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 Function: load a single DNA entry
 Returns : true if successfully loaded
 Args    : a raw sequence string (DNA, RNA, protein)
 Status  : Public

=cut

sub load_sequence_string {
  my $self = shift;
  my ($acc,$seq)  = @_;
  my $offset = 0;
  $self->insert_sequence_chunk($acc,\$offset,\$seq) or return;
  $self->insert_sequence($acc,$offset,$seq) or return;
  1;
}

sub setup_argv {
  my $self = shift;
  my $file_or_directory = shift;
  my @suffixes          = @_;
  no strict 'refs';  # so that we can call fileno() on the argument

  my @argv;

  if (-d $file_or_directory) {
    # Because glob() is broken with long file names that contain spaces
    $file_or_directory = Win32::GetShortPathName($file_or_directory)
      if $^O =~ /^MSWin/i && eval 'use Win32; 1';
    @argv = map { glob("$file_or_directory/*.{$_,$_.gz,$_.Z,$_.bz2}")} @suffixes;
  }elsif (my $fd = fileno($file_or_directory)) {
    open STDIN,"<&=$fd" or $self->throw("Can't dup STDIN");
    @argv = '-';
  } elsif (ref $file_or_directory) {
    @argv = @$file_or_directory;
  } else {
    @argv = $file_or_directory;
  }

  foreach (@argv) {
    if (/\.gz$/) {
      $_ = "gunzip -c $_ |";
    } elsif (/\.Z$/) {
      $_ = "uncompress -c $_ |";
    } elsif (/\.bz2$/) {
      $_ = "bunzip2 -c $_ |";
    }
  }
  @argv;
}

=head2 lock_on_load

 Title   : lock_on_load
 Usage   : $lock = $db->lock_on_load([$lock])
 Function: set write locking during load
 Returns : current value of lock-on-load flag
 Args    : new value of lock-on-load-flag
 Status  : Public

This method is honored by some of the adaptors.  If the value is true,
the tables used by the GFF modules will be locked for writing during
loads and inaccessible to other processes.

=cut

sub lock_on_load {
  my $self = shift;
  my $d = $self->{lock};
  $self->{lock} = shift if @_;
  $d;
}

=head2 meta

 Title   : meta
 Usage   : $value = $db->meta($name [,$newval])
 Function: get or set a meta variable
 Returns : a string
 Args    : meta variable name and optionally value
 Status  : abstract

Get or set a named metavalues for the database.  Metavalues can be
used for database-specific settings.

By default, this method does nothing!

=cut

sub meta {
  my $self = shift;
  my ($name,$value) = @_;
  return;
}

=head2 default_meta_values

 Title   : default_meta_values
 Usage   : %values = $db->default_meta_values
 Function: empty the database
 Returns : a list of tag=>value pairs
 Args    : none
 Status  : protected

This method returns a list of tag=E<gt>value pairs that contain default
meta information about the database.  It is invoked by initialize() to
write out the default meta values.  The base class version returns an
empty list.

For things to work properly, meta value names must be UPPERCASE.

=cut

sub default_meta_values {
  my $self = shift;
  return ();
}


=head2 error

 Title   : error