JAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(AlignmentAnnotation ala) - calls...

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 5e400c0..6dad024 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1351,7 +1351,35 @@ public class AlignmentTest
             "Temperature Factor", null, false, seq, null);
     assertNotNull(ala);
     assertEquals(seq, ala.sequenceRef);
-    assertEquals("", ala.calcId);
+    assertEquals("", ala.getCalcId());
+  }
+
+  @Test(groups = {"Functional"})
+  public void testUpdateFromOrAddAnnotation()
+  {
+    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.getCalcId());
+
+    // Assuming findOrCreateForNullCalcId passed then this should work
+
+    assertTrue(ala == alignment.updateFromOrCopyAnnotation(ala));
+    AlignmentAnnotation updatedAla = new AlignmentAnnotation(ala);
+    updatedAla.description = "updated Description";
+    Assert.assertTrue(
+            ala == alignment.updateFromOrCopyAnnotation(updatedAla));
+    Assert.assertEquals(ala.toString(), updatedAla.toString());
+    updatedAla.calcId = "newCalcId";
+    AlignmentAnnotation newUpdatedAla = alignment
+            .updateFromOrCopyAnnotation(updatedAla);
+    Assert.assertTrue(updatedAla != newUpdatedAla);
+    Assert.assertEquals(updatedAla.toString(), newUpdatedAla.toString());
   }
 
   @Test(groups = "Functional")
@@ -1485,6 +1513,54 @@ public class AlignmentTest
     assertEquals(".PQR...", seq3.getSequenceAsString());
   }
 
+  /**
+   * Test for setHiddenColumns, to check it returns true if the hidden columns
+   * have changed, else false
+   */
+  @Test(groups = { "Functional" })
+  public void testSetHiddenColumns()
+  {
+    AlignmentI al = new Alignment(new SequenceI[] {});
+    assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+    HiddenColumns hc = new HiddenColumns();
+    assertFalse(al.setHiddenColumns(hc)); // no change
+    assertSame(hc, al.getHiddenColumns());
+
+    hc.hideColumns(2, 4);
+    assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+    /*
+     * set a different object but with the same columns hidden
+     */
+    HiddenColumns hc2 = new HiddenColumns();
+    hc2.hideColumns(2, 4);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+    assertSame(hc2, al.getHiddenColumns());
+
+    assertTrue(al.setHiddenColumns(null));
+    assertNull(al.getHiddenColumns());
+    assertTrue(al.setHiddenColumns(hc));
+    assertSame(hc, al.getHiddenColumns());
+
+    al.getHiddenColumns().hideColumns(10, 12);
+    hc2.hideColumns(10, 12);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+
+    /*
+     * hide columns 15-16 then 17-18 in hc
+     * hide columns 15-18 in hc2
+     * these are not now 'equal' objects even though they
+     * represent the same set of columns
+     */
+    assertSame(hc2, al.getHiddenColumns());
+    hc.hideColumns(15, 16);
+    hc.hideColumns(17, 18);
+    hc2.hideColumns(15, 18);
+    assertFalse(hc.equals(hc2));
+    assertTrue(al.setHiddenColumns(hc)); // 'changed'
+  }
+
   @Test(groups = { "Functional" })
   public void testGetWidth()
   {