JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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

diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java
index db21c2f..c38cb1e 100644 (file)
--- a/test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreTest.java
@@ -2,6 +2,7 @@ package jalview.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.SequenceFeature;
@@ -184,58 +185,6 @@ public class FeatureStoreTest
     assertTrue(overlaps.contains(sf));
   }
 
-  /**
-   * Tests for the method that returns false for an attempt to add a feature
-   * that would enclose, or be enclosed by, another feature
-   */
-  @Test(groups = "Functional")
-  public void testAddNonNestedFeature()
-  {
-    FeatureStore fs = new FeatureStore();
-
-    String type = "Domain";
-    SequenceFeature sf1 = new SequenceFeature(type, type, 10, 20,
-            Float.NaN, null);
-    assertTrue(fs.addNonNestedFeature(sf1));
-
-    // co-located feature is ok
-    SequenceFeature sf2 = new SequenceFeature(type, type, 10, 20,
-            Float.NaN, null);
-    assertTrue(fs.addNonNestedFeature(sf2));
-
-    // overlap left is ok
-    SequenceFeature sf3 = new SequenceFeature(type, type, 5, 15, Float.NaN,
-            null);
-    assertTrue(fs.addNonNestedFeature(sf3));
-
-    // overlap right is ok
-    SequenceFeature sf4 = new SequenceFeature(type, type, 15, 25,
-            Float.NaN, null);
-    assertTrue(fs.addNonNestedFeature(sf4));
-
-    // add enclosing feature is not ok
-    SequenceFeature sf5 = new SequenceFeature(type, type, 10, 21,
-            Float.NaN, null);
-    assertFalse(fs.addNonNestedFeature(sf5));
-    SequenceFeature sf6 = new SequenceFeature(type, type, 4, 15, Float.NaN,
-            null);
-    assertFalse(fs.addNonNestedFeature(sf6));
-    SequenceFeature sf7 = new SequenceFeature(type, type, 1, 50, Float.NaN,
-            null);
-    assertFalse(fs.addNonNestedFeature(sf7));
-
-    // add enclosed feature is not ok
-    SequenceFeature sf8 = new SequenceFeature(type, type, 10, 19,
-            Float.NaN, null);
-    assertFalse(fs.addNonNestedFeature(sf8));
-    SequenceFeature sf9 = new SequenceFeature(type, type, 16, 25,
-            Float.NaN, null);
-    assertFalse(fs.addNonNestedFeature(sf9));
-    SequenceFeature sf10 = new SequenceFeature(type, type, 7, 7, Float.NaN,
-            null);
-    assertFalse(fs.addNonNestedFeature(sf10));
-  }
-
   @Test(groups = "Functional")
   public void testGetPositionalFeatures()
   {
@@ -462,9 +411,7 @@ public class FeatureStoreTest
     assertEquals(fs.getFeatureCount(true), 3);
     assertTrue(fs.delete(sf1));
     assertEquals(fs.getFeatureCount(true), 2);
-    // FeatureStore should now only contain features in the NCList
-    assertTrue(fs.nonNestedFeatures.isEmpty());
-    assertEquals(fs.nestedFeatures.size(), 2);
+    assertEquals(fs.features.size(), 2);
     assertFalse(fs.isEmpty());
     assertTrue(fs.delete(sf2));
     assertEquals(fs.getFeatureCount(true), 1);
@@ -693,7 +640,7 @@ public class FeatureStoreTest
   public void testListContains()
   {
     assertFalse(FeatureStore.listContains(null, null));
-    List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> features = new ArrayList<>();
     assertFalse(FeatureStore.listContains(features, null));
 
     SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
@@ -774,7 +721,7 @@ public class FeatureStoreTest
   public void testShiftFeatures()
   {
     FeatureStore fs = new FeatureStore();
-    assertFalse(fs.shiftFeatures(1));
+    assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
     fs.addFeature(sf1);
@@ -790,9 +737,9 @@ public class FeatureStoreTest
     fs.addFeature(sf4);
 
     /*
-     * shift features right by 5
+     * shift all features right by 5
      */
-    assertTrue(fs.shiftFeatures(5));
+    assertTrue(fs.shiftFeatures(0, 5));
 
     // non-positional features untouched:
     List<SequenceFeature> nonPos = fs.getNonPositionalFeatures();
@@ -818,7 +765,7 @@ public class FeatureStoreTest
      * feature at [7-10] should be removed
      * feature at [13-19] should become [1-4] 
      */
-    assertTrue(fs.shiftFeatures(-15));
+    assertTrue(fs.shiftFeatures(0, -15));
     pos = fs.getPositionalFeatures();
     assertEquals(pos.size(), 2);
     SequenceFeatures.sortFeatures(pos, true);
@@ -826,6 +773,32 @@ public class FeatureStoreTest
     assertEquals(pos.get(0).getEnd(), 4);
     assertEquals(pos.get(1).getBegin(), 13);
     assertEquals(pos.get(1).getEnd(), 22);
+
+    /*
+     * shift right by 4 from position 2 onwards
+     * feature at [1-4] unchanged, feature at [13-22] shifts
+     */
+    assertTrue(fs.shiftFeatures(2, 4));
+    pos = fs.getPositionalFeatures();
+    assertEquals(pos.size(), 2);
+    SequenceFeatures.sortFeatures(pos, true);
+    assertEquals(pos.get(0).getBegin(), 1);
+    assertEquals(pos.get(0).getEnd(), 4);
+    assertEquals(pos.get(1).getBegin(), 17);
+    assertEquals(pos.get(1).getEnd(), 26);
+
+    /*
+     * shift right by 4 from position 18 onwards
+     * should be no change
+     */
+    SequenceFeature f1 = pos.get(0);
+    SequenceFeature f2 = pos.get(1);
+    assertFalse(fs.shiftFeatures(18, 4)); // no update
+    pos = fs.getPositionalFeatures();
+    assertEquals(pos.size(), 2);
+    SequenceFeatures.sortFeatures(pos, true);
+    assertSame(pos.get(0), f1);
+    assertSame(pos.get(1), f2);
   }
 
   @Test(groups = "Functional")
@@ -842,8 +815,8 @@ public class FeatureStoreTest
     assertEquals(features.size(), 2);
     assertTrue(features.contains(sf1));
     assertTrue(features.contains(sf2));
-    assertTrue(store.nonNestedFeatures.contains(sf1));
-    assertTrue(store.nestedFeatures.contains(sf2));
+    assertTrue(store.features.contains(sf1));
+    assertTrue(store.features.contains(sf2));
   
     /*
      * delete the first feature