Summary

Bio::Graphics::Glyph - Base class for Bio::Graphics::Glyph objects

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

See Bio::Graphics::Panel.

Description

Bio::Graphics::Glyph is the base class for all glyph objects. Each
glyph is a wrapper around an Bio:SeqFeatureI object, knows how to
render itself on an Bio::Graphics::Panel, and has a variety of
configuration variables.
End developers will not ordinarily work directly with
Bio::Graphics::Glyph objects, but with Bio::Graphics::Glyph::generic
and its subclasses. Similarly, most glyph developers will want to
subclass from Bio::Graphics::Glyph::generic because the latter
provides labeling and arrow-drawing facilities.

Methods

Methods description

None available.

Methods code

sub new {

  my $class = shift;
  my %arg = @_;

  my $feature = $arg{-feature} or $class->throw("No feature $class");
  my $factory = $arg{-factory} || $class->default_factory;
  my $level   = $arg{-level} || 0;
  my $flip    = $arg{-flip};

  my $self = bless {},$class;
  $self->{feature} = $feature;
  $self->{factory} = $factory;
  $self->{level}   = $level;
  $self->{flip}++  if $flip;
  $self->{top} = 0;

  my $panel = $factory->panel;
  my $p_start = $panel->start;
  my $p_end   = $panel->end;

  my @subfeatures;
  my @subglyphs;

  warn $self if DEBUG;
  warn $feature if DEBUG;

  @subfeatures         = $self->subfeat($feature);

  if ($self->option('ignore_sub_part')) {
    my @tmparray;
    foreach (@subfeatures) {
      my $type = $_->method;

      my @ignore_list = split /\s+/, $self->option('ignore_sub_part');
      my $ignore_str  = join('|', @ignore_list);

      unless ($type =~ /$ignore_str/) {
        push @tmparray, $_;
      }
    }
    @subfeatures = @tmparray;
  }

  my @visible_subfeatures = grep {$p_start <= $_->end && $p_end >= $_->start} @subfeatures;

  $self->feature_has_subparts(@subfeatures>0);

  if (@visible_subfeatures) {
    # dynamic glyph resolution
    @subglyphs = map { $_->[0] }
          sort { $a->[1] <=> $b->[1] }
	    map { [$_, $_->left ] }
	      $factory->make_glyph($level+1,@visible_subfeatures);
    $self->{parts}   =\@ subglyphs;
  }

  my ($start,$stop) = ($self->start, $self->stop);
  if (defined $start && defined $stop && $start ne '') {  # more paranoia
    ($start,$stop) = ($stop,$start) if $start > $stop;  # sheer paranoia
    # the +1 here is critical for allowing features to meet nicely at nucleotide resolution
    my ($left,$right) = $factory->map_pt($start,$stop+1);
    $self->{left}    = $left;
    $self->{width}   = $right - $left + 1;
  }

  if (@subglyphs) {
      my $l            = $subglyphs[0]->left;
      # this clashes with the pad_left calculation and is unecessary
      # $self->{left}    = $l if !defined($self->{left}) || $l < $self->{left};
      my $right        = (
			  sort { $b<=>$a } 
			  map {$_->right} @subglyphs)[0];
      my $w            = $right - $self->{left} + 1;
      # this clashes with the pad_right calculation and is unecessary
      # $self->{width}   = $w if !defined($self->{width}) || $w > $self->{width};
  }

  $self->{point} = $arg{-point} ? $self->height : undef;

  return $self;

}

sub parts {

  my $self = shift;
  return unless $self->{parts};
  return wantarray ? @{$self->{parts}} : $self->{parts};

}

sub feature_has_subparts {

  my $self = shift;

  return $self->{feature_has_subparts} = shift if @_;
  return 0 if $self->maxdepth == 0;
  my $feature = $self->feature;
  return 1 if $feature->can('compound') && $feature->compound;
  return $self->{feature_has_subparts};

}

sub feature {

 shift->{feature}

}

sub factory {

 shift->{factory}

}

sub panel {

 shift->factory->panel

}

sub point {

 shift->{point}

}

sub scale {

 shift->factory->scale

}

sub flip {

  my $self      = shift;
  my $d         = $self->{flip};
  $self->{flip} = shift if @_;
  $d;

}

sub start {

  my $self = shift;
  return $self->{start} if exists $self->{start};
  if ($self->{flip}) {
    $self->{start} = defined $self->{feature}->end
                     ? $self->panel->end + 1 - $self->{feature}->end
                     : 0;
  } else {
    $self->{start} = defined $self->{feature}->start
                     ? $self->{feature}->start
		     : $self->panel->offset - 1
  }

  return $self->{start};

}

sub stop {

  my $self = shift;
  return $self->{stop} if exists $self->{stop};
  if ($self->{flip}) {
    $self->{stop} = defined $self->{feature}->start 
      ? $self->panel->end + 1 - $self->{feature}->start
      : $self->panel->offset - 1;
  } else {
    $self->{stop} = defined $self->{feature}->end
      ?  $self->{feature}->end
      : $self->panel->offset+$self->panel->length+1;
  }

  return $self->{stop}

}

sub end {

 shift->stop

}

sub length {

 my $self = shift; $self->stop - $self->start };

}

sub score {

    my $self = shift;
    return $self->{score} if exists $self->{score};
    return $self->{score} = ($self->{feature}->score || 0);

}

sub strand {

    my $self = shift;
    return $self->{strand} if exists $self->{strand};
    return $self->{strand} = ($self->{feature}->strand || 0);

}

sub map_pt {

 shift->{factory}->map_pt(@_)

}

sub map_no_trunc {

 shift->{factory}->map_no_trunc(@_)

}

sub add_feature {

  my $self       = shift;
  my $factory    = $self->factory;

  for my $feature (@_) {
    if (ref $feature eq 'ARRAY') {
      $self->add_group(@$feature);
    } else {
      warn $factory if DEBUG;
      push @{$self->{parts}},$factory->make_glyph(0,$feature);
    }
  }

}

sub add_group {

  my $self = shift;
  my @features = ref($_[0]) eq 'ARRAY' ? @{$_[0]} : @_;
  my $f    = Bio::Graphics::Feature->new(
					 -segments=>\@features,
					 -type => 'group',
					);
  $self->add_feature($f);
  $f;

}

sub top {

  my $self = shift;
  my $g = $self->{top};
  $self->{top} = shift if @_;
  $g;

