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# $Id: Seq.pm,v 1.2 2003/07/16 04:35:03 lapp Exp $
#
# BioPerl module for Bio::DB::Persistent::PrimarySeq
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
# 
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
HideShow 48 lines of Pod
=head1 NAME
Bio::DB::Persistent::PrimarySeq - Proxy object for database PrimarySeq 
                                  representations 
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
This is a proxy object which will ferry calls to/from database for the
heavy stuff (sequence data) while it stores the simple attributes in
memory.  This object is obtained from a DBAdaptor.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
  bioperl-l@bio.perl.org
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via email
or the web:
  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/
=head1 AUTHOR - Hilmar Lapp, Ewan Birney
Email hlapp at gmx.net
Based in idea largely on Bio::DB::Seq by Ewan Birney.
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::Persistent::Seq;
use vars qw(@ISA);
use strict;
use Bio::SeqI;
use Bio::DB::Persistent::PrimarySeq;
@ISA = qw(Bio::DB::Persistent::PrimarySeq);
sub new {
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    # success - we hope
    return $self;
}
HideShow 21 lines of Pod
=head1 Overridden methods
=cut
=head2 primary_key
 Title   : primary_key
 Usage   : $obj->primary_key($newval)
 Function: Get/set the primary key value.
           We override this here from PersistentObjectI in order to
           propagate the primary key to a possibly attached PrimarySeq
           object if PrimarySeqI is implemented by composition.
 Example : 
 Returns : value of primary_key (a scalar)
 Args    : new value (a scalar, optional)
=cut
sub primary_key{
    my ($self,@args) = @_;
    if(@args && $self->obj() && $self->obj()->can('primary_seq')) {
        my $seq = $self->primary_seq();
        if($seq && $seq->isa("Bio::DB::PersistentObjectI")) {
            $seq->primary_key(@args);
        }
    }
    return $self->SUPER::primary_key(@args);
}
1;