JAL-2780 JAL-2781 - patch and first test for AlignmentI.findOrCreateAnnotation

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 1cfa771..4d86bc7 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1300,4 +1300,43 @@ public class AlignmentTest
     AlignmentI alignment = new Alignment(new SequenceI[] { seq });
     alignment.setDataset(alignment);
   }
+
+  @Test(groups = "Functional")
+  public void testAppend()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+    alignment.setGapCharacter('-');
+    SequenceI seq2 = new Sequence("seq1", "KP..L.FQII.");
+    AlignmentI alignment2 = new Alignment(new SequenceI[] { seq2 });
+    alignment2.setGapCharacter('.');
+
+    alignment.append(alignment2);
+
+    assertEquals('-', alignment.getGapCharacter());
+    assertSame(seq, alignment.getSequenceAt(0));
+    assertEquals("KP--L-FQII-", alignment.getSequenceAt(1)
+            .getSequenceAsString());
+
+    // todo test coverage for annotations, mappings, groups,
+    // 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);
+  }
 }