my ($self, $external_db_id, $ensType, $extraType) = @_;

  my $from_sql = '';
  my $where_sql = '';
  my $ID_sql = "oxr.ensembl_id";

  if (defined $extraType) {

	throw('Extra types not accomodated in eFG xref schema');

    if (lc($extraType) eq 'translation') {
      $ID_sql = "tl.translation_id";
    } else {
      $ID_sql = "t.${extraType}_id";
    }

    if (lc($ensType) eq 'translation') {
      $from_sql = 'transcript t, translation tl, ';
      $where_sql = qq(
          t.transcript_id = tl.transcript_id AND
          tl.translation_id = oxr.ensembl_id AND
          t.is_current = 1 AND
      );
    } else {
      $from_sql = 'transcript t, ';
      $where_sql = 't.'.lc($ensType).'_id = oxr.ensembl_id AND '.
          't.is_current = 1 AND ';
    }
  }

 # if (lc($ensType) eq 'gene') {
 #   $from_sql = 'gene g, ';
 #   $where_sql = 'g.gene_id = oxr.ensembl_id AND g.is_current = 1 AND ';
 # } elsif (lc($ensType) eq 'transcript') {
 #   $from_sql = 'transcript t, ';
 #   $where_sql = 't.transcript_id = oxr.ensembl_id AND t.is_current = 1 AND ';
 # } elsif (lc($ensType) eq 'translation') {
 #   $from_sql = 'transcript t, translation tl, ';
  #   $where_sql = qq(
  #       t.transcript_id = tl.transcript_id AND
  #       tl.translation_id = oxr.ensembl_id AND
  #       t.is_current = 1 AND
  #   );
 # }els

  if(lc($ensType) eq 'regulatoryfeature'){
	$from_sql  = 'regulatory_feature rf, ';
	$where_sql = qq( rf.regulatory_feature_id = oxr.ensembl_id AND );
  }
  elsif(lc($ensType) eq 'externalfeature'){
	$from_sql  = 'external_feature ef, ';
	$where_sql = qq( ef.external_feature_id = oxr.ensembl_id AND );
  } 
  elsif(lc($ensType) eq 'annotatedfeature'){
	$from_sql  = 'annotated_feature af, ';
	$where_sql = qq( af.annotated_feature_id = oxr.ensembl_id AND );
  }
  elsif(lc($ensType) eq 'featuretype'){
	$from_sql  = 'featuretype ft, ';
	$where_sql = qq( ft.feature_type_id = oxr.ensembl_id AND );
  }
  elsif(lc($ensType) eq 'probefeature'){
	$from_sql  = 'probe_feature pf, ';
	$where_sql = qq( pf.probe_feature_id = oxr.ensembl_id AND );
  }


  my $query = 
    "SELECT $ID_sql
       FROM $from_sql xref x, object_xref oxr
      WHERE $where_sql x.external_db_id = ? AND
  	     x.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?";

# Increase speed of query by splitting the OR in query into three separate 
# queries. This is because the 'or' statments render the index useless 
# because MySQL can't use any fields in the index.

  my %hash = ();
  my @result = ();


  my $sth = $self->prepare( $query );
  $sth->bind_param(1, "$external_db_id", SQL_VARCHAR);
  $sth->bind_param(2, $ensType, SQL_VARCHAR);
  $sth->execute();
  while( my $r = $sth->fetchrow_array() ) {
    if( !exists $hash{$r} ) {
      $hash{$r} = 1;
      push( @result, $r );
    }
  }
  return @result;
}


1;

  my ( $self, $name, $ensType, $extraType, $external_db_name ) = @_;

  my $from_sql  = '';
  my $where_sql = '';
  my $ID_sql    = "oxr.ensembl_id";

  if ( defined $extraType ) {

	throw('Extra types not accomodated in eFG xref schema');

    if ( lc($extraType) eq 'translation' ) {
      $ID_sql = "tl.translation_id";
    } else {
      $ID_sql = "t.${extraType}_id";
    }

    if ( lc($ensType) eq 'translation' ) {
      $from_sql  = 'transcript t, translation tl, ';
      $where_sql = qq(
          t.transcript_id = tl.transcript_id AND
          tl.translation_id = oxr.ensembl_id AND
          t.is_current = 1 AND
      );
    } else {
      $from_sql  = 'transcript t, ';
      $where_sql = 't.'
        . lc($ensType)
        . '_id = oxr.ensembl_id AND '
        . 't.is_current = 1 AND ';
    }
  }

