Reinstated changes for MySQL 5 compatibility.

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -68,7 +68,7 @@ sub fetch_by_dbID {
            exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
            exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
            xref.info_type, xref.info_text
-    FROM   xref, external_db exDB
+    FROM   (xref, external_db exDB)
     LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
     WHERE  xref.xref_id = ?
     AND    xref.external_db_id = exDB.external_db_id");
@@ -143,7 +143,7 @@ sub fetch_by_db_accession {
            exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
            exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
            xref.info_type, xref.info_text
-    FROM   xref, external_db exDB
+    FROM   (xref, external_db exDB)
     LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
     WHERE  xref.dbprimary_acc = ?
     AND    exDB.db_name = ?
@@ -667,7 +667,7 @@ sub _fetch_by_object_type {
            idt.cigar_line, idt.score, idt.evalue, idt.analysis_id,
            gx.linkage_type,
            xref.info_type, xref.info_text
-    FROM   xref xref, external_db exDB, object_xref oxr 
+    FROM   (xref xref, external_db exDB, object_xref oxr)
     LEFT JOIN external_synonym es on es.xref_id = xref.xref_id 
     LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
     LEFT JOIN go_xref gx on gx.object_xref_id = oxr.object_xref_id