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

  my $ragged = $self->option('ragged_start') 
    ? RAGGED_START_FUZZ 
    : $self->option('ragged_extra');

  return $self->SUPER::pad_left 
    unless $self->draw_target && $ragged && $self->dna_fits;
  my $extra = 0;
  my $target = eval {$self->feature->hit} or return $self->SUPER::pad_left + $extra;
  return $self->SUPER::pad_left + $extra unless $target->start<$target->end && $target->start < $ragged;
  return ($target->start-1) * $self->scale + $extra;
}

sub pad_right {
  my $self = shift;
  return $self->SUPER::pad_right unless $self->level > 0;
  my $ragged = $self->option('ragged_start') 
    ? RAGGED_START_FUZZ 
    : $self->option('ragged_extra');
  return $self->SUPER::pad_right 
    unless $self->draw_target && $ragged && $self->dna_fits;
  my $target = eval {$self->feature->hit} or return $self->SUPER::pad_right;
  return $self->SUPER::pad_right unless $target->end < $target->start && $target->start < $ragged;
  return ($target->end-1) * $self->scale;
}

sub labelwidth {
  my $self = shift;
  return $self->SUPER::labelwidth unless $self->draw_target && $self->dna_fits && $self->label_position eq 'left';
  return $self->{labelwidth} ||= (length($self->label||'')+1) * $self->mono_font->width;
}
sub draw_target {
  my $self = shift;
  return if $self->option('draw_dna');
  return $self->option('draw_target');
}

sub draw_protein_target {
  my $self = shift;
  return if $self->option('draw_protein');
  return $self->option('draw_protein_target');
  return $self->option('draw_target');
}

sub height {
  my $self = shift;
  my $height = $self->SUPER::height;
  return $height unless $self->draw_target || $self->draw_protein_target;
  if ($self->draw_target) {
    return $height unless $self->dna_fits;
  }
  if ($self->draw_protein_target) {
    return $height unless $self->protein_fits;
  }
  my $fontheight = $self->mono_font->height;
  return $fontheight if $fontheight > $height;
}

# group sets connector to 'solid'
sub connector {
  my $self = shift;
  return $self->SUPER::connector(@_) if $self->all_callbacks;
  return ($self->SUPER::connector(@_) || 'solid');
}

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

sub maxdepth {
  my $self = shift;
  my $md   = $self->Bio::Graphics::Glyph::maxdepth;
  return $md if defined $md;
  return 1;
}

# this was willfully confusing
#sub fontcolor {
#  my $self = shift;
#  return $self->SUPER::fontcolor unless $self->draw_target;# || $self->option('draw_dna');
#  return $self->SUPER::fontcolor unless $self->dna_fits;
#  return $self->bgcolor;
#}

# Override _subfeat() method to make it appear that a top-level feature that
# has no subfeatures appears as a feature that has a single subfeature.
# Otherwise at high mags gaps will be drawn as components rather than
# as connectors.  Because of differing representations of split features
# in Bio::DB::GFF::Feature and Bio::SeqFeature::Generic, there is
# some breakage of encapsulation here.
sub _subfeat {
    my $self    = shift;
    my $feature = shift;

    my @subfeat = $self->SUPER::_subfeat($feature);

    if (!@subfeat && $self->option('split_on_cigar')) {
	my $cigar   = $self->_get_cigar($feature);
	if ($cigar && @$cigar) {
	    return $self->_split_on_cigar($feature,$cigar);
	}
    }

    return @subfeat if @subfeat;
    if ($self->level == 0 && !@subfeat && !$self->feature_has_subparts) {
	return $self->feature;
    } else {
	return;
    }
}

sub _split_on_cigar {
    my $self = shift;
    my ($feature,$cigar) = @_;

    my $source_start = $feature->start;
    my $source_end   = $feature->end;
    my $ss  = $feature->strand;
    my $ts  = $feature->hit->strand;

    # Render -/- alignments on the + strand
    if ($ss == -1 && $ts == -1) {
        $ss = 1;
    }

    my $target_start = eval {$feature->hit->start} || return $feature;