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	push(@file,$file);
    }
   
    my $out = Bio::SeqIO::MultiFile->new( '-format' => $self->_file_format , -files => \@file);
    return $out;
}

=head2 get_all_primary_ids

 Title   : get_all_primary_ids
 Usage   : @ids = $seqdb->get_all_primary_ids()
 Function: gives an array of all the primary_ids of the 
           sequence objects in the database. These
           maybe ids (display style) or accession numbers
           or something else completely different - they
           *are not* meaningful outside of this database
           implementation.
 Example :
 Returns : an array of strings
 Args    : none


=cut

sub get_all_primary_ids {
   my ($self,@args) = @_;
    my $db = $self->db;
   
   # the problem is here that we have indexed things both on
   # accession number and name. 

   # We could take two options
   # here - loop over the database, returning only one copy of each
   # id that points to the same byte position, or we rely on semantics
   # of accession numbers.

   # someone is going to index a database with no accession numbers.
   # doh!. We have to uniquify the index...

   my( %bytepos );
   while (my($id, $rec) = each %$db) {
       if( $id =~ /^__/ ) {
           # internal info
           next;
       }
       my ($file, $begin) = $self->unpack_record( $rec );
       
       $bytepos{"$file:$begin"} = $id;
   }

   return values %bytepos;
}


=head2 get_Seq_by_primary_id

 Title   : get_Seq_by_primary_id
 Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
 Function: Gets a Bio::Seq object by the primary id. The primary
           id in these cases has to come from $db->get_all_primary_ids.
           There is no other way to get (or guess) the primary_ids
           in a database.

           The other possibility is to get Bio::PrimarySeqI objects
           via the get_PrimarySeq_stream and the primary_id field
           on these objects are specified as the ids to use here.
 Returns : A Bio::Seq object
 Args    : primary id (as a string)
 Throws  : "acc does not exist" exception


=cut

sub get_Seq_by_primary_id {
   my ($self,$id) = @_;
   return $self->fetch($id);
}

1;