X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=1d1ebd67d596d194a82af033a131229aee1476db;hb=bd7b3138379c2db8507fe7e8d25f5a921e2d9df7;hp=ddba94991a40f1a7927abc7131410e36cbb91e2f;hpb=53ef0b8b1f5cad886db96520528e367aadec2712;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index ddba949..1d1ebd6 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -248,7 +248,9 @@ public class AlignmentTest
                   if (raiseAssert)
                   {
                     Assert.fail(message
-                            + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                            + " DBRefEntry " + dbr + " for sequence "
+                            + seqds
+                            + " in alignment has map to sequence not in dataset");
                   }
                   return false;
                 }
@@ -669,6 +671,17 @@ public class AlignmentTest
     // third found.. so
     assertFalse(iter.hasNext());
 
+    // search for annotation on one sequence with a particular label - expect
+    // one
+    SequenceI sqfound;
+    anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+            "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    // expect reference to sequence 1 in the alignment
+    assertTrue(sqfound == iter.next().sequenceRef);
+    assertFalse(iter.hasNext());
+
     // null on all parameters == find all annotations
     anns = al.findAnnotations(null, null, null);
     iter = anns.iterator();
@@ -1323,6 +1336,24 @@ public class AlignmentTest
     // hidden sequences, properties
   }
 
+  /**
+   * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+   * an annotation with a null calcId
+   * 
+   */
+  @Test(groups = "Functional")
+  public void testFindOrCreateForNullCalcId()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+    AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+            "Temperature Factor", null, false, seq, null);
+    assertNotNull(ala);
+    assertEquals(seq, ala.sequenceRef);
+    assertEquals("", ala.calcId);
+  }
+
   @Test(groups = "Functional")
   public void testPropagateInsertions()
   {