JAL-2046 RFC on addSequenceFeature behaviour after deriveSequence

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 95755ee..0e9ab28 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -395,9 +395,9 @@ public class SequenceTest
     assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
 
     assertNull(sq.sequenceFeatures);
-    // assertNull(derived.sequenceFeatures);
+    assertNull(derived.sequenceFeatures);
+    // derived sequence should access dataset sequence features
     assertNotNull(sq.getSequenceFeatures());
-    // derived sequence has a copy of the sequence features (is this right?)
     assertArrayEquals(sq.getSequenceFeatures(),
             derived.getSequenceFeatures());
   }
@@ -471,6 +471,8 @@ public class SequenceTest
     seq1.setDescription("description");
     seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
             1.3d));
+    // JAL-2046 - what is the contract for using a derived sequence's
+    // addSequenceFeature ?
     seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
             12.4f, "group"));
     seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
@@ -518,7 +520,11 @@ public class SequenceTest
     // copy has a copy of the sequence feature:
     SequenceFeature[] sfs = copy.getSequenceFeatures();
     assertEquals(1, sfs.length);
-    assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
+    if (seq1.getDatasetSequence()!=null && copy.getDatasetSequence()==seq1.getDatasetSequence()) {
+      assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
+    } else {
+      assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
+    }
     assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
 
     // copy has a copy of the PDB entry