}

sub left {

  my $self = shift;
  return $self->{left} - $self->pad_left;

}

sub right {

  my $self = shift;
  return $self->left + $self->layout_width - 1;

}

sub bottom {

  my $self = shift;
  $self->top + $self->layout_height - 1;

}

sub height {

  my $self = shift;
  return $self->{height} if exists $self->{height};
  my $baseheight = $self->option('height');  # what the factory says
  return $self->{height} = $baseheight;

}

sub width {

  my $self = shift;
  my $g = $self->{width};
  $self->{width} = shift if @_;
  $g;

}

sub layout_height {

  my $self = shift;
  return $self->layout;

}

sub layout_width {

  my $self = shift;
  return $self->width + $self->pad_left + $self->pad_right;

}

sub calculate_boundaries {

return shift->bounds(@_);

}

sub bounds {

  my $self = shift;
  my ($dx,$dy) = @_;
  $dx += 0; $dy += 0;
  ($dx + $self->{left},
   $dy + $self->top    + $self->pad_top,
   $dx + $self->{left} + $self->{width} - 1,
   $dy + $self->bottom - $self->pad_bottom);

}

sub box {

  my $self = shift;
  my @result = ($self->left,$self->top,$self->right,$self->bottom);
  return @result;

}

sub unfilled_box {

  my $self = shift;
  my $gd   = shift;
  my ($x1,$y1,$x2,$y2,$fg,$bg,$lw) = @_;
  $lw = $self->linewidth;

  unless ($fg) {
      $fg ||= $self->fgcolor;
  $fg = $self->set_pen($lw,$fg) if $lw > 1;
  }

  unless ($bg) {
      $bg ||= $self->bgcolor;
      $bg = $self->set_pen($lw,$bg) if $lw > 1;
  }

  # draw a box
  $gd->rectangle($x1,$y1,$x2,$y2,$fg);

  # if the left end is off the end, then cover over
  # the leftmost line
  my ($width) = $gd->getBounds;

  $gd->line($x1,$y1+$lw,$x1,$y2-$lw,$bg)
    if $x1 < $self->panel->pad_left;

  $gd->line($x2,$y1+$lw,$x2,$y2-$lw,$bg)
    if $x2 > $width - $self->panel->pad_right;

}

sub boxes {

  my $self = shift;

  my ($left,$top,$parent) = @_;
  $top  += 0; $left += 0;
  my @result;

  $self->layout;
  $parent         ||= $self;
  my $subparts = $self->box_subparts || 0;

  for my $part ($self->parts) {
    my $type = $part->feature->primary_tag || '';
    if ($type eq 'group' or $subparts > $part->level) {
      push @result,$part->boxes($left,$top+$self->top+$self->pad_top,$parent);
      next if $type eq 'group';
    }
    my ($x1,$y1,$x2,$y2) = $part->box;
    $x2++ if $x1==$x2;
    push @result,[$part->feature,
		  $left + $x1,$top+$self->top+$self->pad_top+$y1,
		  $left + $x2,$top+$self->top+$self->pad_top+$y2,
		  $parent];
  }

  return wantarray ? @result :\@ result;

}

sub box_subparts {

  my $self = shift;
  return $self->{box_subparts} if exists $self->{box_subparts};
  return $self->{box_subparts} = $self->_box_subparts;

}

sub _box_subparts {

 shift->option('box_subparts')

}

sub pad_top {

  my $self = shift;
  return 0;

}

sub pad_bottom {

  my $self = shift;
  return 0;

}

sub pad_left {

  my $self = shift;
  my @parts = $self->parts or return 0;
  my $max = 0;
  foreach (@parts) {
    my $pl = $_->pad_left;
    $max = $pl if $max < $pl;
  }
  $max;

}

sub pad_right {

  my $self = shift;
  my @parts = $self->parts or return 0;
  my $max = 0;
  foreach (@parts) {
    my $pr = $_->pad_right;
    $max = $pr if $max < $pr;
  }
  $max;

}

sub move {

  my $self = shift;
  my ($dx,$dy) = @_;
  $self->{left} += $dx;
  $self->{top}  += $dy;

  # because the feature parts use *absolute* not relative addressing
  # we need to move each of the parts horizontally, but not vertically
  $_->move($dx,0) foreach $self->parts;

}

sub option {

  my $self = shift;
  my $option_name = shift;
  my @args = ($option_name,@{$self}{qw(partno total_parts)});
  my $factory = $self->{factory} or return;
  return $factory->option($self,@args)

}

sub code_option {

  my $self = shift;
  my $option_name = shift;
  my $factory = $self->factory or return;
  $factory->get_option($option_name);

}

sub configure {

  my $self = shift;
  my $factory = $self->factory;
  my $option_map = $factory->option_map;
  while (@_) {
    my $option_name  = shift;
    my $option_value = shift;
    ($option_name = lc $option_name) =~ s/^-//;
    $option_map->{$option_name} = $option_value;
  }

}

sub color {

  my $self = shift;
  my $color = shift;
  my $index = $self->option($color);
  # turn into a color index
  return $self->factory->translate_color($index) if defined $index;
  return 0;

}

sub connector {

  return shift->option('connector',@_);

}

sub bump {

  my $self = shift;
  return $self->option('bump');

}

sub hbumppad {

  my $self = shift;
  return $self->{_hbumppad} if exists $self->{_hbumppad};
  return $self->{_hbumppad}= $self->option('hbumppad');

}

sub fgcolor {

  my $self  = shift;
  my $index   = $self->option('color') || $self->option('fgcolor');
  $index = 'black' unless defined $index;
  $self->factory->translate_color($index);

}

sub fillcolor {

    my $self = shift;
    return $self->bgcolor;

}

sub bgcolor {

  my $self = shift;
  my $bgcolor = $self->option('bgcolor');
  my $index = defined $bgcolor ? $bgcolor : $self->option('fillcolor');
  $index = 'white' unless defined $index;
  $self->factory->translate_color($index);

