use Bio::EnsEMBL::Registry;

  my $homology_adaptor = $reg->get_adaptor("Multi", "compara", "Homology");

  ## Please, refer to Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor
  ## to see how to get a Member from the database. Also, you can
  ## find alternative ways to fetch homologies in the POD for the
  ## Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor module.

  my $homologies = $homology_adaptor->fetch_all_by_Member($member);

  foreach my $this_homology (@$homologies) {
    my $homologue_genes = $this_homology->gene_list();
    print join(" and ", @$homologue_genes), " are ",
        $this_homology->description, "\n";
  }

  my ($codon) = @_;
  
  if (defined $FOURD_CODONS{$codon}) {
    return 1;
  }

  return 0;

  my ($codon) = @_;
  
  if (defined $TWOD_CODONS{$codon}) {
    return 1;
  }

  return 0;

  my $self = shift;

  $self->{'_ancestor_node_id'} = shift if(@_);
  $self->{'_ancestor_node_id'} = '' unless($self->{'_ancestor_node_id'});
  return $self->{'_ancestor_node_id'};

  my ($self, $dn, $apply_threshold_on_ds) = @_;

  $self->{'_dn'} = $dn if (defined $dn);
  $apply_threshold_on_ds = 1 unless (defined $apply_threshold_on_ds);

  unless (defined $self->ds(undef, $apply_threshold_on_ds)) {
    return undef;
  }

  return $self->{'_dn'};

  my $self = shift;
  my $apply_threshold_on_ds = shift;
  
  $apply_threshold_on_ds = 1 unless (defined $apply_threshold_on_ds);

  my $ds = $self->ds(undef, $apply_threshold_on_ds);
  my $dn = $self->dn(undef, $apply_threshold_on_ds);

  unless (defined $dn &&
          defined $ds &&
          $ds !=0) {
    return undef;
  }

  unless (defined $self->{'_dnds_ratio'}) {
    $self->{'_dnds_ratio'} = sprintf("%.5f",$dn/$ds);
  }

  return $self->{'_dnds_ratio'};

  my ($self, $ds, $apply_threshold_on_ds) = @_;

  $self->{'_ds'} = $ds if (defined $ds);
  $apply_threshold_on_ds = 1 unless (defined $apply_threshold_on_ds);

  if (defined $self->{'_ds'} && 
      defined $self->{'_threshold_on_ds'} &&
      $self->{'_ds'} > $self->{'_threshold_on_ds'}) {
    
    if ($apply_threshold_on_ds) {
      return undef;
    } else {
      warning("Threshold on ds values is switched off. Be aware that you may obtain saturated ds values that are not to be trusted, neither the dn/ds ratio\n");
    }
  }

  return $self->{'_ds'};

  my $self = shift;
  my @genes;
  foreach my $member_attribute (@{$self->get_all_Member_Attribute}) {
    my ($member, $attribute) = @{$member_attribute};
    push @genes, $member;
  }
  return\@ genes;

  my $self = shift;
  
  my $sa = Bio::SimpleAlign->new();

  #Hack to try to work with both bioperl 0.7 and 1.2:
  #Check to see if the method is called 'addSeq' or 'add_seq'
  my $bio07 = 0;
  if(!$sa->can('add_seq')) {
    $bio07 = 1;
  }

  my $ma = $self->adaptor->db->get_MemberAdaptor;

  my %member_seqstr;
  foreach my $member_attribute (@{$self->get_all_Member_Attribute}) {
    my ($member, $attribute) = @{$member_attribute};
    my $peptide_member = $ma->fetch_by_dbID($attribute->peptide_member_id);
    my $seqstr;
    $seqstr = $attribute->cdna_alignment_string($peptide_member);
    next if(!$seqstr);
#    print STDERR $seqstr,"\n";
    my @tmp_tab = split /\s+/, $seqstr;
#    print STDERR "tnp_tab 0: ", $tmp_tab[0],"\n";
    $member_seqstr{$peptide_member->stable_id} =\@ tmp_tab;
  }
  
