X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=2adefc901bfb076043bbd4fa339f482f868fab07;hb=e6798fd04b1d7a35836a2e84deae5a94a35b88b9;hp=68933bd956c76715cc3ac7a69ee9e9237fe1362a;hpb=bc096ecbcd3cf4bbf17a24f9e9df88806789d688;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 68933bd..2adefc9 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -620,6 +620,67 @@ public class AlignmentTest
     assertFalse(iter.hasNext());
   }
 
+  /**
+   * Test method that returns annotations that match on reference sequence,
+   * label, or calcId.
+   */
+  @Test(groups = { "Functional" })
+  public void testFindAnnotations_bySeqLabelandorCalcId()
+  {
+    // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test
+    /* Note - this is an incomplete test - need to check null or
+     * non-null [ matches, not matches ] behaviour for each of the three
+     * parameters..*/
+
+    // search for a single, unique calcId with wildcards on other params
+    Iterable<AlignmentAnnotation> anns = al.findAnnotations(null,
+            "CalcIdForD.melanogaster.2", null);
+    Iterator<AlignmentAnnotation> iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    AlignmentAnnotation ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // save reference to test sequence reference parameter
+    SequenceI rseq = ann.sequenceRef;
+
+    // search for annotation associated with a single sequence
+    anns = al.findAnnotations(rseq, null, null);
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a non-existant calcId
+    anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null);
+    iter = anns.iterator();
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a particular label - expect three
+    anns = al.findAnnotations(null, null, "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    // third found.. so
+    assertFalse(iter.hasNext());
+
+    // null on all parameters == find all annotations
+    anns = al.findAnnotations(null, null, null);
+    iter = anns.iterator();
+    int n = al.getAlignmentAnnotation().length;
+    while (iter.hasNext())
+    {
+      n--;
+      iter.next();
+    }
+    assertTrue("Found " + n + " fewer annotations from search.", n == 0);
+  }
+
   @Test(groups = { "Functional" })
   public void testDeleteAllAnnotations_includingAutocalculated()
   {
@@ -1260,4 +1321,34 @@ public class AlignmentTest
     assertEquals(a.getHiddenSequences().getSize(), 1);
   }
 
+  @Test(
+    groups = "Functional",
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testSetDataset_selfReference()
+  {
+    SequenceI seq = new Sequence("a", "a");
+    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
+  }
 }