Summary

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

Package variables

Included modules

Inherit

Bio::Graphics::Glyph::segmented_keyglyph

Synopsis

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

Description

This glyph is used for drawing features that consist of discontinuous
segments. Unlike "graded_segments" or "alignment", the segments are a
uniform color and not dependent on the score of the segment. 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

Methods

Methods description

None available.

Methods code

sub connector {

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

}

sub bump {

  my $self = shift;
  return $self->SUPER::bump(@_) if $self->all_callbacks;
  return 0;

}

sub label {

  my $self = shift;
  return $self->SUPER::label(@_) if $self->all_callbacks;
  return unless $self->{level} == 0;
  return $self->SUPER::label(@_);

}

sub description {

  my $self = shift;
  return $self->SUPER::description(@_) if $self->all_callbacks;
  return unless $self->{level} == 0;
  return $self->SUPER::description(@_);

}

sub _subseq {

  my $self    = shift;
  my $feature = shift;
  my @subseq  = $self->SUPER::_subseq($feature);
  return @subseq if @subseq;
  if ($self->level == 0 && !@subseq && !eval{$feature->compound}) {
    my($start,$end) = ($feature->start,$feature->end);
    ($start,$end) = ($end,$start) if $start > $end; # to keep Bio::Location::Simple from bitching
    return Bio::Location::Simple->new(-start=>$start,-end=>$end);
  } else {
    return;
  }

}

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.