Update the 'get_all_StructuralVariations' method

modules/Bio/EnsEMBL/Slice.pm

@@ -76,6 +76,8 @@ use Bio::EnsEMBL::StrainSlice;
 use Bio::EnsEMBL::Mapper::RangeRegistry;
 use Bio::EnsEMBL::SeqRegionSynonym;
 
+use Bio::EnsEMBL::Variation::Utils::Constants qw(%VARIATION_CLASSES);
+
 # use Data::Dumper;
 
 my $reg = "Bio::EnsEMBL::Registry";
@@ -1807,9 +1809,19 @@ sub get_all_StructuralVariations{
 	
 	# Get the attrib_id
 	my $at_adaptor = $variation_db->get_AttributeAdaptor;
-	my $SO_term   = $at_adaptor->SO_term_for_SO_accession($sv_class);
+	
+	# Find the SO term associated with the SO accession number ($sv_class)
+	my $SO_term = '';
+	foreach my $term (%VARIATION_CLASSES) {
+		if ($VARIATION_CLASSES{$term}->{'SO_accession'} eq $sv_class) {
+			$SO_term = $term;
+			last;
+		}
+	}
+	
+	# Attrib ID of the SO term
 	my $attrib_id = $at_adaptor->attrib_id_for_type_value('SO_term',$SO_term);
-		
+
 	if (!$attrib_id) {
 		warning("The Sequence Ontology accession number is not found in the database");
   	return [];