diff variant_effect_predictor/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,141 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 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 <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::ProxySNPAdaptor
+
+=head1 SYNOPSIS
+
+Designed as an abstraction over the database specific SNPAdaptors. This
+is written right now to serve as a replacement for a core SNPadaptor
+which doesn''t even exist yet and probably never will since SNPs are
+taken from external databases. In the future some sort of DBRegistry may
+remove the need for this class.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::DBSQL::ProxySNPAdaptor;
+
+use strict;
+
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+
+use vars ('@ISA', '$AUTOLOAD');
+
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+
+=head2 fetch_attributes_only
+
+  Arg [1]    : int refsnp_id
+  Arg [2]    : (optional) string source
+  Example    : none
+  Description: Retrieves a snp objcet from the SNP database but does not
+               populate the location information.  This is necessary given 
+               the current state of the snp database because location 
+               information has to be retrieved differently for different 
+               species!
+  Returntype : Bio::EnsEMBL::SNP
+  Exceptions : none
+  Caller     : snpview
+
+=cut
+
+
+
+sub fetch_attributes_only{
+    my ( $self, @args ) = @_;
+
+  my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');
+  my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP');
+
+  if( defined $snp_db ) {
+      my $snp_adaptor = $snp_db->get_SNPAdaptor();
+      return $snp_adaptor->fetch_attributes_only( @args );
+  }
+
+  if( defined $lite_db ) {
+      my $snp_adaptor = $lite_db->get_SNPAdaptor();
+      return $snp_adaptor->fetch_attributes_only( @args );
+  }
+
+}
+
+
+
+
+=head2 AUTOLOAD
+
+  Arg [1]    : list of arbitrary values @args
+               a list of arguments to pass to the request method
+  Example    : -
+  Description: AUTOLOAD method should not be called directly.  It is called
+               implicitly when a method requested from this class cannot be
+               found. This method first tries to execute the requested method
+               in the primary adaptor.  If the method cannot be found then 
+               it searches the other attached databases for equivalent adaptors
+               and tries then one at a time.
+  Returntype : arbitrary
+  Exceptions : thrown if the requested method cannot be found on the primary
+               adaptor or on any of the attached databases.
+  Caller     : called implicitly by perl
+
+=cut
+
+sub AUTOLOAD {
+  my ($self, @args) =  @_;
+  
+  #determine the method which was called
+  my $method = $AUTOLOAD;
+  
+  #strip out fully qualified method name
+  $method =~ s/.*:://;
+
+  my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');
+  my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP');
+
+  if( defined $lite_db ) {
+      my $snp_adaptor = $lite_db->get_SNPAdaptor();
+      if($snp_adaptor->can($method)) {
+	  return $snp_adaptor->$method(@args);
+      } 
+  }
+
+  if( defined $snp_db ) {
+      my $snp_adaptor = $snp_db->get_SNPAdaptor();
+      if($snp_adaptor->can($method)) {
+	  return $snp_adaptor->$method(@args);
+      }
+  }
+
+
+
+  throw("The requested method $method could not be found in lite or snp" );
+}
+
+sub DESTROY {
+}
+
+1;
+
+__END__