view release on metacpan or  search on metacpan

lib/Bio/DB/GFF/Feature.pm  view on Meta::CPAN

	    $self->{stop}  = $high
	      if (!defined($self->{stop}))  || $high  > $self->{stop};
	  } else {
	    $self->{start} = $high
	      if (!defined($self->{start})) || $high > $self->{start};
	    $self->{stop}  = $low
	      if (!defined($self->{stop}))  || $low  < $self->{stop};
	  }
	}

	# fix up endpoints of targets too (for homologies only)
	my $h = $feat->group;
	next unless $h && $h->isa('Bio::DB::GFF::Homol');
	next unless $g && $g->isa('Bio::DB::GFF::Homol');

	($start,$stop) = ($h->{start},$h->{stop});
	if ($shrink && !$tfirst++) {
	    $g->{start} = $start;
	    $g->{stop}  = $stop;
	} else {
	  if ($start <= $stop) {

lib/Bio/DB/GFF/Feature.pm  view on Meta::CPAN

sub gff_string {
  my $self = shift;
  my $version = $self->version;

  # gff3_string and gff_string are synonymous if the version is set to 3
  return $self->gff3_string(@_) if $version == 3;

  my ($start,$stop) = ($self->start,$self->stop);

  # the defined() tests prevent uninitialized variable warnings, when dealing with clone objects
  # whose endpoints may be undefined
  ($start,$stop) = ($stop,$start) if defined($start) && defined($stop) && $start > $stop;

  my ($class,$name) = ('','');
  my $strand = ('-','.','+')[$self->strand+1];

  my @group;

  if (my $t = $self->target) {
    push @group, $version == 2.5 ? $self->flatten_target($t,2.5) 
                                 : $self->flatten_target($t);

lib/Bio/DB/GFF/Feature.pm  view on Meta::CPAN

 Status  : Public

=cut

sub gff3_string {
  my $self = shift;
  my ($recurse,$parent) = @_;
  my ($start,$stop) = ($self->start,$self->stop);

  # the defined() tests prevent uninitialized variable warnings, when dealing with clone objects
  # whose endpoints may be undefined
  ($start,$stop) = ($stop,$start) if defined($start) && defined($stop) && $start > $stop;

  my $strand = ('-','.','+')[$self->strand+1];
  my $ref = $self->refseq;
  my $n   = ref($ref) ? $ref->name : $ref;
  my $phase = $self->phase;
  $phase = '.' unless defined $phase;

  my ($class,$name) = ('','');
  my @group;