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

In addition, the alignment glyph recognizes the following
glyph-specific options:

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

  -max_score  Maximum value of the	   Calculated
              feature's "score" attribute

  -min_score  Minimum value of the         Calculated
              feature's "score" attribute

If max_score and min_score are not specified, then the glyph will
calculate the local maximum and minimum scores at run time.

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 $self->all_callbacks || !$self->is_recursive;
  return unless $self->subseq($self->feature);
  return $self->SUPER::label(@_);

}

sub description {

  my $self = shift;
  return $self->SUPER::description(@_) if $self->all_callbacks || !$self->is_recursive;
  return unless $self->subseq($self->feature);
  return $self->SUPER::description(@_);

}

General documentation

Please report them.

Bio::Graphics::Panel,
Bio::Graphics::Track,
Bio::Graphics::Glyph::anchored_arrow,
Bio::Graphics::Glyph::arrow,
Bio::Graphics::Glyph::box,
Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2,

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.