}

sub getfont {

  my $self    = shift;
  my $option  = shift || 'font';
  my $default = shift;

  my $font = $self->option($option) || $default;
  return unless $font;

  my $img_class = $self->image_class;

  unless (UNIVERSAL::isa($font,$img_class . '::Font')) {
    my $ref    = {
		  gdTinyFont       => $img_class->gdTinyFont(),
		  gdSmallFont      => $img_class->gdSmallFont(),
		  gdMediumBoldFont => $img_class->gdMediumBoldFont(),
		  gdLargeFont      => $img_class->gdLargeFont(),
		  gdGiantFont      => $img_class->gdGiantFont(),
    		 };

    my $gdfont = $ref->{$font};
    $self->configure($option => $gdfont);
    return $gdfont;
  }
  return $font;

}

sub font {

  my $self = shift;
  return $self->getfont('font','gdSmallFont');

}

sub fontcolor {

  my $self = shift;
  my $fontcolor = $self->color('fontcolor');
  return defined $fontcolor ? $fontcolor : $self->fgcolor;

}

sub font2color {

  my $self = shift;
  my $font2color = $self->color('font2color');
  return defined $font2color ? $font2color : $self->fgcolor;

}

sub tkcolor {

 # "track color"  my $self = shift;
  $self->option('tkcolor') or return;
  return $self->color('tkcolor')

}

sub connector_color {

  my $self = shift;
  $self->color('connector_color') || $self->fgcolor;

}

sub image_class {

 shift->{factory}->{panel}->{image_class};

}

sub polygon_package {

 shift->{factory}->{panel}->{polygon_package};

}

sub layout_sort {

    my $self = shift;
    my $sortfunc;

    my $opt = $self->code_option("sort_order");

    if (!$opt) {
       $sortfunc = sub { $a->left <=> $b->left };
    } elsif (ref $opt eq 'CODE') {
      $self->throw('sort_order subroutines must use the $$ prototype') unless prototype($opt) eq '$$';
      $sortfunc = $opt;
    } elsif ($opt =~ /^sub\s+\{/o) {
       $sortfunc = eval $opt;
    } else {
       # build $sortfunc for ourselves:
       my @sortbys = split(/\s*\|\s*/o, $opt);
       $sortfunc = 'sub { ';
       my $sawleft = 0;

       # not sure I can make this schwartzian transformed
       for my $sortby (@sortbys) {
	 if ($sortby eq "left" || $sortby eq "default") {
	   $sortfunc .= '($a->left <=> $b->left) || ';
	   $sawleft++;
	 } elsif ($sortby eq "right") {
	   $sortfunc .= '($a->right <=> $b->right) || ';
	 } elsif ($sortby eq "low_score") {
	   $sortfunc .= '($a->score <=> $b->score) || ';
	 } elsif ($sortby eq "high_score") {
	   $sortfunc .= '($b->score <=> $a->score) || ';
	 } elsif ($sortby eq "longest") {
	   $sortfunc .= '(($b->length) <=> ($a->length)) || ';
	 } elsif ($sortby eq "shortest") {
	   $sortfunc .= '(($a->length) <=> ($b->length)) || ';
	 } elsif ($sortby eq "strand") {
	   $sortfunc .= '($b->strand <=> $a->strand) || ';
	 } elsif ($sortby eq "name") {
	   $sortfunc .= '($a->feature->display_name cmp $b->feature->display_name) || ';
	 }
       }
       unless ($sawleft) {
           $sortfunc .= ' ($a->left <=> $b->left) ';
       } else {
           $sortfunc .= ' 0';
       }
       $sortfunc .= '}';
       $sortfunc = eval $sortfunc;
    }

    # cache this
    # $self->factory->set_option(sort_order => $sortfunc);

    my @things = sort $sortfunc @_;
    return @things;

}

sub layout {

  my $self = shift;
  return $self->{layout_height} if exists $self->{layout_height};

  my @parts = $self->parts;
  return $self->{layout_height} = $self->height + $self->pad_top + $self->pad_bottom unless @parts;

  my $bump_direction = $self->bump;
  my $bump_limit = $self->option('bump_limit') || -1;

  $_->layout foreach @parts;  # recursively lay out

  # no bumping requested, or only one part here
  if (@parts == 1 || !$bump_direction) {
    my $highest = 0;
    foreach (@parts) {
      my $height = $_->layout_height;
      $highest   = $height > $highest ? $height : $highest;
    }
    return $self->{layout_height} = $highest + $self->pad_top + $self->pad_bottom;
  }

  my (%bin1,%bin2);
  my $limit = 0;

  for my $g ($self->layout_sort(@parts)) {

    my $height = $g->{layout_height};

    # Simple +/- 2 bumping.  Every feature gets its very own line
    if (abs($bump_direction) >= 2) {
      $g->move(0,$limit);
      $limit += $height + BUMP_SPACING if $bump_direction > 0;
      $limit -= $height + BUMP_SPACING if $bump_direction < 0;
      next;
    }

    # we get here for +/- 1 bumping
    my $pos = 0;
    my $bumplevel = 0;
    my $left   = $g->left;
    my $right  = $g->right;

    while (1) {

      # stop bumping if we've gone too far down
      if ($bump_limit > 0 && $bumplevel++ >= $bump_limit) {
	$g->{overbumped}++;  # this flag can be used to suppress label and description
	foreach ($g->parts) {
	  $_->{overbumped}++;
	}
	last;
      }

      # look for collisions
      my $bottom = $pos + $height;
      $self->collides(\%bin1,CM1,CM2,$left,$pos,$right,$bottom) or last;
      my $collision = $self->collides(\%bin2,CM3,CM4,$left,$pos,$right,$bottom) or last;

      if ($bump_direction > 0) {
	$pos += $collision->[3]-$collision->[1] + BUMP_SPACING;    # collision, so bump
      } else {
	$pos -= BUMP_SPACING;
      }

      $pos++ if $pos % 2; # correct for GD rounding errors
    }

    $g->move(0,$pos);
    $self->add_collision(\%bin1,CM1,CM2,$left,$g->top,$right,$g->bottom);
    $self->add_collision(\%bin2,CM3,CM4,$left,$g->top,$right,$g->bottom);
  }

  # If -1 bumping was allowed, then normalize so that the top glyph is at zero
  if ($bump_direction < 0) {
    my $topmost;
    foreach (@parts) {
      my $top  = $_->top;
      $topmost = $top if !defined($topmost) or $top < $topmost;
    }
    my $offset = - $topmost;
    $_->move(0,$offset) foreach @parts;
  }

