Merge pull request #269 from Ensembl/bugfix/multispecies_pf

backport ENSCORESW-2767: multi-species support for protein feature

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -522,6 +522,7 @@ sub _generate_sql {
   # coord_system).
   if (    $self->is_multispecies()
        && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
+       && !$self->isa('Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor')
        && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
   {
     # We do a check to see if there is already seq_region

modules/t/proteinFeatureAdaptor.t

@@ -38,9 +38,22 @@ my $pfa = $dba->get_ProteinFeatureAdaptor();
 ok($pfa && ref($pfa) && $pfa->isa('Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor'));
 
 my $pfs = $pfa->fetch_all_by_translation_id(21724);
+ok(@$pfs == 15);
+
+#check if the pfa is multispecies
+isnt($pfa->is_multispecies(), 0, "Adaptor is not multispecies");
+
+#set it to multispecies mode to test if it works for collection dbs
+$pfa->is_multispecies(1);
 
+#check if the pfa is multispecies
+is($pfa->is_multispecies(), 1, "Adaptor is multispecies");
+$pfs = $pfa->fetch_all_by_translation_id(21724);
 ok(@$pfs == 15);
 
+#set it back to single species mode
+$pfa->is_multispecies(0);
+
 sub print_features {
   my $features = shift;
   foreach my $f (@$features) {