  #if ( lc($ensType) eq 'gene' ) {
  #  $from_sql  = 'gene g, ';
  #  $where_sql = 'g.gene_id = oxr.ensembl_id AND g.is_current = 1 AND ';
  #} elsif ( lc($ensType) eq 'transcript' ) {
  #  $from_sql = 'transcript t, ';
  #  $where_sql =
  #    't.transcript_id = oxr.ensembl_id AND t.is_current = 1 AND ';
  #} elsif ( lc($ensType) eq 'translation' ) {
  #  $from_sql  = 'transcript t, translation tl, ';
  #  $where_sql = qq(
  #      t.transcript_id = tl.transcript_id AND
  #      tl.translation_id = oxr.ensembl_id AND
  #      t.is_current = 1 AND
  #  );
  #}
  #


  if(lc($ensType) eq 'regulatoryfeature'){
	$from_sql  = 'regulatory_feature rf, ';
	$where_sql = qq( rf.regulatory_feature_id = oxr.ensembl_id AND );
  }
  elsif(lc($ensType) eq 'externalfeature'){
	$from_sql  = 'external_feature ef, ';
	$where_sql = qq( ef.external_feature_id = oxr.ensembl_id AND );
  } 
  elsif(lc($ensType) eq 'annotatedfeature'){
	$from_sql  = 'annotated_feature af, ';
	$where_sql = qq( af.annotated_feature_id = oxr.ensembl_id AND );
  }
  elsif(lc($ensType) eq 'featuretype'){
	$from_sql  = 'featuretype ft, ';
	$where_sql = qq( ft.feature_type_id = oxr.ensembl_id AND );
  }
  elsif(lc($ensType) eq 'probefeature'){
	$from_sql  = 'probe_feature pf, ';
	$where_sql = qq( pf.probe_feature_id = oxr.ensembl_id AND );
  }

  

  if ( defined($external_db_name) ) {
    # Involve the 'external_db' table to limit the hits to a particular
    # external database.

    $from_sql .= 'external_db xdb, ';
    $where_sql .=
        'xdb.db_name LIKE '
      . $self->dbc()->db_handle()->quote( $external_db_name . '%' )
      . ' AND xdb.external_db_id = x.external_db_id AND';
  }

  my @queries = (
    "SELECT $ID_sql
       FROM $from_sql xref x, object_xref oxr
      WHERE $where_sql x.dbprimary_acc = ? AND
             x.xref_id = oxr.xref_id AND
             oxr.ensembl_object_type= ?",
    "SELECT $ID_sql 
       FROM $from_sql xref x, object_xref oxr
      WHERE $where_sql x.display_label = ? AND
             x.xref_id = oxr.xref_id AND
             oxr.ensembl_object_type= ?"
  );

  if ( defined $external_db_name ) {
    # If we are given the name of an external database, we need to join
    # between the 'xref' and the 'object_xref' tables on 'xref_id'.

    push @queries, "SELECT $ID_sql
       FROM $from_sql xref x, object_xref oxr, external_synonym syn
      WHERE $where_sql syn.synonym = ? AND
             x.xref_id = oxr.xref_id AND
             oxr.ensembl_object_type= ? AND
             syn.xref_id = oxr.xref_id";
  } else {
    # If we weren't given an external database name, we can get away
    # with less joins here.

    push @queries, "SELECT $ID_sql
       FROM $from_sql object_xref oxr, external_synonym syn
      WHERE $where_sql syn.synonym = ? AND
             oxr.ensembl_object_type= ? AND
             syn.xref_id = oxr.xref_id";
  }

  # Increase speed of query by splitting the OR in query into three
  # separate queries.  This is because the 'or' statments render the
  # index useless because MySQL can't use any fields in it.

  my %hash   = ();
  my @result = ();

  foreach (@queries) {
    my $sth = $self->prepare($_);
    $sth->bind_param( 1, "$name",  SQL_VARCHAR );
    $sth->bind_param( 2, $ensType, SQL_VARCHAR );
    $sth->execute();

    while ( my $r = $sth->fetchrow_array() ) {
      if ( !exists $hash{$r} ) {
        $hash{$r} = 1;
        push( @result, $r );
      }
    }
  }

  return @result;
} ## end sub _type_by_external_id

  my ( $self, $gene) = @_;
 
  if(! (ref($gene) && $gene->isa('Bio::EnsEMBL::Gene'))) {
    throw("Bio::EnsEMBL::Gene argument expected.");
  }

  throw('Not yet implemented for eFG');


  #This is going to be a bit of a work around as we should really have a separate fetch method
  #fetch_all_by_external_name_object_type?
  #No!! Because this simply pulls back the xrefs, not the object xrefs!!
  #This is the same for the fetch_by_dbID method???