  # find new height
  my $bottom = 0;
  foreach (@parts) {
    $bottom = $_->bottom if $_->bottom > $bottom;
  }
  # return $self->{layout_height} = $self->pad_bottom + $self->pad_top + $bottom - $self->top  + 1;
  return $self->{layout_height} = $bottom + $self->pad_top + $self->pad_bottom;

}

sub collides {

  my $self = shift;
  my ($occupied,$cm1,$cm2,$left,$top,$right,$bottom) = @_;
  my @keys = $self->_collision_keys($cm1,$cm2,$left,$top,$right,$bottom);
  my $hspacing = $self->hbumppad || 0;
  my $collides = 0;
  for my $k (@keys) {
    next unless exists $occupied->{$k};
    for my $bounds (@{$occupied->{$k}}) {
      my ($l,$t,$r,$b) = @$bounds;
      next unless $right+$hspacing >= $l and $left-$hspacing <= $r 
	and $bottom >= $t and $top <= $b;
      $collides = $bounds;
      last;
    }
  }
  $collides;

}

sub add_collision {

  my $self = shift;
  my ($occupied,$cm1,$cm2,$left,$top,$right,$bottom) = @_;
  my $value = [$left,$top,$right+2,$bottom];
  my @keys = $self->_collision_keys($cm1,$cm2,@$value);
  push @{$occupied->{$_}},$value foreach @keys;

}

sub _collision_keys {

  my $self = shift;
  my ($binx,$biny,$left,$top,$right,$bottom) = @_;
  my @keys;
  my $bin_left   = int($left/$binx);
  my $bin_right  = int($right/$binx);
  my $bin_top    = int($top/$biny);
  my $bin_bottom = int($bottom/$biny);
  for (my $x=$bin_left;$x<=$bin_right; $x++) {
    for (my $y=$bin_top;$y<=$bin_bottom; $y++) {
      push @keys,join(',',$x,$y);
    }
  }
  @keys;

}

sub draw {

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

  my $connector = $self->connector;

  if (my @parts = $self->parts) {

    # invoke sorter if user wants to sort always and we haven't already sorted
    # during bumping.
    @parts = $self->layout_sort(@parts) if !$self->bump && $self->option('always_sort');

    my $x = $left;
    my $y = $top  + $self->top + $self->pad_top;

    $self->draw_connectors($gd,$x,$y) if $connector && $connector ne 'none';

    my $last_x;
    for (my $i=0; $i<@parts; $i++) {
      # lie just a little bit to avoid lines overlapping and make the picture prettier
      my $fake_x = $x;
      $fake_x-- if defined $last_x && $parts[$i]->left - $last_x == 1;
      $parts[$i]->draw($gd,$fake_x,$y,$i,scalar(@parts));
      $last_x = $parts[$i]->right;
    }
  }

  else {  # no part
    $self->draw_connectors($gd,$left,$top)
      if $connector && $connector ne 'none'; # && $self->{level} == 0;
    $self->draw_component($gd,$left,$top,$partno,$total_parts) unless $self->feature_has_subparts;
  }

}

sub level {

  shift->{level};

}

sub draw_connectors {

  my $self = shift;

  return if $self->{overbumped};
  my $gd = shift;
  my ($dx,$dy) = @_;
  my @parts = sort { $a->left <=> $b->left } $self->parts;
  for (my $i = 0; $i < @parts-1; $i++) {
    # don't let connectors double-back on themselves
    next if ($parts[$i]->bounds)[2] > ($parts[$i+1]->bounds)[0];
    $self->_connector($gd,$dx,$dy,$parts[$i]->bounds,$parts[$i+1]->bounds);
  }

  # extra connectors going off ends
  if (@parts) {
    my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
    my($xl,$xt,$xr,$xb) = $parts[0]->bounds;
    $self->_connector($gd,$dx,$dy,$x1,$xt,$x1,$xb,$xl,$xt,$xr,$xb)      if $x1 < $xl;
    my ($xl2,$xt2,$xr2,$xb2) = $parts[-1]->bounds;

    my $feature = $self->feature;
    my @p       = map {$_->feature} @parts;
    $self->_connector($gd,$dx,$dy,$parts[-1]->bounds,$x2,$xt2,$x2,$xb2) if $x2 > $xr2;
  } else {
    my ($x1,$y1,$x2,$y2) = $self->bounds($dx,$dy);
    $self->draw_connector($gd,$y1,$y2,$x1,$y1,$y2,$x2);
  }

}

sub hilite_color {

  my $self         = shift;
  return     if $self->level; # only highlite top level glyphs
  my $index   = $self->option('hilite') or return;
  $self->factory->translate_color($index);

}

sub draw_highlight {

  my $self              = shift;
  my ($gd,$left,$top)   = @_;
  my $color  = $self->hilite_color or return;
  my @bounds = $self->bounds;
  $gd->filledRectangle($bounds[0]+$left - 3,
		       $bounds[1]+$top  - 3,
		       $bounds[2]+$left + 3,
		       $bounds[3]+$top  + 3,
		       $color);

}

sub _connector {

  my $self = shift;
  my ($gd,
      $dx,$dy,
      $xl,$xt,$xr,$xb,
      $yl,$yt,$yr,$yb) = @_;
  my $left   = $dx + $xr;
  my $right  = $dx + $yl;
  my $top1     = $dy + $xt;
  my $bottom1  = $dy + $xb;
  my $top2     = $dy + $yt;
  my $bottom2  = $dy + $yb;

  # restore this comment if you don't like the group dash working
  # its way backwards.
  return if $right-$left < 1 && !$self->isa('Bio::Graphics::Glyph::group');

  $self->draw_connector($gd,
			$top1,$bottom1,$left,
			$top2,$bottom2,$right,
		       );

}

sub draw_connector {

  my $self   = shift;
  my $gd     = shift;

  my $color          = $self->connector_color;
  my $connector_type = $self->connector or return;

  if ($connector_type eq 'hat') {
    $self->draw_hat_connector($gd,$color,@_);
  } elsif ($connector_type eq 'solid') {
    $self->draw_solid_connector($gd,$color,@_);
  } elsif ($connector_type eq 'dashed') {
    $self->draw_dashed_connector($gd,$color,@_);
  } elsif ($connector_type eq 'quill') {
    $self->draw_quill_connector($gd,$color,@_);
  } elsif ($connector_type eq 'crossed') {
    $self->draw_crossed_connector($gd,$color,@_);
  } else {
    ; # draw nothing
  }

