added is_ref to see if gene is the reference gene

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -942,6 +942,23 @@ sub fetch_all_alt_alleles {
   return [];
 }
 
+sub is_ref{
+  my ( $self, $gene_id) = @_;
+  my $is_not_ref;
+
+  # easier to find if it is not an alt_Allele do this and then negate it.
+  my $sth = $self->prepare("select count(1) from alt_allele where gene_id = $gene_id and is_ref = 0");
+  $sth->execute();
+  $sth->bind_columns(\$is_not_ref);
+  $sth->fetch;
+
+  if(defined($is_not_ref) and $is_not_ref){
+    return 0;
+  }
+ 
+  return 1;
+}
+
 
 =head2 store_alt_alleles
 

modules/Bio/EnsEMBL/Gene.pm

@@ -1468,6 +1468,27 @@ sub load {
   }
 }
 
+=head2 is_ref
+
+  Description: getter setter for the gene attribute is_ref
+  Arg [1]    : (optional) 1 or 0
+  return     : boolean
+
+=cut
+
+sub is_reference{
+  my ( $self, $is_ref) = @_;
+
+  if(defined($is_ref)){
+    $self->{'is_ref'} = $is_ref;
+  }
+  else{
+    $self->{'is_ref'} = $self->adaptor->is_ref($self->dbID);
+  }	
+  return $self->{'is_ref'};
+}
+
+
 =head2 summary_as_hash
 
   Example       : $gene_summary = $gene->summary_as_hash();