SNPAdaptor.pm

=head1 LICENSE

  Copyright (c) 1999-2011 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <dev@ensembl.org>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut

=head1 NAME

Bio::EnsEMBL::DBSQL::GeneLiteAdaptor - 
MySQL Database queries to retrieve genes quickly from denormalized tables.

=head1 SYNOPSIS

=head1 METHODS

=cut


package Bio::EnsEMBL::Lite::SNPAdaptor;

use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::DBEntry;
use Bio::EnsEMBL::SNP;

use vars '@ISA';


@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);


=head2 fetch_all_by_Slice

  Arg  1    : Bio::EnsEMBL::Slice $slice
              The slice we want SNPs on
  Function  : retrieve all the SNPs on this slice. 
              uses Lite databases transcript to get info
  Returntype: listreference of Bio::EnsEMBL::ExternalData::Variation
  Exceptions: none
  Caller    : Bio::EnsEMBL::Slice

=cut

sub fetch_all_by_Slice {
  my ($self, $slice ) = @_;

  my @snps;

  my $from_strand = $slice->strand();

  # warn "LITE snps....";
  # wherever this slice is, it needs to be converted to
  # a toplevel slices since all snps in the lite database 
  # are stored on toplevel seqregions

  my @projection = @{$slice->project('toplevel')};