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sub _config_path {
  my $self = shift;
  $self->_catfile($self->_config_name);
}

sub _catfile {
  my $self = shift;
  my $component = shift;
  File::Spec->catfile($self->directory,$self->dbname,$component);
}

sub _config_name { CONFIG_FILE_NAME }

sub _path2fileno {
  my $self = shift;
  my $path = shift;
  return $self->add_flat_file($path)
    unless exists $self->{flat_flat_file_no}{$path};
  $self->{flat_flat_file_no}{$path};
}

sub _fileno2path {
  my $self = shift;
  my $fileno = shift;
  $self->{flat_flat_file_path}{$fileno};
}

sub _files {
  my $self = shift;
  my $paths = $self->{flat_flat_file_no};
  return keys %$paths;
}

=head2 fetch

  Title   : fetch
  Usage   : $index->fetch( $id )
  Function: Returns a Bio::Seq object from the index
  Example : $seq = $index->fetch( 'dJ67B12' )
  Returns : Bio::Seq object
  Args    : ID

Deprecated.  Use get_Seq_by_id instead.

=cut

sub fetch { shift->get_Seq_by_id(@_) }


=head2 To Be Implemented in Subclasses

The following methods MUST be implemented by subclasses.

=cut

# create real live Bio::Seq object
sub get_Seq_by_id {
  my $self = shift;
  my $id   = shift;
  $self->throw_not_implemented;
}


# fetch array of Bio::Seq objects
sub get_Seq_by_acc {
  my $self = shift;
  return $self->get_Seq_by_id(shift) if @_ == 1;
  my ($ns,$key) = @_;

  $self->throw_not_implemented;
}

sub fetch_raw {
  my ($self,$id,$namespace) = @_;
  $self->throw_not_implemented;
}

sub default_file_format {
  my $self = shift;
  $self->throw_not_implemented;
}

sub _store_index {
   my $self = shift;
   my ($ids,$file,$offset,$length) = @_;
   $self->throw_not_implemented;
}

=head2 May Be Overridden in Subclasses

The following methods MAY be overridden by subclasses.

=cut

sub default_primary_namespace {
  return "ACC";
}

sub default_secondary_namespaces {
  return;
}

sub seq_to_ids {
  my $self = shift;
  my $seq  = shift;
  my %ids;
  $ids{$self->primary_namespace} = $seq->accession_number;
  \%ids;
}

sub DESTROY {
  my $self = shift;
  $self->close;
}


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