my $self = shift;
  
  my (@coords, $out_id, $out_cs);
  # Query is genomic
  if ( $_[4] eq $self->{'genomic'} ) {
    @coords = $self->{'_mapper'}->genomic2pep(@_[1 .. 3]);
    $out_id = $self->{'peptide_id'};
    $out_cs = $self->{'peptide_cs'};
  # Query is peptide
  } elsif ( $_[4] eq $self->{'peptide'} ) {
    @coords = $self->{'_mapper'}->pep2genomic(@_[1 .. 2]);
    $out_id = $self->{'genomic_id'};
    $out_cs = $self->{'genomic_cs'};
  } else {
    throw($_[4].' is neither the genomic or peptide coordinate system');
  }
  
  for my $c ( @coords ) {
    if ($c->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
      $c->id( $out_id );
      $c->coord_system( $out_cs ); # TranscriptMapper doesn't set this
    }
  }
  return @coords;
}

1;

  my ( $proto, $from, $to, $from_cs, $to_cs, $transcript ) = @_;
  my $class = ref $proto || $proto;
  
  my $self = {
    '_mapper' => Bio::EnsEMBL::TranscriptMapper->new( $transcript->transfer($transcript->slice->seq_region_Slice) ),
    'from'    => $from,
    'to'      => $to,
    'from_cs' => $from_cs,
    'to_cs'   => $to_cs,
  };
  bless $self, $class;
  
  my $is_forward = $to_cs->name =~ m/peptide/;
  $self->{'genomic_id'} = $transcript->slice->seq_region_name;
  $self->{'peptide_id'} = $transcript->translation->stable_id;
  $self->{'genomic'}    = $is_forward ? $from : $to;
  $self->{'peptide'}    = $is_forward ? $to   : $from;
  $self->{'genomic_cs'} = $is_forward ? $from_cs : $to_cs;
  $self->{'peptide_cs'} = $is_forward ? $to_cs   : $from_cs;
  
  return $self;