fetch_attributes only needs to come from SNP if possible

modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm

@@ -34,6 +34,43 @@ 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
@@ -63,26 +100,25 @@ sub 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');
-  
-  #
-  # First try the primary adaptor
-  #
+
   if( defined $lite_db ) {
       my $snp_adaptor = $lite_db->get_SNPAdaptor();
       if($snp_adaptor->can($method)) {
 	  return $snp_adaptor->$method(@args);
       } 
   }
-  
-  my $snp_adaptor = $snp_db->get_SNPAdaptor();
-  if($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" );
 }
 

modules/Bio/EnsEMBL/DBSQL/StatementHandle.pm

@@ -32,7 +32,7 @@ use Bio::EnsEMBL::Utils::Exception qw(warning stack_trace_dump);
 use DBD::mysql;
 use DBI;
 
-# use Time::HiRes qw(time);
+ use Time::HiRes qw(time);
 
 @ISA = qw(DBI::st);
 
@@ -76,32 +76,32 @@ sub sql {
 #
 # uncomment this for printing out handy debug information (every query)
 #
-# sub execute {
-#   my $self = shift;
+ sub execute {
+   my $self = shift;
 
-#   my $sql = $self->sql();
+   my $sql = $self->sql();
 
 
-#   my @chrs = split(//, $sql);
+   my @chrs = split(//, $sql);
 
-#   my $j = 0;
-#   for(my $i =0; $i < @chrs; $i++) {
-#     $chrs[$i] = $_[$j++] if($chrs[$i] eq '?' && defined($_[$j]));
-#   }
+   my $j = 0;
+   for(my $i =0; $i < @chrs; $i++) {
+     $chrs[$i] = $_[$j++] if($chrs[$i] eq '?' && defined($_[$j]));
+   }
 
-#   my $str = join('', @chrs);
+   my $str = join('', @chrs);
 
-#   my $time = time;
-#   print STDERR "\nSQL:\n$str\n\n";
+   my $time = time;
+   print STDERR "\nSQL:\n$str\n\n";
 
-# #  print STDERR stack_trace_dump(), "\n";
+ #  print STDERR stack_trace_dump(), "\n";
 
-#   my $res = $self->SUPER::execute(@_);
-#   $time = time - $time;
-#   print STDERR "DONE ($time)\n";
+   my $res = $self->SUPER::execute(@_);
+   $time = time - $time;
+   print STDERR "DONE ($time)\n";
 
-#   return $res;
-# }
+   return $res;
+ }
 
 
 sub DESTROY {

modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm

@@ -202,7 +202,7 @@ sub fetch_all_by_Slice_transcript_ids {
   return $snps;
 }
 
-sub fetch_attributes_only{
+sub fetch_attributes_only_lite{
   my $self = shift;
 
   my $refsnp_id = shift;