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 Title   : fh
 Usage   : $obj->fh
 Function:
 Example : $fh = $obj->fh;      # make a tied filehandle
           $feature = <$fh>;   # read a feature object
           print $fh $feature; # write a feature object
 Returns : filehandle tied to Bio::FeatureIO class
 Args    : none

=cut


sub fh {
  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;
}

# _initialize is chained for all FeatureIO classes

sub _initialize {
    my($self, %arg) = @_;

    # flush is initialized by the Root::IO init

    # initialize the IO part
    $self->seq($arg{-seq});
    $self->_initialize_io(%arg);
}

=head2 next_feature

 Title   : next_feature
 Usage   : $feature = stream->next_feature
 Function: Reads the next feature object from the stream and returns it.

           Certain driver modules may encounter entries in the stream
           that are either misformatted or that use syntax not yet
           understood by the driver. If such an incident is
           recoverable, e.g., by dismissing a feature of a feature
           table or some other non-mandatory part of an entry, the
           driver will issue a warning. In the case of a
           non-recoverable situation an exception will be thrown.  Do
           not assume that you can resume parsing the same stream
           after catching the exception. Note that you can always turn
           recoverable errors into exceptions by calling
           $stream->verbose(2).

 Returns : a Bio::SeqFeatureI feature object
 Args    : none

See L<Bio::Root::RootI>, L<Bio::SeqFeatureI>

=cut

sub next_feature {
   my ($self, $seq) = @_;
   $self->throw_not_implemented;
}

=head2 write_feature

 Title   : write_feature
 Usage   : $stream->write_feature($feature)
 Function: writes the $feature object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::SeqFeature object

=cut

sub write_feature {
    my ($self, $seq) = @_;
    $self->throw_not_implemented();
}

=head2 _load_format_module

 Title   : _load_format_module
 Usage   : *INTERNAL FeatureIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :

=cut

sub _load_format_module {
    my ($self, $format) = @_;
    my $class = ref($self) || $self;
    my $module = $class."::$format";#"Bio::Feature::" . $format;
    my $ok;

    eval {
	$ok = $self->_load_module($module);
    };
    if ( $@ ) {
    print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the FeatureIO system please see the FeatureIO docs.
This includes ways of checking for formats at compile time, not run time
END
  ;
  }
  return $ok;
}

=head2 seq

 Title   : seq
 Usage   : $obj->seq() OR $obj->seq($newSeq)
 Example :
 Returns : Bio::SeqI object
 Args    : newSeq (optional)

=cut

sub seq {
  my $self = shift;
  my $val = shift;

  $self->{'seq'} = $val if defined($val);
  return $self->{'seq'};
}

=head2 _filehandle

 Title   : _filehandle
 Usage   : $obj->_filehandle($newval)
 Function: This method is deprecated. Call _fh() instead.
 Example :
 Returns : value of _filehandle
 Args    : newvalue (optional)