}

sub draw_hat_connector {

  my $self = shift;
  my $gd   = shift;
  my $color = shift;
  my ($top1,$bottom1,$left,$top2,$bottom2,$right) = @_;

  cluck "gd object is $gd" unless ref $gd;

  my $center1  = ($top1 + $bottom1)/2;
  my $quarter1 = $top1 + ($bottom1-$top1)/4;
  my $center2  = ($top2 + $bottom2)/2;
  my $quarter2 = $top2 + ($bottom2-$top2)/4;

  if ($center1 != $center2) {
    $self->draw_solid_connector($gd,$color,@_);
    return;
  }

  if ($right - $left > 4) {  # room for the inverted "V"
      my $middle = $left + int(($right - $left)/2);
      $gd->line($left,$center1,$middle,$top1,$color);
      $gd->line($middle,$top1,$right-1,$center1,$color);
    } elsif ($right-$left > 1) { # no room, just connect
      $gd->line($left,$quarter1,$right-1,$quarter1,$color);
    }

}

sub draw_solid_connector {

  my $self = shift;
  my $gd   = shift;
  my $color = shift;
  my ($top1,$bottom1,$left,$top2,$bottom2,$right) = @_;

  my $center1  = ($top1 + $bottom1)/2;
  my $center2  = ($top2 + $bottom2)/2;

  $gd->line($left,$center1,$right,$center2,$color);

}

sub draw_dashed_connector {

  my $self = shift;
  my $gd   = shift;
  my $color = shift;
  my ($top1,$bottom1,$left,$top2,$bottom2,$right) = @_;

  my $center1  = ($top1 + $bottom1)/2;
  my $center2  = ($top2 + $bottom2)/2;
  my $image_class   = $self->panel->image_class;
  my $gdTransparent = $image_class->gdTransparent;
  my $gdStyled      = $image_class->gdStyled;
  $gd->setStyle($color,$color,$gdTransparent,$gdTransparent);
  $gd->line($left,$center1,$right,$center2,$gdStyled);

}

sub draw_quill_connector {

  my $self = shift;
  my $gd   = shift;
  my $color = shift;
  my ($top1,$bottom1,$left,$top2,$bottom2,$right) = @_;

  my $center1  = ($top1 + $bottom1)/2;
  my $center2  = ($top2 + $bottom2)/2;

  $gd->line($left,$center1,$right,$center2,$color);
  my $direction = $self->feature->strand;
  return unless $direction;
  $direction *= -1 if $self->{flip};

  if ($direction > 0) {
    my $start = $left+4;
    my $end   = $right-1;
    for (my $position=$start; $position <= $end; $position += QUILL_INTERVAL) {
      $gd->line($position,$center1,$position-2,$center1-2,$color);
      $gd->line($position,$center1,$position-2,$center1+2,$color);
    }
  } else {
    my $start = $left+1;
    my $end   = $right-4;
    for (my $position=$start; $position <= $end; $position += QUILL_INTERVAL) {
      $gd->line($position,$center1,$position+2,$center1-2,$color);
      $gd->line($position,$center1,$position+2,$center1+2,$color);
    }
  }

}

sub draw_crossed_connector {

  my $self = shift;
  my $gd = shift;
  my $color = shift;
  my ($top1,$bottom1,$left,$top2,$bottom2,$right) = @_;

  #Draw the horizontal line
  my $center1  = ($top1 + $bottom1)/2;
  my $center2  = ($top2 + $bottom2)/2;

  $gd->line($left,$center1,$right,$center2,$color);

  #Extra validations
  ($left, $right)   = ($right, $left)   if ($right < $left);
  ($top1, $bottom1) = ($bottom1, $top1) if ($bottom1 < $top1);
  ($top2, $bottom2) = ($bottom2, $top2) if ($bottom2 < $top2);

  #Draw the "X"
  my $middle = int(($right - $left) / 2) + $left;
  my $midLen = int(($bottom1 - $top1) / 2);

  $gd->line($middle-$midLen,$top1,   $middle+$midLen,$bottom2,$color);
  $gd->line($middle-$midLen,$bottom1,$middle+$midLen,$top2,$color);

}

sub filled_box {

  my $self = shift;
  my $gd = shift;
  my ($x1,$y1,$x2,$y2,$bg,$fg,$lw) = @_;

  $bg ||= $self->bgcolor;
  $fg ||= $self->fgcolor;
  $lw ||= $self->option('linewidth') || 1;

  $gd->filledRectangle($x1,$y1,$x2,$y2,$bg);
  $fg = $self->set_pen($lw,$fg) if $lw > 1;

  # draw a box
  $gd->rectangle($x1,$y1,$x2,$y2,$fg);

  # if the left end is off the end, then cover over
  # the leftmost line
  my ($width) = $gd->getBounds;

  $bg = $self->set_pen($lw,$bg) if $lw > 1;

  $gd->line($x1,$y1+$lw,$x1,$y2-$lw,$bg)
    if $x1 < $self->panel->pad_left;

  $gd->line($x2,$y1+$lw,$x2,$y2-$lw,$bg)
    if $x2 > $width - $self->panel->pad_right;

}

sub filled_oval {

  my $self = shift;
  my $gd = shift;
  my ($x1,$y1,$x2,$y2,$bg,$fg,$lw) = @_;
  my $cx = ($x1+$x2)/2;
  my $cy = ($y1+$y2)/2;

  $fg ||= $self->fgcolor;
  $bg ||= $self->bgcolor;
  $lw ||= $self->linewidth;

  $fg = $self->set_pen($lw) if $lw > 1;

  # Maintain backwards compatability with gd 1.8.4
  # which does not support the ellipse methods.
  # can() method fails with GD::SVG...
  if ($gd->can('ellipse') || $gd =~ /SVG/ ) {
    $gd->filledEllipse($cx,$cy,$x2-$x1,$y2-$y1,$bg);
    # Draw the edge around the ellipse
    $gd->ellipse($cx,$cy,$x2-$x1,$y2-$y1,$fg);
  } else {
    $gd->arc($cx,$cy,$x2-$x1,$y2-$y1,0,360,$fg);
    $gd->fillToBorder($cx,$cy,$fg,$bg);
  }

