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GFF format), and I<subtype> is a description of how the feature was
derived (the "source" field of the GFF format).  Either of these
fields can be absent, and either can be a regular expression.  More
advanced filtering is not supported, but is provided by the Sanger
Centre's GFF module.

The order of the features in the returned list is not specified.  To
obtain features sorted by position, use this idiom:

  @features = sort { $a->start <=> $b->start } $seq->features;

=head2 feature_list()

  my $list = $seq->feature_list();

This method returns a summary list of the features that cross the
sequence in the form of a L<Ace::Feature::List> object.  From the
L<Ace::Feature::List> object you can obtain the list of feature names
and the number of each type.  The feature list is obtained from the
ACeDB server with a single short transaction, and therefore has much
less overhead than features().

See L<Ace::Feature::List> for more details.

=head2 transcripts()

This returns a list of Ace::Sequence::Transcript objects, which are
specializations of Ace::Sequence::Feature.  See L<Ace::Sequence::Transcript>
for details.

=head2 clones()

This returns a list of Ace::Sequence::Feature objects containing
reconstructed clones.  This is a nasty hack, because ACEDB currently
records clone ends, but not the clones themselves, meaning that we
will not always know both ends of the clone.  In this case the missing
end has a synthetic position of -99,999,999 or +99,999,999.  Sorry.

=head2 gff()

  $gff = $seq->gff();
  $gff = $seq->gff(-abs      => 1,
                   -features => ['exon','intron:GeneFinder']);

This method returns a GFF file as a scalar.  The following arguments
are optional:

=over 4

=item -abs

Ordinarily the feature entries in the GFF file will be returned in
coordinates relative to the start of the I<Ace::Sequence> object.
Position 1 will be the start of the sequence object, and the "+"
strand will be the sequence object's natural orientation.  However if
a true value is provided to B<-abs>, the coordinate system used will
be relative to the start of the source sequence, i.e. the native ACeDB
Sequence object (usually a cosmid sequence or a link).  

If a reference sequence was provided when the I<Ace::Sequence> was
created, it will be used by default to set the coordinate system.
Relative coordinates can be reenabled by providing a false value to
B<-abs>.  

Ordinarily the coordinate system manipulations automatically "do what
you want" and you will not need to adjust them.  See also the abs()
method described below.

=item -features

The B<-features> argument filters the features according to a list of
types and subtypes.  The format is identical to the one described for
the features() method.  A single filter may be provided as a scalar
string.  Multiple filters may be passed as an array reference.

=back

See also the GFF() method described next.

=head2 GFF()

  $gff_object = $seq->gff;
  $gff_object = $seq->gff(-abs      => 1,
                   -features => ['exon','intron:GeneFinder']);

The GFF() method takes the same arguments as gff() described above,
but it returns a I<GFF::GeneFeatureSet> object from the GFF.pm
module.  If the GFF module is not installed, this method will generate 
a fatal error.

=head2 absolute()

 $abs = $seq->absolute;
 $abs = $seq->absolute(1);

This method controls whether the coordinates of features are returned
in absolute or relative coordinates.  "Absolute" coordinates are
relative to the underlying source or reference sequence.  "Relative"
coordinates are relative to the I<Ace::Sequence> object.  By default,
coordinates are relative unless new() was provided with a reference
sequence.  This default can be examined and changed using absolute().

=head2 automerge()

  $merge = $seq->automerge;
  $seq->automerge(0);

This method controls whether groups of features will automatically be
merged together by the features() call.  If true (the default), then
the left and right end of clones will be merged into "clone" features,
introns, exons and CDS entries will be merged into
Ace::Sequence::Transcript objects, and similarity entries will be
merged into Ace::Sequence::GappedAlignment objects.

=head2 db()

  $db = $seq->db;

Returns the L<Ace> database accessor associated with this sequence.

=head1 SEE ALSO

L<Ace>, L<Ace::Object>, L<Ace::Sequence::Feature>,
L<Ace::Sequence::FeatureList>, L<GFF>

=head1 AUTHOR

Lincoln Stein <lstein@cshl.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

Many thanks to David Block <dblock@gene.pbi.nrc.ca> for finding and
fixing the nasty off-by-one errors.

Copyright (c) 1999, Lincoln D. Stein

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

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