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Ace/Graphics/Track.pm  view on Meta::CPAN

		    factory  => $glyph_factory,         # the glyph class associated with this track
		    glyphs   => undef,                  # list of glyphs
		   },$class;
  $self->add_feature($_) foreach @$features;
  $self;
}

# control bump direction:
#    +1   => bump downward
#    -1   => bump upward
#     0   => no bump
sub bump {
  my $self = shift;
  $self->factory->option('bump',@_);
}

# add a feature (or array ref of features) to the list
sub add_feature {
  my $self       = shift;
  my $feature    = shift;
  if (ref($feature) eq 'ARRAY') {
    my $name     = ++$self->{group_name};
    $self->{group_ids}{$name} = $feature;
  } else {
    push @{$self->{features}},$feature;
  }
}

# link a set of features together so that they bump as a group
sub add_group {
  my $self     = shift;
  my $features = shift;
  ref($features) eq 'ARRAY' or croak("Usage: Ace::Graphics::Track->add_group(\$arrayref)");
  $self->add_feature($features);
}

# delegate lineheight to the glyph
sub lineheight {
  shift->{factory}->height(@_);
}

# the scale is horizontal, measured in pixels/bp
sub scale {
  my $self = shift;
  my $g = $self->{scale};
  $self->{scale} = shift if @_;
  $g;
}

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

# set scale by a segment
sub scale_to_segment {
  my $self = shift;
  my ($segment,$desired_width) = @_;
  $self->set_scale(abs($segment->length),$desired_width);
}

sub set_scale {
  my $self = shift;
  my ($bp,$desired_width) = @_;
  $desired_width ||= 512;
  $self->scale($desired_width/$bp);
  $self->width($desired_width);
}

# return the glyph class
sub factory {
  my $self = shift;
  my $g = $self->{factory};
  $self->{factory} = shift if @_;
  $g;
}

# return boxes for each of the glyphs
# will be an array of four-element [$feature,l,t,r,b] arrays
sub boxes {
  my $self = shift;
  my ($left,$top) = @_;
  $top  += 0; $left += 0;
  my @result;

  my $glyphs = $self->layout;

  for my $g (@$glyphs) {
    my ($l,$t,$r,$b) = $g->box;
    push @result,[$g->feature,$left+$l,$top+$t,$left+$r,$top+$b];

  }

  return wantarray ? @result : \@result;
}

# synthesize a key glyph
sub keyglyph {
  my $self = shift;
  my $scale = 1/$self->scale;  # base pairs/pixel
  # two segments, at pixels 0->50, 60->80
  my $offset = $self->offset;
  my $feature = Ace::Graphics::Fk->new(-segments=>[ [ 0*$scale +$offset,50*$scale+$offset],
						    [60*$scale+$offset, 80*$scale+$offset]
						    ],
				       -name => $self->option('key'),
				       -strand => '+1');
  my $factory = $self->factory->clone;
  $factory->scale($self->scale);
  $factory->width($self->width);
  $factory->option(label=>1);  # turn on labels
  return $factory->glyph($feature);
}

# draw glyphs onto a GD object at the indicated position
sub draw {
  my $self = shift;
  my ($gd,$left,$top) = @_;
  $top  += 0;  $left += 0;
  my $glyphs = $self->layout;

  # draw background
  my $bgcolor = $self->factory->bgcolor;
  # $gd->filledRectangle($left,$top,$left+$self->width,$top+$self->height,$bgcolor);

  if (my $label = $self->factory->option('track_label')) {
    my $font = $self->factory->font;
    my $y = $top + ($self->height-$font->height)/2;
    my $x = $left - length($label) * $font->width;
    $gd->string($font,$x,$y,$label,$self->factory->fontcolor);
  }
  $_->draw($gd,$left,$top) foreach @$glyphs;

  if ($self->factory->option('connectgroups')) {
    $_->draw($gd,$left,$top) foreach @{$self->{groups}};
  }
}

# lay out -- this uses the infamous bump algorithm
sub layout {
  my $self = shift;
  my $force = shift || 0;
  return $self->{glyphs} if $self->{glyphs} && !$force;

  my $f = $self->{features};
  my $factory = $self->factory;
  $factory->scale($self->scale);  # set the horizontal scale
  $factory->width($self->width);

  # create singleton glyphs
  my @singletons = map { $factory->glyph($_) } @$f;

  # create linked groups of glyphs
  my @groups;
  if (my $groups = $self->{group_ids}) {
    my $groupfactory = Ace::Graphics::GlyphFactory->new('group');
    for my $g (values %$groups) {
      my @g = map { $factory->glyph($_) } @$g;
      push @groups,$groupfactory->glyph(\@g);
    }
  }

  return $self->{glyphs} = [] unless @singletons || @groups;

  # run the bumper on the groups
  $self->_bump([@singletons,@groups]) if $self->bump;

  # merge the singletons and groups and sort them horizontally
  my @glyphs = sort {$a->left <=> $b->left } @singletons,map {$_->members} @groups;

  # If -1 bumping was allowed, then normalize so that the top glyph is at zero
  my ($topmost) = sort {$a->top <=> $b->top} @glyphs;
  my $offset = 0 - $topmost->top;
  $_->move(0,$offset) foreach @glyphs;

  $self->{groups}        = \@groups;
  return $self->{glyphs} = \@glyphs;
}

# bumper - glyphs already sorted left to right
sub _bump {
  my $self   = shift;
  my $glyphs = shift;
  my $bump_direction = $self->bump;  # +1 means bump down, -1 means bump up

  my @occupied;
  my $rightmost = -2;
  for my $g (sort { $a->left <=> $b->left} @$glyphs) {