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Summary

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

Package variables

Included modules

Inherit

Bio::Graphics::Glyph::segments

Synopsis

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

Description

This is identical to the "alignment" glyph, and is used for
drawing features that consist of discontinuous segments. The
color intensity of each segment is proportionate to the score. 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
  ------      -----------                  -------

  -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 bgcolor {

   my $self = shift;
  return $self->{partcolor} || $self->SUPER::bgcolor;

}

sub calculate_color {

  my $self = shift;
  my ($s,$rgb,$min_score,$span) = @_;
  return map { 255 - (255-$_) * min(max( ($s-$min_score)/$span, 0), 1) } @$rgb;

}

sub draw {

  my $self = shift;

  # bail out if this isn't the right kind of feature
  # handle both das-style and Bio::SeqFeatureI style,
  # which use different names for subparts.
  my @parts = $self->parts;
  @parts    = $self if !@parts && $self->level == 0;
  return $self->SUPER::draw(@_) unless @parts;

  # figure out the colors
  my $max_score = $self->option('max_score');
  my $min_score = $self->option('min_score');
  unless (defined $max_score && defined $min_score) {
    for my $part (@parts) {
      my $s = eval { $part->feature->score };
      next unless defined $s;
      $max_score = $s if !defined $max_score or $s > $max_score;
      $min_score = $s if !defined $min_score or $s < $min_score;
    }
  }

  return $self->SUPER::draw(@_)
    unless defined($max_score) && defined($min_score)
      && $min_score < $max_score;

  my $span = $max_score - $min_score;

  # allocate colors
  my $fill   = $self->bgcolor;
  my ($red,$green,$blue) = $self->panel->rgb($fill);

  foreach my $part (@parts) {
    my $s = eval { $part->feature->score };
    unless (defined $s) {
      $part->{partcolor} = $fill;
      next;
    }
    my ($r,$g,$b) = $self->calculate_color($s,[$red,$green,$blue],$min_score,$span);
    my $idx      = $self->panel->translate_color($r,$g,$b);
    $part->{partcolor} = $idx;
  }
  $self->SUPER::draw(@_);

}

sub fgcolor {

   my $self = shift;
  return $self->{partcolor} || $self->SUPER::fgcolor;
}

1;

}

sub keyglyph {

  my $self = shift;

  my $scale = 1/$self->scale;  # base pairs/pixel

  # two segments, at pixels 0->50, 60->80
  my $offset = $self->panel->offset;

  my $feature =
    Bio::Graphics::Feature->new(
				-segments=>[ [ 0*$scale +$offset,20*$scale+$offset],
					     [ 30*$scale +$offset,50*$scale+$offset],
					     [60*$scale+$offset, 80*$scale+$offset]
					   ],
				-name => $self->option('key'),
				-strand => '+1');
  ($feature->segments)[0]->score(10);
  ($feature->segments)[1]->score(50);
  ($feature->segments)[2]->score(100);
  my $factory = $self->factory->clone;
  $factory->set_option(label => 1);
  $factory->set_option(bump  => 0);
  $factory->set_option(connector  => 'solid');
  return $factory->make_glyph($feature);
}

# component draws a shaded box

}

sub max {

 $_[0] > $_[1] ? $_[0] : $_[1]

}

sub subseq {

  my $class = shift;
  my $feature = shift;
  return $feature->segments        if $feature->can('segments');
  return $feature->sub_SeqFeature  if $feature->can('sub_SeqFeature');
  return;
}

# synthesize a key glyph

}

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.