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lib/Bio/DB/Das/Chado/Segment/Feature.pm  view on Meta::CPAN

	my($start,$stop,$strand) = $feat->adjust_bounds;
	$self->{strand} = $strand unless defined $self->{strand};
	if ($start <= $stop) {
	  $self->{start} = $start if !defined($self->{start}) || $start < $self->{start};
	  $self->{stop}  = $stop  if !defined($self->{stop})  || $stop  > $self->{stop};
	} else {
	  $self->{start} = $start if !defined($self->{start}) || $start > $self->{start};
	  $self->{stop}  = $stop  if !defined($self->{stop})  || $stop  < $self->{stop};
	}

	# fix up endpoints of targets too (for homologies only)
#	my $h = $feat->group;
#	next unless $h && $h->isa('Bio::DB::GFF::Homol'); # always false (for now)
#	next unless $g && $g->isa('Bio::DB::GFF::Homol');
#	($start,$stop) = ($h->{start},$h->{stop});
#	if ($h->strand >= 0) {
#	  $g->{start} = $start if !defined($g->{start}) || $start < $g->{start};
#	  $g->{stop}  = $stop  if !defined($g->{stop})  || $stop  > $g->{stop};
#	} else {
#	  $g->{start} = $start if !defined($g->{start}) || $start > $g->{start};
#	  $g->{stop}  = $stop  if !defined($g->{stop})  || $stop  < $g->{stop};