  #_fetch_by_external_id
  #The problem here is that we want to return ox info aswell.
  #Just rewrite _fetch_by_object_type

  my ( $self, $trans) = @_;

  throw('Not implemented in eFG, maybe you want the core DBEntryAdaptor?');  


  if(! $trans->isa('Bio::EnsEMBL::Transcript')){
	throw('Must provide a valid stored Bio::EnsEMBL::Transcript');
  }
  #Thsi method doesn't work like this and just returns the xref with no object_xref info/join.
  $self->fetch_by_db_accession($trans->stable_id, 'ensembl_core_Gene');

  my ( $self, $trans) = @_;
  throw('Not implemented in eFG, maybe you want the core DBEntryAdaptor?');  
}

#Haven't we replaced these for eFG feature with a direct call in the object/object_adaptor?

  my ( $self, $external_name, $external_db_name ) = @_;

  return
    $self->_type_by_external_id( $external_name, 'AnnotatedFeature', undef,
                                 $external_db_name );

  my ( $self, $external_name, $external_db_name ) = @_;

  return
    $self->_type_by_external_id( $external_name, 'ExternalFeature', undef,
                                 $external_db_name );

  my ( $self, $external_name, $external_db_name ) = @_;

  return $self->_type_by_external_id( $external_name, 'FeatureType', 
									  undef, $external_db_name );

   my ($self,$external_db_id) = @_;

throw('Not implemented in eFG, maybe you want the core DBEntryAdaptor?');



   my %T = map { ($_, 1) }
       $self->_type_by_external_db_id( $external_db_id, 'Translation', 'gene' ),
       $self->_type_by_external_db_id( $external_db_id, 'Transcript',  'gene' ),
       $self->_type_by_external_db_id( $external_db_id, 'Gene' );
   return keys %T;

  my ( $self, $external_name, $external_db_name ) = @_;

throw('Not implemented in eFG, maybe you want the core DBEntryAdaptor?');



  my %T = map { ( $_, 1 ) }
    $self->_type_by_external_id( $external_name, 'Translation', 'gene',
                                 $external_db_name ),
    $self->_type_by_external_id( $external_name, 'Transcript', 'gene',
                                 $external_db_name ),
    $self->_type_by_external_id( $external_name, 'Gene', undef,
                                 $external_db_name );

  return keys %T;

  my ( $self, $external_name, $external_db_name ) = @_;

  return
    $self->_type_by_external_id( $external_name, 'ProbeFeature', undef,
                                 $external_db_name );

   my ($self,$external_db_id) = @_;

   my %T = map { ($_, 1) }
            $self->_type_by_external_db_id( $external_db_id, 'RegulatoryFeature' );
   return keys %T;

  my ( $self, $external_name, $external_db_name ) = @_;

 
  return $self->_type_by_external_id( $external_name, 'RegulatoryFeature', 
									  undef, $external_db_name );

  my ( $self, $external_name, $external_db_name ) = @_;

throw('Not implemented in eFG, maybe you want the core DBEntryAdaptor?');



  my %T = map { ( $_, 1 ) }
    $self->_type_by_external_id( $external_name, 'Translation',
                                 'transcript',   $external_db_name
    ),
    $self->_type_by_external_id( $external_name, 'Transcript', undef,
                                 $external_db_name );

  return keys %T;

  my ( $self, $external_name, $external_db_name ) = @_;

  throw('Not implemented in eFG, maybe you want the core DBEntryAdaptor?');


  return
    $self->_type_by_external_id( $external_name, 'Translation', undef,
                                 $external_db_name );

  Arg [1]    : string $dbname - The name of the database which the provided
               accession is for.
  Arg [2]    : string $accession - The accesion of the external reference to
               retrieve.
  Example    : my $xref = $dbea->fetch_by_db_accession('Interpro','IPR003439');
               print $xref->description(), "\n" if($xref);
  Description: Retrieves a DBEntry (xref) via the name of the database it is
               from and its primary accession in that database. Undef is
               returned if the xref cannot be found in the database.
  Returntype : Bio::EnsEMBL::DBSQL::DBEntry
  Exceptions : thrown if arguments are incorrect
  Caller     : general, domainview
  Status     : Stable

  Arg [1]    : string $ensID
  Arg [2]    : string $ensType
  			   (object type to be returned) 
  Arg [3]    : optional $exdbname (external database name)
  Arf [4]    : optional $exdb_type (external database type)
  Example    : $self->_fetch_by_object_type( $translation_id, 'Translation' )
  Description: Fetches DBEntry by Object type
  Returntype : arrayref of DBEntry objects; may be of type IdentityXref if
               there is mapping data, or GoXref if there is linkage data.
  Exceptions : none
  Caller     : fetch_all_by_Gene
               fetch_all_by_Translation
               fetch_all_by_Transcript
  Status     : Stable