}

sub oval {

  my $self = shift;
  my $gd = shift;
  my ($x1,$y1,$x2,$y2) = @_;
  my $cx = ($x1+$x2)/2;
  my $cy = ($y1+$y2)/2;

  my $fg = $self->fgcolor;
  my $linewidth = $self->linewidth;
  $fg = $self->set_pen($linewidth) if $linewidth > 1;

  # Maintain backwards compatability with gd 1.8.4 which does not
  # support the ellipse method.
  if ($gd->can('ellipse') || $gd =~ /SVG/ ) {
    $gd->ellipse($cx,$cy,$x2-$x1,$y2-$y1,$fg);
  } else {
    $gd->arc($cx,$cy,$x2-$x1,$y2-$y1,0,360,$fg);
  }

}

sub filled_arrow {

  my $self = shift;
  my $gd   = shift;
  my $orientation = shift;
  my ($x1,$y1,$x2,$y2,$fg,$bg)  = @_;

  $orientation *= -1 if $self->{flip};

  my ($width) = $gd->getBounds;
  my $indent = $y2-$y1 < $x2-$x1 ? $y2-$y1 : ($x2-$x1)/2;

  return $self->filled_box($gd,@_)
    if ($orientation == 0)
      or ($x1 < 0 && $orientation < 0)
        or ($x2 > $width && $orientation > 0)
	  or ($indent <= 0)
	    or ($x2 - $x1 < 3);

  $fg   ||= $self->fgcolor;
  $bg   ||= $self->bgcolor;
  my $pkg  = $self->polygon_package;
  my $poly = $pkg->new();
  if ($orientation >= 0) {
    $poly->addPt($x1,$y1);
    $poly->addPt($x2-$indent,$y1);
    $poly->addPt($x2,($y2+$y1)/2);
    $poly->addPt($x2-$indent,$y2);
    $poly->addPt($x1,$y2);
  } else {
    $poly->addPt($x2,$y1);
    $poly->addPt($x2,$y2);
    $poly->addPt($x1+$indent,$y2);
    $poly->addPt($x1,($y2+$y1)/2);
    $poly->addPt($x1+$indent,$y1);
  }
  $gd->filledPolygon($poly,$bg);
  $gd->polygon($poly,$fg);

  # blunt it a bit if off the end
  # good idea - but isn't inuitive
  # if ($orientation >= 0 && $x2 > $width - $self->panel->pad_right) {
  # $gd->filledRectangle($x2-3,$y1,$x2,$y2,$self->panel->bgcolor);
  #}

}

sub linewidth {

  shift->option('linewidth') || 1;

}

sub fill {

  my $self = shift;
  my $gd   = shift;
  my ($x1,$y1,$x2,$y2) = @_;
  if ( ($x2-$x1) >= 2 && ($y2-$y1) >= 2 ) {
    $gd->fill($x1+1,$y1+1,$self->bgcolor);
  }

}

sub set_pen {

  my $self = shift;
  my ($linewidth,$color) = @_;
  $linewidth ||= $self->linewidth;
  $color     ||= $self->fgcolor;
  return $color unless $linewidth > 1;
  $self->panel->set_pen($linewidth,$color);

}

sub draw_component {

  my $self = shift;
  my ($gd,$left,$top,$partno,$total_parts) = @_;
  my($x1,$y1,$x2,$y2) = $self->bounds($left,$top);

  # clipping
  my $panel = $self->panel;
  return unless $x2 >= $panel->left and $x1 <= $panel->right;

  if ($self->option('strand_arrow') || $self->option('stranded')) {
    $self->filled_arrow($gd,$self->feature->strand,
			$x1, $y1,
			$x2, $y2)
  } else {
    $self->filled_box($gd,
		      $x1, $y1,
		      $x2, $y2)
  }

}

sub no_subparts {

  return shift->option('no_subparts');

}

sub maxdepth {

  my $self = shift;

  my $maxdepth =  $self->option('maxdepth');
  return $maxdepth if defined $maxdepth;

  # $feature->compound is an artefact from aggregators. Sadly, an aggregated feature can miss
  # parts that are out of the query range - this is a horrible mis-feature. Aggregated features have
  # a compound flag to hack around this.
  my $feature = $self->feature;
  return 1 if $feature->can('compound') && $feature->compound;

  return;

}

sub exceeds_depth {

  my $self = shift;
  my $max_depth     = $self->maxdepth;
  return unless defined $max_depth;

  my $current_depth = $self->level || 0;
  return $current_depth >= $max_depth;

}

sub subfeat {

  my $self    = shift;
  my $feature = shift;

  return $self->_subfeat($feature) unless ref $self;  # protect against class invocation

  return if $self->level == 0 && $self->no_subparts;
  return if $self->exceeds_depth;

  return @{$self->{cached_subfeat}{$feature}} if exists $self->{cached_subfeat}{$feature};
  my @ss = $self->_subfeat($feature);
  $self->{cached_subfeat}{$feature} =\@ ss;
  @ss;

}

sub _subfeat {

  my $class   = shift;
  my $feature = shift;

  return $feature->segments     if $feature->can('segments');

  my @split = eval { my $id   = $feature->location->seq_id;
		     my @subs = $feature->location->sub_Location;
		     grep {$id eq $_->seq_id} @subs;
		   };

  return @split if @split;

  # Either the APIs have changed, or I got confused at some point...
  return $feature->get_SeqFeatures         if $feature->can('get_SeqFeatures');
  return $feature->sub_SeqFeature          if $feature->can('sub_SeqFeature');
  return;

}

sub keyglyph {

  my $self = shift;
  my $feature = $self->make_key_feature;
  my $factory = $self->factory->clone;
  $factory->set_option(label       => 1);
  $factory->set_option(description => 0);
  $factory->set_option(bump  => 0);
  $factory->set_option(connector  => 'solid');
  return $factory->make_glyph(0,$feature);

}

sub make_key_feature {

  my $self = shift;

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

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

  my $feature =
    Bio::Graphics::Feature->new(-start =>0 * $scale +$offset,
				-end   =>80*$scale+$offset,
				-name => $self->make_key_name(),
				-strand => '+1');
  return $feature;

}

sub make_key_name {

  my $self = shift;

  # breaking encapsulation - this should be handled by the panel
  my $key      = $self->option('key') || '';
  return $key unless $self->panel->add_category_labels;

  my $category = $self->option('category');
  my $name     = defined $category ? "$key ($category)" : $key;
  return $name;

