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  my $db      = shift || $self->db;

  my $parent = $self->parent;
  my $start = $self->start(1);
  my $end   = $self->end(1);
  ($start,$end) = ($end,$start) if $start > $end;  #flippity floppity

  my $coord   = "-coords $start $end";

  # BAD BAD HACK ALERT - CHECKS THE QUERY THAT IS PASSED DOWN
  # ALSO MAKES THINGS INCOMPATIBLE WITH PRIOR 4.9 servers.
#  my $opt     = $command =~ /seqfeatures/ ? '-nodna' : '';
  my $opt = '-noclip';

  my $query = "gif seqget $parent $opt $coord ; $command";
  warn $query if $self->debug;

  return $db->raw_query("gif seqget $parent $opt $coord ; $command");
}

# utility function -- reverse complement
sub _complement {
  my $dna = shift;
  $$dna =~ tr/GATCgatc/CTAGctag/;
  $$dna = scalar reverse $$dna;
}

sub _feature_filter {
  my $self = shift;
  my $features = shift;
  return '' unless $features;
  my $opt = '';
  $opt = '+feature ' . join('|',@$features) if ref($features) eq 'ARRAY' && @$features;
  $opt = "+feature $features" unless ref $features;
  $opt;
}

1;

=head1 NAME

Ace::Sequence - Examine ACeDB Sequence Objects

=head1 SYNOPSIS

    # open database connection and get an Ace::Object sequence
    use Ace::Sequence;

    $db  = Ace->connect(-host => 'stein.cshl.org',-port => 200005);
    $obj = $db->fetch(Predicted_gene => 'ZK154.3');

    # Wrap it in an Ace::Sequence object 
    $seq = Ace::Sequence->new($obj);

    # Find all the exons
    @exons = $seq->features('exon');

    # Find all the exons predicted by various versions of "genefinder"
    @exons = $seq->features('exon:genefinder.*');

    # Iterate through the exons, printing their start, end and DNA
    for my $exon (@exons) {
      print join "\t",$exon->start,$exon->end,$exon->dna,"\n";
    }

    # Find the region 1000 kb upstream of the first exon
    $sub = Ace::Sequence->new(-seq=>$exons[0],
                              -offset=>-1000,-length=>1000);

    # Find all features in that area
    @features = $sub->features;

    # Print its DNA
    print $sub->dna;

    # Create a new Sequence object from the first 500 kb of chromosome 1
    $seq = Ace::Sequence->new(-name=>'CHROMOSOME_I',-db=>$db,
			      -offset=>0,-length=>500_000);

    # Get the GFF dump as a text string
    $gff = $seq->gff;

    # Limit dump to Predicted_genes
    $gff_genes = $seq->gff(-features=>'Predicted_gene');

    # Return a GFF object (using optional GFF.pm module from Sanger)
    $gff_obj = $seq->GFF;

=head1 DESCRIPTION

I<Ace::Sequence>, and its allied classes L<Ace::Sequence::Feature> and
L<Ace::Sequence::FeatureList>, provide a convenient interface to the
ACeDB Sequence classes and the GFF sequence feature file format.

Using this class, you can define a region of the genome by using a
landmark (sequenced clone, link, superlink, predicted gene), an offset
from that landmark, and a distance.  Offsets and distances can be
positive or negative.  This will return an I<Ace::Sequence> object.
Once a region is defined, you may retrieve its DNA sequence, or query
the database for any features that may be contained within this
region.  Features can be returned as objects (using the
I<Ace::Sequence::Feature> class), as GFF text-only dumps, or in the
form of the GFF class defined by the Sanger Centre's GFF.pm module.

This class builds on top of L<Ace> and L<Ace::Object>.  Please see
their manual pages before consulting this one.

=head1 Creating New Ace::Sequence Objects, the new() Method

 $seq = Ace::Sequence->new($object);

 $seq = Ace::Sequence->new(-source  => $object,
                           -offset  => $offset,
                           -length  => $length,
			   -refseq  => $reference_sequence);

 $seq = Ace::Sequence->new(-name    => $name,
			   -db      => $db,
                           -offset  => $offset,
                           -length  => $length,
			   -refseq  => $reference_sequence);

In order to create an I<Ace::Sequence> you will need an active I<Ace>
database accessor.  Sequence regions are defined using a "source"
sequence, an offset, and a length.  Optionally, you may also provide a
"reference sequence" to establish the coordinate system for all
inquiries.  Sequences may be generated from existing I<Ace::Object>
sequence objects, from other I<Ace::Sequence> and
I<Ace::Sequence::Feature> objects, or from a sequence name and a
database handle.

The class method named new() is the interface to these facilities.  In
its simplest, one-argument form, you provide new() with a
previously-created I<Ace::Object> that points to Sequence or