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      $v_range = 0;
      $v_start = 255;
    }
    elsif ( $start_color eq 'white' ) { # end black
      $s_range = 0;
      $s_start = 0;
      $v_range = -255;
      $v_start = 255;
    }
    elsif ( $stop_color eq 'white' ) { # start black
      $s_range = 0;
      $s_start = 0;
      $v_range = 255;
      $v_start = 0;
    }
    elsif ( _isa_color($start_color) ) { # end black
      $s_range = 255;
      $s_start = 0;
      $v_range = 255;
      $v_start = 0;
    }
    elsif ( _isa_color($stop_color) ) { # start black
      $s_range = -255;
      $s_start = 255;
      $v_range = -255;
      $v_start = 255;
    }

  }

  # store gradient info
  $self->h_range($h_range);
  $self->h_start($h_start);
  $self->s_start($s_start);
  $self->v_start($v_start);
  $self->s_range($s_range);
  $self->v_range($v_range);

  # store score info
  $self->peak_score_range($max - $min);
  $self->min_peak_score($min);
  $self->max_peak_score($max);

  # store color extremes
  my @low_rgb  = $self->HSVtoRGB(@$hsv_start);
  my @high_rgb = $self->HSVtoRGB(@$hsv_stop);
  $self->low_hsv($hsv_start);
  $self->high_rgb(\@high_rgb);
  $self->low_rgb(\@low_rgb);
  return 1;
}


sub _isa_color {
  my $color = shift;
  return $color =~ /white|black|FFFFFF|000000/i ? 0 : 1;
}

sub level { -1 }

# Need to override this so we have a nice image map for overlayed peaks
sub boxes {
    my $self = shift;
    my($left,$top,$parent) = @_;

    return if $self->glyph_subtype eq 'density'; # No boxes for density plot
    my @boxes = $self->SUPER::boxes(@_);
    
    if (my $rects = $self->{peak_cache}) {
	push @boxes,[@$_,$parent] foreach @$rects;
    }
    return wantarray ? @boxes : \@boxes;
}


# Modified and fused functions from wiggle_density.pm and wiggle_xyplot.pm
sub _draw_wigfile {
    my $self = shift;
    my $feature = shift;
    my $wig     = shift;

    $wig->smoothing($self->get_smoothing);
    $wig->window($self->smooth_window);

    my ($gd,$left,$top) = @_;
    my ($start,$end) = $self->effective_bounds($feature); 

    if ($self->glyph_subtype eq 'density') {
     my ($x1,$y1,$x2,$y2) = $self->bounds($left,$top);
     $self->draw_segment($gd,
                         $start,$end,
                         $wig,$start,$end,
                         1,1,
                         $x1,$y1,$x2,$y2);
     $self->Bio::Graphics::Glyph::xyplot::draw_label(@_)       if $self->option('label');
     $self->draw_description(@_) if $self->option('description');
    } else {
     my ($start,$end) = $self->effective_bounds($feature);
     $self->wig($wig);
     my $parts = $self->create_parts_for_dense_feature($wig,$start,$end);
     $self->draw_plot($parts,@_);
    }
}

sub peaks {
    my $self = shift;
    return @{$self->{_peaks}} if $self->{_peaks};

    my $feature = $self->feature;
    my $db = $feature->object_store;
    my ($p_type) = eval{$feature->get_tag_values('peak_type')};

    unless ($db && $p_type) {
	$self->{_peaks}	 = [];
	return;
    }

    my @peaks = $db->features(-seq_id => $feature->segment->ref,
			      -start  => $self->panel->start,
			      -end    => $self->panel->end,
			      -type   => $p_type); 

    $self->{_peaks} = \@peaks;
    return @{$self->{_peaks}};
}

1;

=head1 NAME

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

=head1 SYNOPSIS

See 
L<Bio::Graphics::Glyph>, L<Bio::Graphics::Glyph::wiggle_xyplot> and L<Bio::Graphics::Glyph::heat_map>.

=head1 DESCRIPTION

This glyph draws peak calls (features with discreet boundaries,
i.e. putative transcription sites, over signal graph (wiggle_xyplot)
requires a special load gff file that uses attributes 'wigfile' and 'peak_type'

B<Example:>

2L  chip_seq  vista  5407   23011573  .  .  .  Name=ChipSeq Exp 1;wigfile=SomeWigFile.wigdb;peak_type=binding_site:exp1

The glyph will draw the wiggle file first, than overlay the peaks (if there are any)
over signal graph. Elsewhere in the GFF3 file, there should be one or more features 
of type "binding_site:exp1", e.g.:

2L  exp1  binding_site  91934  92005  .  .  .

Options like 'balloon hover' and 'link' are available to customize
interaction with peaks in detail view.

B<BigWig support:>

Supported bigwig format also requires another attribute to be supplied
in load gff file (fasta) which specifies sequence index file for the
organism in use. The data file should have the 'bw' extension - it is
used to detect the BigWig format by vista_plot

3L  chip_seq  vista   1    24543530  .  .  .   Name=ChipSeq Exp 2;wigfile=SomeBigWigFile.bw;peak_type=binding_site:exp2;fasta=YourOrganism.fasta

Note that all attributes should be present in load gff, as the code currently does not handle situation when
only some of the attributes are in gff. To omit peak or signal drawing use "" (i.e. peak_type="")
In both cases, the stanza code will look the same (only essential parameters shown):

 [VISTA_PLOT]
 feature         = vista:chip_seq
 glyph           = vista_plot
 label           = 1 
 smoothing       = mean
 smoothing_window = 10
 bump density    = 250
 autoscale       = local
 variance_band   = 1
 max_peak        = 255
 min_peak        = 1
 peakwidth       = 3
 start_color     = lightgray
 end_color       = black
 pos_color       = blue
 neg_color       = orange
 bgcolor         = orange
 alpha           = 80
 fgcolor         = black
 database        = database_with_load_gff_data
 box_subparts    = 1
 bicolor_pivot   = min
 key             = VISTA plot 

=head1 OPTIONS

Options are the same as for wiggle_xyplot and heat_map

B<Additional parameters:>

B<alpha>
set transparency for peak area.

B<glyph_subtype>
Display only 'peaks', 'signal', 'density' or 'peaks+signal'. 
Aliases for 'peaks+signal' include "both" and "vista".

B<Recommended global settings:>