JAL-3383 JAL-3253-applet

[jalview.git] / test / jalview / datamodel / features / SequenceFeaturesTest.java

diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index 32987b0..30b1402 100644 (file)
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -889,11 +889,11 @@ public class SequenceFeaturesTest
      * no type specified - get all types stored
      * they are returned in keyset (alphabetical) order
      */
-    Map<String, FeatureStore> featureStores = (Map<String, FeatureStore>) PA
+    Map<String, FeatureStoreI> featureStores = (Map<String, FeatureStoreI>) PA
             .getValue(sf, "featureStore");
 
-    Iterable<FeatureStore> types = sf.varargToTypes();
-    Iterator<FeatureStore> iterator = types.iterator();
+    Iterable<FeatureStoreI> types = sf.varargToTypes();
+    Iterator<FeatureStoreI> iterator = types.iterator();
     assertTrue(iterator.hasNext());
     assertSame(iterator.next(), featureStores.get("Cath"));
     assertTrue(iterator.hasNext());
@@ -1161,7 +1161,7 @@ public class SequenceFeaturesTest
   public void testShiftFeatures()
   {
     SequenceFeatures store = new SequenceFeatures();
-    assertFalse(store.shiftFeatures(1));
+    assertFalse(store.shiftFeatures(0, 1));
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
     store.add(sf1);
@@ -1179,7 +1179,7 @@ public class SequenceFeaturesTest
     /*
      * shift features right by 5
      */
-    assertTrue(store.shiftFeatures(5));
+    assertTrue(store.shiftFeatures(0, 5));
   
     // non-positional features untouched:
     List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
@@ -1208,7 +1208,7 @@ public class SequenceFeaturesTest
      * feature at [7-10] should be removed
      * feature at [13-19] should become [1-4] 
      */
-    assertTrue(store.shiftFeatures(-15));
+    assertTrue(store.shiftFeatures(0, -15));
     pos = store.getPositionalFeatures();
     assertEquals(pos.size(), 2);
     SequenceFeatures.sortFeatures(pos, true);
@@ -1218,6 +1218,35 @@ public class SequenceFeaturesTest
     assertEquals(pos.get(1).getBegin(), 13);
     assertEquals(pos.get(1).getEnd(), 22);
     assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+    /*
+     * shift right by 4 from column 2
+     * feature at [1-4] should be unchanged
+     * feature at [13-22] should become [17-26] 
+     */
+    assertTrue(store.shiftFeatures(2, 4));
+    pos = store.getPositionalFeatures();
+    assertEquals(pos.size(), 2);
+    SequenceFeatures.sortFeatures(pos, true);
+    assertEquals(pos.get(0).getBegin(), 1);
+    assertEquals(pos.get(0).getEnd(), 4);
+    assertEquals(pos.get(0).getType(), "Metal");
+    assertEquals(pos.get(1).getBegin(), 17);
+    assertEquals(pos.get(1).getEnd(), 26);
+    assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+    /*
+     * shift right from column 18
+     * should be no updates
+     */
+    SequenceFeature f1 = pos.get(0);
+    SequenceFeature f2 = pos.get(1);
+    assertFalse(store.shiftFeatures(18, 6));
+    pos = store.getPositionalFeatures();
+    assertEquals(pos.size(), 2);
+    SequenceFeatures.sortFeatures(pos, true);
+    assertSame(pos.get(0), f1);
+    assertSame(pos.get(1), f2);
   }
 
   @Test(groups = "Functional")
@@ -1232,4 +1261,18 @@ public class SequenceFeaturesTest
     assertTrue(store.isOntologyTerm("junk", new String[] {}));
     assertTrue(store.isOntologyTerm("junk", (String[]) null));
   }
+
+  @Test(groups = "Functional")
+  public void testDeleteAll()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+    assertFalse(store.hasFeatures());
+    store.deleteAll();
+    assertFalse(store.hasFeatures());
+    store.add(new SequenceFeature("Cath", "Desc", 12, 20, 0f, "Group"));
+    store.add(new SequenceFeature("Pfam", "Desc", 6, 12, 2f, "Group2"));
+    assertTrue(store.hasFeatures());
+    store.deleteAll();
+    assertFalse(store.hasFeatures());
+  }
 }