transcript2 documentation.

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. 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)

  -strand_arrow Whether to indicate            0 (false)
                 strandedness

  -hilite       Highlight color                undef (no color)

In addition, the alignment glyph recognizes the following
glyph-specific options:

  Option         Description                  Default
  ------         -----------                  -------

  -arrow_length  Length of the directional   8
                 arrow.

sub extra_arrow_length {

  my $self = shift;
#  return 0 unless $self->{level} == 0;
  my $strand = $self->feature->strand || 0;
  $strand *= -1 if $self->{flip};
  return 0 unless $strand < 0;
  my $first = ($self->parts)[0] || $self;
  my @rect  = $first->bounds();
  my $width = abs($rect[2] - $rect[0]);
  return 0 if $width >= MIN_WIDTH_FOR_ARROW;
  return $self->arrow_length;

}

sub pad_left {

   my $self = shift;
#   return 0 unless $self->{level} == 0;
   my $pad = $self->Bio::Graphics::Glyph::generic::pad_left;
   my $extra_arrow_length = $self->extra_arrow_length;
   if ($self->label_position eq 'left' && $self->label) {
     return $extra_arrow_length+$pad;
   } else {
     return $extra_arrow_length > $pad ? $extra_arrow_length : $pad;
   }

}

sub pad_right {

  my $self = shift;
#  return 0 unless $self->{level} == 0;
  my $pad = $self->Bio::Graphics::Glyph::generic::pad_right;
  return $pad if $self->{level} > 0;
  my $last = ($self->parts)[-1] || $self;
  my @rect  = $last->bounds();
  my $width = abs($rect[2] - $rect[0]);
  return $self->SUPER::pad_right if $width < MIN_WIDTH_FOR_ARROW;
  return $pad

}

sub draw_connectors {

  my $self = shift;
  my ($gd,$dx,$dy) = @_;

  my $part;
  my $strand = $self->feature->strand;
  $strand   *= -1 if $self->{flip};  #sigh
  if (my @parts  = $self->parts) {
    $part   = $strand >= 0 ? $parts[-1] : $parts[0];
  } elsif ($self->feature_has_subparts) {
    # 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 ($filled) {
    my ($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 {
      $self->SUPER::draw_component($gd,@_);
    }
  }

  else {
    $self->SUPER::draw_component($gd,@_);
  }

}

extra_arrow_length	No description	Code
pad_left	No description	Code
pad_right	No description	Code
draw_connectors	No description	Code
draw_component	No description	Code
bump	No description	Code