JAL-2232 some fix / partial fix of failing tests

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 50f38b6..759f527 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -80,11 +80,11 @@ public class CrossRefTest
      * Just the protein refs:
      */
     found = DBRefUtils.selectDbRefs(false, refs);
-    assertEquals(3, found.length);
+    assertEquals(4, found.length);
     assertSame(ref1, found[0]);
     assertSame(ref2, found[1]);
     assertSame(ref4, found[2]);
-    // assertSame(ref9, found[3]); ENSEMBL not protein
+    assertSame(ref9, found[3]);
   }
 
   /**
@@ -121,8 +121,9 @@ public class CrossRefTest
     seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
     sources = new CrossRef(new SequenceI[] { seq }, al)
             .findXrefSourcesForSequences(false);
-    assertEquals(4, sources.size());
-    assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+    // method is patched to remove EMBL from the sources to match
+    assertEquals(3, sources.size());
+    assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
 
     /*
      * add a sequence to the alignment which has a dbref to UNIPROT|A1234
@@ -140,8 +141,9 @@ public class CrossRefTest
     al.addSequence(seq2);
     sources = new CrossRef(new SequenceI[] { seq, seq2 }, al)
             .findXrefSourcesForSequences(false);
-    assertEquals(3, sources.size());
-    assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString());
+    // method removed EMBL from sources to match
+    assertEquals(2, sources.size());
+    assertEquals("[EMBLCDS, GENEDB]", sources.toString());
   }
 
   /**
@@ -624,7 +626,7 @@ public class CrossRefTest
      */
     final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG");
     DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20");
-    dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
+    dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
             new MapList(map2)));
     x07547.addDBRef(dbref7);
     DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4");