  my $seqstr_length;
  foreach my $seqid (keys %member_seqstr) {
    unless (defined $seqstr_length) {
 #     print STDERR $member_seqstr{$seqid}->[0],"\n";
      $seqstr_length = scalar @{$member_seqstr{$seqid}};
      next;
    }
    unless ($seqstr_length == scalar @{$member_seqstr{$seqid}}) {
      die "Length of dna alignment are not the same, $seqstr_length and " . scalar @{$member_seqstr{$seqid}} ." respectively for homology_id " . $self->dbID . "\n";
    }
  }
  
  my %FourD_member_seqstr;
  for (my $i=0; $i < $seqstr_length; $i++) {
    my $FourD_codon = 1;
    my $FourD_aminoacid;
    foreach my $seqid (keys %member_seqstr) {
      if (FourD_codon($member_seqstr{$seqid}->[$i])) {
        if (defined $FourD_aminoacid && 
            $FourD_aminoacid eq $FOURD_CODONS{$member_seqstr{$seqid}->[$i]}) {
#          print STDERR "YES ",$FOURD_CODONS{$member_seqstr{$seqid}->[$i]}," ",$member_seqstr{$seqid}->[$i],"\n";
          next;
        } elsif (defined $FourD_aminoacid) {
#          print STDERR "NO ",$FOURD_CODONS{$member_seqstr{$seqid}->[$i]}," ",$member_seqstr{$seqid}->[$i],"\n";
          $FourD_codon = 0;
          last;
        } else {
          $FourD_aminoacid = $FOURD_CODONS{$member_seqstr{$seqid}->[$i]};
#          print STDERR $FOURD_CODONS{$member_seqstr{$seqid}->[$i]}," ",$member_seqstr{$seqid}->[$i]," ";
        }
        next;
      } else {
#        print STDERR "NO ",$CODONS{$member_seqstr{$seqid}->[$i]}," ",$member_seqstr{$seqid}->[$i],"\n";
        $FourD_codon = 0;
        last;
      }
    }
    next unless ($FourD_codon);
    foreach my $seqid (keys %member_seqstr) {
      $FourD_member_seqstr{$seqid} .= substr($member_seqstr{$seqid}->[$i],2,1);
    }
  }
  
  foreach my $seqid (keys %FourD_member_seqstr) {
  
    my $seq = Bio::LocatableSeq->new(-SEQ    => $FourD_member_seqstr{$seqid},
                                     -START  => 1,
                                     -END    => length($FourD_member_seqstr{$seqid}),
                                     -ID     => $seqid,
                                     -STRAND => 0);
    
    if($bio07) {
      $sa->addSeq($seq);
    } else {
      $sa->add_seq($seq);
    }
  }
  
  return $sa;

  my $self = shift;
  my $alignment = shift;
  my $changeSelenos = shift;
  unless (defined $changeSelenos) {
      $changeSelenos = 0;
  }
  
  my $sa = Bio::SimpleAlign->new();

  #Hack to try to work with both bioperl 0.7 and 1.2:
  #Check to see if the method is called 'addSeq' or 'add_seq'
  my $bio07 = 0;
  if(!$sa->can('add_seq')) {
    $bio07 = 1;
  }

  my $ma = $self->adaptor->db->get_MemberAdaptor;

  foreach my $member_attribute (@{$self->get_all_Member_Attribute}) {
    my ($member, $attribute) = @{$member_attribute};
    if ($member->chr_name =~ /mt/i) {
      # codeml icodes
      #      0:universal code (default)
      if ($member->taxon->classification =~ /vertebrata/i) {
        #      1:mamalian mt
        $sa->{_special_codeml_icode} = 1;
      } else {
        #      4:invertebrate mt
        $sa->{_special_codeml_icode} = 4;
      }
    }
    my $peptide_member = $ma->fetch_by_dbID($attribute->peptide_member_id);
    my $seqstr;
    my $alphabet = 'protein';
    if (defined $alignment && $alignment =~ /^cdna$/i) {
      $seqstr = $attribute->cdna_alignment_string($peptide_member,$changeSelenos);
      $seqstr =~ s/\s+//g;
      $alphabet = 'dna';
    } else {
      $seqstr = $attribute->alignment_string($peptide_member);
    }
    next if(!$seqstr);
    my $cigar_start = $attribute->cigar_start;
    my $cigar_end = $attribute->cigar_end;
    $cigar_start = 1 unless (defined $cigar_start && $cigar_start != 0);
    unless (defined $cigar_end && $cigar_end != 0) {
      $cigar_end = $peptide_member->seq_length;
      $cigar_end = $cigar_end*3 if (defined $alignment && $alignment =~ /^cdna$/i);
    }
    #print STDERR "cigar_start $cigar_start cigar_end $cigar_end\n";
    my $seq = Bio::LocatableSeq->new(-SEQ    => $seqstr,
                                     -ALPHABET  => $alphabet,
                                     -START  => $cigar_start,
                                     -END    => $cigar_end,
                                     -ID     => $peptide_member->stable_id,
                                     -STRAND => 0);

