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  my $self = shift;

  return $self->{'uniquename'} = shift if @_;
  return $self->{'uniquename'};
}

=head2 is_analysis()

  Title   : is_analysis
  Usage   : $obj->is_analysis($newval)
  Function: holds feature.is_analysis
  Returns : value of is_analysis (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

=cut

sub is_analysis {
  my $self = shift;
  return $self->{'is_analysis'} = shift if defined($_[0]);

  my $dbh = $self->factory->dbh;
  my $fid = $self->feature_id;
  my $sth = $dbh->prepare("SELECT is_analysis FROM feature WHERE feature_id =?");
  $sth->execute($fid);

  my ($is_analysis) = $sth->fetchrow_array;

  $sth->finish;
  return $self->{'is_analysis'} = $is_analysis;
} 


######################################################################
# ISA Bio::SeqFeatureI
######################################################################

=head1 SeqFeatureI methods

Bio::DB::Das::Chado::Segment::Feature implements the Bio::SeqFeatureI
interface.  Methods described below, see Bio:SeqFeatureI for more
details.

=cut

=head2 attach_seq()

 Title   : attach_seq
 Usage   : $sf->attach_seq($seq)
 Function: Attaches a Bio::Seq object to this feature. This
           Bio::Seq object is for the *entire* sequence: ie
           from 1 to 10000
 Example :
 Returns : TRUE on success
 Args    : a Bio::PrimarySeqI compliant object

=cut

sub attach_seq {
  my ($self) = @_;

  $self->throw_not_implemented();
}

=head2 display_name()

  Title   : display_name
  Function: aliased to uniquename() for Bio::SeqFeatureI compatibility

=cut

*display_name = \&group;

=head2 entire_seq()

 Title   : entire_seq
 Usage   : $whole_seq = $sf->entire_seq()
 Function: gives the entire sequence that this seqfeature is attached to
 Example :
 Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
           sequence attached
 Args    : none


=cut

sub entire_seq {
    my $self = shift;
    $self->SUPER::seq();
}

=head2 get_all_tags()

  Title   : get_all_tags
  Function: aliased to all_tags() for Bio::SeqFeatureI compatibility

=cut

*get_all_tags = \&all_tags;

=head2 get_SeqFeatures()

  Title   : get_SeqFeatures
  Function: aliased to sub_SeqFeature() for Bio::SeqFeatureI compatibility

=cut

*get_SeqFeatures = \&sub_SeqFeature;

=head2 get_tag_values()

  Title   : get_tag_values
  Usage   : $feature->get_tag_values
  Function: Returns values associated with a particular tag
  Returns : A list of values
  Args    : A string (the name of the tag)


=cut

sub get_tag_values {
  my $self = shift;
  my $tag  = shift;

  my @return = $self->attributes($tag);
  return @return;
}

=head2 get_tagset_values()

  Title   : get_tagset_values
  Usage   :
  Function: ???
  Returns :
  Args    :


=cut

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

  $self->throw_not_implemented();
}

=head2 gff_string()

  Title   : gff_string
  Usage   :
  Function: ???
  Returns :
  Args    :


=cut

sub gff_string {
  my $self = shift;
  my $recurse = shift;
  my $feature_id=$self->feature_id; 

  my $gff_init_query = "SELECT ref,source,type,fstart,fend,score,strand,phase FROM gff3view WHERE feature_id=$feature_id"; 
  my @row_ary = $self->factory->dbh->selectrow_array($gff_init_query);
  my $string = join("\t",@row_ary)."\t";

  my $gff_atts_query = "SELECT type,attribute from gff3atts where feature_id=?";
  my $sth = $self->factory->dbh->prepare($gff_atts_query);
  $sth->execute($feature_id);

  while (my $hashref = $sth->fetchrow_hashref()) {
      my $attribute = uri_escape($$hashref{'attribute'});
      next unless $attribute;
      $string .= "$$hashref{'type'}=$attribute;";
  } 

  if ($recurse) {
      foreach($self->sub_SeqFeature) {
          $string .= "\n";
          $string .= $_->gff_string(1);
      }
  }

  return $string;
}

=head2 has_tag()

  Title   : has_tag
  Usage   :
  Function: ???
  Returns :
  Args    :


=cut

sub has_tag { 
  my $self = shift;
  my $tag  = shift;
  my %tags = map {$_=>1} $self->all_tags;
  return $tags{$tag};
}

=head2 primary_tag()

  Title   : primary_tag
  Function: aliased to type() for Bio::SeqFeatureI compatibility

=cut

*primary_tag = \&method;

=head2 seq()

  Title   : seq
  Usage   :
  Function: ???
  Returns :
  Args    :

=cut

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

=head2 seq_id()

  Title   : seq_id
  Usage   : $obj->seq_id($newval)
  Function: Set or get the name of the reference sequence that the feature 
            resides on.
  Returns : value of seq_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)


=cut

sub seq_id {
  my $self = shift;

  return $self->{'seq_id'} = shift if @_;
  return $self->{'seq_id'} if defined $self->{'seq_id'};

  #OK, no seq_id found, we'll try to find one.

  my $feature_id = $self->feature_id;
  return unless $feature_id;

  my $query =<<END
  SELECT COALESCE(f.name,f.uniquename) AS seq_id
  FROM feature f join featureloc fl ON (f.feature_id = fl.srcfeature_id) 
  WHERE fl.feature_id = $feature_id AND fl.rank = 0
END
;

  my ($seq_id) = $self->factory->dbh->selectrow_array($query);

  return $self->{'seq_id'} = $seq_id;
}

######################################################################
# ISA Bio::SeqFeatureI
######################################################################

=head1 Bio::RangeI methods

Bio::SeqFeatureI in turn ISA Bio::RangeI.  Bio::RangeI interface
methods described below, L<Bio::RangeI> for details.

=cut

=head2 end()

  Title   : end
  Function: inherited, L<Bio::DB::Das::Chado::Segment>

=cut

=head2 start()

  Title   : start
  Function: inherited, L<Bio::DB::Das::Chado::Segment>