Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphaf...

diff --combined RELEASE
index c29f144,5c19bf1..bc0c6dd
--- 1/RELEASE
--- 2/RELEASE
+++ b/RELEASE
@@@ -1,2 -1,2 +1,2 @@@
--jalview.release=releases/Release_2_11_2_Branch
 -jalview.version=2.11.2.6
++jalview.release=releases/Release_2_11_3_Branch
 +jalview.version=2.11.3

diff --combined test/jalview/ws/dbsources/UniprotTest.java
index a7eedf1,176cddc..7eb3b75
--- 1/test/jalview/ws/dbsources/UniprotTest.java
--- 2/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@@ -224,14 -224,22 +224,25 @@@ public class UniprotTes
      res = DBRefUtils.searchRefsForSource(seq.getDBRefs(),
              DBRefSource.UNIPROT);
      assertEquals(2, res.size());
 +    res = DBRefUtils.searchRefs(seq.getDBRefs(), "AAK85932");
 +    assertEquals(1, res.size());
 +    assertTrue("1".equals(res.get(0).getVersion()));
      /*
       * NB this test fragile - relies on ordering being preserved
       */
      assertTrue(res.get(0).isCanonical());
      assertFalse(res.get(1).isCanonical());
+ 
+     // check version is preserved for EMBLCDS
+     res = DBRefUtils.searchRefs(seq.getDBRefs(), "AAK85932");
+     assertEquals(1, res.size());
+     // Ideally we would expect AAK85932.1 -> AAK85932
+     // assertTrue("1".equals(res.get(0).getVersion()));
+     // but it also passes through DBrefUtils.ensurePrimaries which adds
+     // (promoted) to the version string
+     // FIXME: Jim needs to specify what (promoted) means !! - or perhaps we just
+     // ignore it !
+     assertEquals("1 (promoted)", (res.get(0).getVersion()));
    }
  
    /**