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lib/Bio/Graphics/Glyph/transcript2.pm  view on Meta::CPAN

    # no parts -- so draw an intron spanning whole thing
    my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
    $self->_connector($gd,$dx,$dy,$x1,$y1,$x1,$y2,$x2,$y1,$x2,$y2);
    $part = $self;
  } else {
    return;
  }
  my @rect   = $part->bounds();
  my $width  = abs($rect[2] - $rect[0]);
  my $filled = $width >= MIN_WIDTH_FOR_ARROW;

  if ($filled) {
    $self->Bio::Graphics::Glyph::generic::draw_connectors(@_);
  } else {
    $self->SUPER::draw_connectors(@_);
  }
}

sub draw_component {
  my $self = shift;
  return unless $self->level > 0;

  my $gd = shift;
  my ($left,$top) = @_;
  my @rect = $self->bounds(@_);

  my $f      = $self->feature;
  my $strand = $f->strand;
  my $str    = $strand * ($self->{flip} ? -1 : 1);

  my $width = abs($rect[2] - $rect[0]);
  my $filled = defined($self->{partno}) && $width >= MIN_WIDTH_FOR_ARROW;
  my ($pwidth) = $gd->getBounds;
  $filled = 0 if $str < 0 && $rect[0] < $self->panel->pad_left;
  $filled = 0 if $str > 0 && $rect[2] > $pwidth - $self->panel->pad_right;

  if ($self->stranded && $filled) {
    my ($first,$last)  = ($self->{partno} == 0 , $self->{partno} == $self->{total_parts}-1);
    ($first,$last)     = ($last,$first) if $self->{flip};

    if ($strand < 0 && $first) { # first exon, minus strand transcript
      $self->filled_arrow($gd,-1,@rect);
    } elsif ($strand >= 0 && $last) { # last exon, plus strand
      $self->filled_arrow($gd,+1,@rect);
    } else {
	$self->filled_box($gd,@rect);
    }
  }

  else {
      $self->filled_box($gd,@rect);
  }

  # copied from generic::draw_component
  $self->draw_translation($gd,@_) if $self->{cds_translation}; # created earlier by calculate_cds()
  $self->draw_sequence($gd,@_)    if $self->option('draw_dna') && $self->dna_fits;
}

sub bump {
  my $self = shift;
  return $self->SUPER::bump(@_) if $self->all_callbacks;
  return 0;  # never allow our components to bump
}

1;


__END__

=head1 NAME

Bio::Graphics::Glyph::transcript2 - The "transcript2" glyph

=head1 SYNOPSIS

  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

=head1 DESCRIPTION

This glyph is used for drawing transcripts.  It is like "transcript"
except that if there is sufficient room the terminal exon is shaped
like an arrow in order to indicate the direction of transcription.  If
there isn't enough room, a small arrow is drawn.

=head2 OPTIONS

The following options are standard among all Glyphs.  See
L<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

  -hilite       Highlight color                undef (no color)

In addition, the alignment glyph recognizes the following