAME

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Bio::Graphics::Glyph::pinsertion - The "Drosophila P-element Insertion" glyph

SYNOPSIS

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

DESCRIPTION

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This glyph was designed to show P-element insertions in the Drosophila genome, but in fact is suitable for any type of zero-width feature. Also see the triangle glyph.

OPTIONS

In addition to the generic options, this glyph recognizes:

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

 -insertion_width  Width of glyph in pixels    3

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>, Shengqiang Shu <sshu@bdgp.lbl.gov>

Copyright (c) 2001 Cold Spring Harbor Laboratory, BDGP

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::pinsertion;
# package to use for drawing P insertion as a triangle
# p insertion is a point (one base).

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

sub box {
  my $self = shift;
  my $half = $self->insertion_width/2;
  return ($self->left-$half,$self->top,$self->right+$half,$self->bottom);
}

sub insertion_width {
  my $self = shift;
  return $self->option('insertion_width') || 6;
}

# override draw method
sub draw {
  my $self = shift;

  my $gd = shift;
  my ($left,$top) = @_;

  my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);

  my $height = $self->height;

  my $half = $self->insertion_width/2;
  my $fill = $self->bgcolor;
  my $border = $self->fgcolor;

  my $poly_pkg = $self->polygon_package;
  my $poly     = $poly_pkg->new();
  if ($self->feature->strand > 0) { #plus strand
      $poly->addPt($x1 - $half, $y1);
      $poly->addPt($x1 + ($half), $y1);
      $poly->addPt($x1, $y2); #pointer down
  } else {
      $poly->addPt($x1, $y1); #pointer up
      $poly->addPt($x1 - $half, $y2);
      $poly->addPt($x1 + ($half), $y2);
  }
  $gd->filledPolygon($poly,$fill);
  $gd->polygon($poly,$border);

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


1;