    if($bio07) {
      $sa->addSeq($seq);
    } else {
      $sa->add_seq($seq);
    }
  }

  return $sa;

  my $self = shift;

  my @pafs;
  throw("homology must have a valid adaptor and db in order to get peptide_align_features")
    unless($self->adaptor and $self->adaptor->db);
  my $pafDBA = $self->adaptor->db->get_PeptideAlignFeatureAdaptor;
  
  foreach my $RefArrayOfMemberAttributeArrayRef ($self->get_Member_Attribute_by_source("ENSEMBLGENE")) {
    foreach my $memAttributeArrayRef (@{$RefArrayOfMemberAttributeArrayRef}) {
      my $member = $memAttributeArrayRef->[0];
      my $attribute = $memAttributeArrayRef->[1];

      if($attribute->peptide_align_feature_id) {
        my $paf = $pafDBA->fetch_by_dbID($attribute->peptide_align_feature_id);
        push @pafs, $paf;
      }
    }
  }
  return\@ pafs;

  my $self = shift;
  my $species_name = shift;
  
  foreach my $member_attribute (@{$self->get_all_Member_Attribute}) {
    my ($member, $attribute) = @{$member_attribute};
    return 1 if($member->genome_db->name eq $species_name);
  }
  return 0;

  my $self = shift;
  return $self->{'_homology_key'} if(defined($self->{'_homology_key'}));
  
  my @genes;
  foreach my $member_attribute (@{$self->get_all_Member_Attribute}) {
    my ($member, $attribute) = @{$member_attribute};
    push @genes, $member;
  }
  @genes = sort {$a->taxon_id <=> $b->taxon_id || $a->stable_id cmp $b->stable_id} @genes;
  @genes = map ($_->stable_id, @genes);

  my $homology_key = join('_', @genes);
  return $homology_key;

  my $self = shift;
  $self->{'_lnl'} = shift if(@_);
  return $self->{'_lnl'};

  my $self = shift;
  $self->{'_n'} = shift if(@_);
  return $self->{'_n'};

  my $self = shift;

  $self->{'_ancestor_node_id'} = shift if(@_);
  $self->{'_ancestor_node_id'} = '' unless($self->{'_ancestor_node_id'});
  return $self->{'_ancestor_node_id'};

  my $self = shift;
  
  printf("Homology %d,%s,%s : ", $self->dbID, $self->description, $self->subtype);
  foreach my $member_attribute (@{$self->get_all_Member_Attribute}) {
    my ($member, $attribute) = @{$member_attribute};
    printf("%s(%d)\t", $member->stable_id, $member->dbID);
  }
  print("\n");

  my $self = shift;
  $self->{'_s'} = shift if(@_);
  return $self->{'_s'};

  my $self = shift;
  # deprecate("Use taxonomy_level() instead.");
  return $self->taxonomy_level(@_);

  my $self = shift;

  my $ancestor_node_id = $self->ancestor_node_id;
  my $tree_dba = $self->adaptor->db->get_ProteinTreeAdaptor;
  my $ancestor = $tree_dba->fetch_node_by_node_id($ancestor_node_id);

  return $ancestor->get_tagvalue('taxon_alias') || undef;

  my $self = shift;
  $self->{'_subtype'} = shift if(@_);
  $self->{'_subtype'} = '' unless($self->{'_subtype'});
  return $self->{'_subtype'};

  my $self = shift;
  $self->{'_threshold_on_ds'} = shift if(@_);
  return $self->{'_threshold_on_ds'};

  my $self = shift;

  $self->{'_tree_node_id'} = shift if(@_);
  $self->{'_tree_node_id'} = '' unless($self->{'_tree_node_id'});
  return $self->{'_tree_node_id'};
  
}


1;