}

sub all_callbacks {

  my $self = shift;
  return $self->{all_callbacks} if exists $self->{all_callbacks}; # memoize
  return $self->{all_callbacks} = $self->_all_callbacks;

}

sub _all_callbacks {

  my $self = shift;
  my $track_level = $self->option('all_callbacks');
  return $track_level if defined $track_level;
  return $self->panel->all_callbacks;

}

sub subpart_callbacks {

  my $self = shift;
  return $self->{subpart_callbacks} if exists $self->{subpart_callbacks}; # memoize
  return $self->{subpart_callbacks} = $self->_subpart_callbacks;

}

sub _subpart_callbacks {

  my $self = shift;
  return 1 if $self->all_callbacks;
  my $do_subparts = $self->option('subpart_callbacks');
  return $self->{level} == 0 || ($self->{level} > 0 && $do_subparts);

}

sub default_factory {

  croak "no default factory implemented";

}

sub finished {

  my $self = shift;
  delete $self->{factory};
  foreach (@{$self->{parts} || []}) {
    $_->finished;
  }
  delete $self->{parts};

}

General documentation

Bio::Graphics::Glyph objects are constructed automatically by an
Bio::Graphics::Glyph::Factory, and are not usually created by
end-developer code.
    Given a sequence feature, creates an Bio::Graphics::Glyph object to
display it. The -feature argument points to the Bio:SeqFeatureI
object to display, and -factory indicates an
Bio::Graphics::Glyph::Factory object from which the glyph will fetch
all its run-time configuration information. Factories are created and
manipulated by the Bio::Graphics::Panel object.
    A standard set of options are recognized. See OPTIONS.

Once a glyph is created, it responds to a large number of methods. In
this section, these methods are grouped into related categories.
Retrieving glyph context:
    Get the Bio::Graphics::Glyph::Factory associated with this object.
This cannot be changed once it is set.
    Get the Bio::Graphics::Panel associated with this object. This cannot
be changed once it is set.
    Get the sequence feature associated with this object. This cannot be
changed once it is set.
    Add the list of features to the glyph, creating subparts. This is
most common done with the track glyph returned by
Ace::Graphics::Panel->add_track().
    This is similar to add_feature(), but the list of features is treated
as a group and can be configured as a set.
    When you are finished with a glyph, you can call its finished() method
in order to break cycles that would otherwise cause memory leaks.
finished() is typically only used by the Panel object.
Retrieving glyph options:
    These methods return the configured foreground, background, font,
alternative font, and fill colors for the glyph in the form of a
GD::Image color index.
    This method returns a color to be used to flood-fill the entire glyph
before drawing (currently used by the "track" glyph).
    Return the width of the glyph, not including left or right padding.
This is ordinarily set internally based on the size of the feature and
the scale of the panel.
    Returns the width of the glyph including left and right padding.
    Returns the height of the glyph, not including the top or bottom
padding. This is calculated from the "height" option and cannot be
changed.
    Return the font for the glyph.
    Return the value of the indicated option.
    Given a symbolic or #RRGGBB-form color name, returns its GD index.
    The "level" is the nesting level of the glyph.
Groups are level -1, top level glyphs are level 0,
subparts (e.g. exons) are level 1 and so forth.
Setting an option:
    You may change a glyph option after it is created using set_option().
This is most commonly used to configure track glyphs.
Retrieving information about the sequence:
    These methods return the start and end of the glyph in base pair
units.
    Returns the offset of the segment (the base pair at the far left of
the image).
    Returns the length of the sequence segment.
Retrieving formatting information:
    These methods return the top, left, bottom and right of the glyph in
pixel coordinates.
    Returns the height of the glyph. This may be somewhat larger or
smaller than the height suggested by the GlyphFactory, depending on
the type of the glyph.
    Get the scale for the glyph in pixels/bp.
    Return the height of the label, if any.
    Return a human-readable label for the glyph.
These methods are called by Bio::Graphics::Track during the layout
process:
    Move the glyph in pixel coordinates by the indicated delta-x and
delta-y values.
    Return the current position of the glyph.
These methods are intended to be overridden in subclasses:
    Calculate the height of the glyph.
    Calculate the left side of the glyph.
    Calculate the right side of the glyph.
    Optionally offset the glyph by the indicated amount and draw it onto
the GD::Image object.
    Draw the label for the glyph onto the provided GD::Image object,
optionally offsetting by the amounts indicated in $left and $right.
    This returns the maximum number of levels of feature subparts that the
glyph will recurse through. For example, returning 0 indicates that
the glyph will only draw the top-level feature. Returning 1 indicates
that it will only draw the top-level feature and one level of
subfeatures. Returning 2 will descend down two levels. Overriding this
method will speed up rendering by avoiding creating of a bunch of
subglyphs that will never be drawn.
    The default behavior is to return undef (unlimited levels of descent)
unless the -maxdepth option is passed, in which case this number is
returned.
    Note that Bio::Graphics::Glyph::generic overrides maxdepth() to return
0, meaning no descent into subparts will be performed.
These methods are useful utility routines:
    Map the indicated base position, given in base pair units, into
pixels, using the current scale and glyph position.
    Draw a filled rectangle with the appropriate foreground and fill
colors, and pen width onto the GD::Image object given by $gd, using
the provided rectangle coordinates.
    As above, but draws an oval inscribed on the rectangle.
    Returns true if descending into another level of subfeatures will
exceed the value returned by maxdepth().

The following options are standard among all Glyphs. See individual
glyph pages for more options.

  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                 undef (false)

  -connector_color
                Connector color                black

  -strand_arrow Whether to indicate            undef (false)
                 strandedness

  -label        Whether to draw a label	       undef (false)

  -description  Whether to draw a description  undef (false)

  -no_subparts  Set to true to prevent         undef (false)
                drawing of the subparts
                of a feature.

  -ignore_sub_part Give the types/methods of   undef
                subparts to ignore (as a 
                space delimited list).

  -maxdepth     Specifies the maximum number   undef (unlimited) 
                child-generations to decend
                when getting subfeatures

  -sort_order   Specify layout sort order      "default"

  -always_sort  Sort even when bumping is off  undef (false)

  -bump_limit   Maximum number of levels to bump undef (unlimited)

  -hilite       Highlight color                undef (no color)

  -link, -title, -target
               These options are used when creating imagemaps
               for display on the web.  See Bio::Graphics::Panel/"Creating Imagemaps".

