[ENSCORESW-475] fixing the dbentry return to prioritise genes, transcripts and...

[ENSCORESW-475] fixing the dbentry return to prioritise genes, transcripts and translations found on reference slices

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -837,12 +837,12 @@ sub fetch_all_by_external_name {
 
   my @ids = $entryAdaptor->list_gene_ids_by_extids($external_name, $external_db_name, $override);
 
-  my %genes_by_dbIDs =
-	map { $_->dbID(), $_ } @{$self->fetch_all_by_dbID_list(\@ids)};
+  my %genes_by_dbIDs = map { $_->dbID(), $_ } @{$self->fetch_all_by_dbID_list(\@ids)};
 
-  my @result = map { $genes_by_dbIDs{$_} } @ids;
-
-  return \@result;
+  my @features = map { $genes_by_dbIDs{$_} } @ids;
+  my @reference = grep { $_->slice()->is_reference() } @features;
+  my @non_reference = grep { ! $_->slice()->is_reference() } @features;
+  return [ @reference, @non_reference ];
 }
 
 =head2 fetch_all_by_description

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -519,7 +519,10 @@ sub fetch_all_by_external_name {
     $entryAdaptor->list_transcript_ids_by_extids( $external_name,
                                                   $external_db_name, $override );
 
-  return $self->fetch_all_by_dbID_list( \@ids );
+  my @features = @{ $self->fetch_all_by_dbID_list( \@ids ) };
+  my @reference = grep { $_->slice()->is_reference() } @features;
+  my @non_reference = grep { ! $_->slice()->is_reference() } @features;
+  return [ @reference, @non_reference ];
 }
 
 =head2 fetch_all_by_GOTerm

modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm

@@ -313,16 +313,23 @@ sub fetch_all_by_external_name {
 
   my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
 
-  my @out;
+  my @reference;
+  my @non_reference;
   foreach my $id (@ids) {
     my $transcript = $transcript_adaptor->fetch_by_translation_id($id);
 
     if ( defined($transcript) ) {
-      push @out, $self->fetch_by_Transcript($transcript);
+      my $translation = $self->fetch_by_Transcript($transcript);
+      if($transcript->slice()->is_reference()) {
+        push(@reference, $translation);
+      }
+      else {
+        push(@non_reference, $translation);
+      }
     }
   }
 
-  return \@out;
+  return [@reference, @non_reference];
 }
 
 =head2 fetch_all_by_GOTerm