For glyphs that consist of multiple segments, the -connector option
controls what's drawn between the segments. The default is undef (no
connector). Options include:

   "hat"     an upward-angling conector
   "solid"   a straight horizontal connector
   "quill"   a decorated line with small arrows indicating strandedness
             (like the UCSC Genome Browser uses)
   "dashed"  a horizontal dashed line.
   "crossed" a straight horizontal connector with an "X" on it
              (Can be used when segments are not yet validated
               by some internal experiments...)

The -connector_color option controls the color of the connector, if
any.
The label is printed above the glyph. You may pass an anonymous
subroutine to -label, in which case the subroutine will be invoked
with the feature as its single argument. and is expected to return
the string to use as the description. If you provide the numeric
value "1" to -description, the description will be read off the
feature's seqname(), info() and primary_tag() methods will be called
until a suitable name is found. To create a label with the
text "1", pass the string "1 ". (A 1 followed by a space).
The description is printed below the glyph. You may pass an anonymous
subroutine to -description, in which case the subroutine will be
invoked with the feature as its single argument and is expected to
return the string to use as the description. If you provide the
numeric value "1" to -description, the description will be read off
the feature's source_tag() method. To create a description with the
text "1", pass the string "1 ". (A 1 followed by a space).
In the case of ACEDB Ace::Sequence feature objects, the feature's
info(), Brief_identification() and Locus() methods will be called to
create a suitable description.
The -strand_arrow option, if true, requests that the glyph indicate
which strand it is on, usually by drawing an arrowhead. Not all
glyphs will respond to this request. For historical reasons,
-stranded is a synonym for this option.
sort_order: By default, features are drawn with a layout based only on the
position of the feature, assuring a maximal "packing" of the glyphs
when bumped. In some cases, however, it makes sense to display the
glyphs sorted by score or some other comparison, e.g. such that more
"important" features are nearer the top of the display, stacked above
less important features. The -sort_order option allows a few
different built-in values for changing the default sort order (which
is by "left" position): "low_score" (or "high_score") will cause
features to be sorted from lowest to highest score (or vice versa).
"left" (or "default") and "right" values will cause features to be
sorted by their position in the sequence. "longer" (or "shorter")
will cause the longest (or shortest) features to be sorted first, and
"strand" will cause the features to be sorted by strand: "+1"
(forward) then "0" (unknown, or NA) then "-1" (reverse).
In all cases, the "left" position will be used to break any ties. To
break ties using another field, options may be strung together using a
"|" character; e.g. "strand|low_score|right" would cause the features
to be sorted first by strand, then score (lowest to highest), then by
"right" position in the sequence.
Finally, a subroutine coderef with a $$ prototype can be provided. It
will receive two glyph as arguments and should return -1, 0 or 1
(see Perl's sort() function for more information). For example, to
sort a set of database search hits by bits (stored in the features'
"score" fields), scaled by the log of the alignment length (with
"start" position breaking any ties):

  sort_order = sub ($$) {
    my ($glyph1,$glyph2) = @_;
    my $a = $glyph1->feature;
    my $b = $glyph2->feature;
    ( $b->score/log($b->length)
          <=>
      $a->score/log($a->length) )
          ||
    ( $a->start <=> $b->start )
  }

It is important to remember to use the $$ prototype as shown in the
example. Otherwise Bio::Graphics will quit with an exception. The
arguments are subclasses of Bio::Graphics::Glyph, not the features
themselves. While glyphs implement some, but not all, of the feature
methods, to be safe call the two glyphs' feature() methods in order to
convert them into the actual features.
The '-always_sort' option, if true, will sort features even if bumping
is turned off. This is useful if you would like overlapping features
to stack in a particular order. Features towards the end of the list
will overlay those towards the beginning of the sort order.
The -hilite option draws a colored box behind each feature using the
indicated color. Typically you will pass it a code ref that returns a
color name. For example:

  -hilite => sub { my $name = shift->display_name; 
                   return 'yellow' if $name =~ /XYZ/ }

The -no_subparts option will prevent the glyph from searching its
feature for subfeatures. This may enhance performance if you know in
advance that none of your features contain subfeatures.

By convention, subclasses are all lower-case. Begin each subclass
with a preamble like this one:

 package Bio::Graphics::Glyph::crossbox;

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

Then override the methods you need to. Typically, just the draw()
method will need to be overridden. However, if you need additional
room in the glyph, you may override calculate_height(),
calculate_left() and calculate_right(). Do not directly override
height(), left() and right(), as their purpose is to cache the values
returned by their calculating cousins in order to avoid time-consuming
recalculation.
A simple draw() method looks like this:

 sub draw {
  my $self = shift;
  $self->SUPER::draw(@_);
  my $gd = shift;

  # and draw a cross through the box
  my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
  my $fg = $self->fgcolor;
  $gd->line($x1,$y1,$x2,$y2,$fg);
  $gd->line($x1,$y2,$x2,$y1,$fg);
 }

This subclass draws a simple box with two lines criss-crossed through
it. We first call our inherited draw() method to generate the filled
box and label. We then call calculate_boundaries() to return the
coordinates of the glyph, disregarding any extra space taken by
labels. We call fgcolor() to return the desired foreground color, and
then call $gd->line() twice to generate the criss-cross.
For more complex draw() methods, see Bio::Graphics::Glyph::transcript
and Bio::Graphics::Glyph::segments.
Please avoid using a specific image class (via "use GD" for example)
within your glyph package. Instead, rely on the image package passed
to the draw() method. This approach allows for future expansion of
supported image classes without requiring glyph redesign. If you need
access to the specific image classes such as Polygon, Image, or Font,
generate them like such:

 sub draw {
  my $self = shift;
  my $image_class = shift;

  my $polygon_package = $self->polygon_package->new()
  ...
  }

Please report them.

Bio::DB::GFF::Feature,
Ace::Sequence,
Bio::Graphics::Panel,
Bio::Graphics::Track,
Bio::Graphics::Glyph::anchored_arrow,
Bio::Graphics::Glyph::arrow,
Bio::Graphics::Glyph::box,
Bio::Graphics::Glyph::dna,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2,
Bio::Graphics::Glyph::wormbase_transcript
Bio::Graphics::Glyph::xyplot
Bio::Graphics::Glyph::whiskerplot

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.