JAL-3383 code and unit test tweaks

[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 bc179f6..db0fabf 100644 (file)
--- a/test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreTest.java
@@ -4,6 +4,7 @@ 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 static org.testng.Assert.fail;
 
 import jalview.datamodel.SequenceFeature;
 
@@ -34,21 +35,21 @@ public class FeatureStoreTest
     fs.addFeature(new SequenceFeature("", "", 15, 25, Float.NaN, null));
     fs.addFeature(new SequenceFeature("", "", 20, 35, Float.NaN, null));
 
-    List<SequenceFeature> overlaps = fs.findOverlappingFeatures(1, 9);
+    List<SequenceFeature> overlaps = fs.findFeatures(1, 9);
     assertTrue(overlaps.isEmpty());
 
-    overlaps = fs.findOverlappingFeatures(8, 10);
+    overlaps = fs.findFeatures(8, 10);
     assertEquals(overlaps.size(), 2);
     assertEquals(overlaps.get(0).getEnd(), 20);
     assertEquals(overlaps.get(1).getEnd(), 20);
 
-    overlaps = fs.findOverlappingFeatures(12, 16);
+    overlaps = fs.findFeatures(12, 16);
     assertEquals(overlaps.size(), 3);
     assertEquals(overlaps.get(0).getEnd(), 20);
     assertEquals(overlaps.get(1).getEnd(), 20);
     assertEquals(overlaps.get(2).getEnd(), 25);
 
-    overlaps = fs.findOverlappingFeatures(33, 33);
+    overlaps = fs.findFeatures(33, 33);
     assertEquals(overlaps.size(), 1);
     assertEquals(overlaps.get(0).getEnd(), 35);
   }
@@ -66,25 +67,25 @@ public class FeatureStoreTest
     fs.addFeature(sf4);
     SequenceFeature sf5 = addFeature(fs, 35, 36);
 
-    List<SequenceFeature> overlaps = fs.findOverlappingFeatures(1, 9);
+    List<SequenceFeature> overlaps = fs.findFeatures(1, 9);
     assertTrue(overlaps.isEmpty());
 
-    overlaps = fs.findOverlappingFeatures(10, 15);
+    overlaps = fs.findFeatures(10, 15);
     assertEquals(overlaps.size(), 2);
     assertTrue(overlaps.contains(sf1));
     assertTrue(overlaps.contains(sf2));
 
-    overlaps = fs.findOverlappingFeatures(45, 60);
+    overlaps = fs.findFeatures(45, 60);
     assertEquals(overlaps.size(), 1);
     assertTrue(overlaps.contains(sf1));
 
-    overlaps = fs.findOverlappingFeatures(32, 38);
+    overlaps = fs.findFeatures(32, 38);
     assertEquals(overlaps.size(), 3);
     assertTrue(overlaps.contains(sf1));
     assertTrue(overlaps.contains(sf2));
     assertTrue(overlaps.contains(sf5));
 
-    overlaps = fs.findOverlappingFeatures(15, 25);
+    overlaps = fs.findFeatures(15, 25);
     assertEquals(overlaps.size(), 4);
     assertTrue(overlaps.contains(sf1));
     assertTrue(overlaps.contains(sf2));
@@ -103,30 +104,30 @@ public class FeatureStoreTest
     SequenceFeature sf5 = addFeature(fs, 60, 100);
     SequenceFeature sf6 = addFeature(fs, 70, 70);
 
-    List<SequenceFeature> overlaps = fs.findOverlappingFeatures(200, 200);
+    List<SequenceFeature> overlaps = fs.findFeatures(200, 200);
     assertTrue(overlaps.isEmpty());
 
-    overlaps = fs.findOverlappingFeatures(1, 9);
+    overlaps = fs.findFeatures(1, 9);
     assertEquals(overlaps.size(), 1);
     assertTrue(overlaps.contains(sf2));
 
-    overlaps = fs.findOverlappingFeatures(5, 18);
+    overlaps = fs.findFeatures(5, 18);
     assertEquals(overlaps.size(), 2);
     assertTrue(overlaps.contains(sf1));
     assertTrue(overlaps.contains(sf2));
 
-    overlaps = fs.findOverlappingFeatures(30, 40);
+    overlaps = fs.findFeatures(30, 40);
     assertEquals(overlaps.size(), 3);
     assertTrue(overlaps.contains(sf1));
     assertTrue(overlaps.contains(sf3));
     assertTrue(overlaps.contains(sf4));
 
-    overlaps = fs.findOverlappingFeatures(80, 90);
+    overlaps = fs.findFeatures(80, 90);
     assertEquals(overlaps.size(), 2);
     assertTrue(overlaps.contains(sf4));
     assertTrue(overlaps.contains(sf5));
 
-    overlaps = fs.findOverlappingFeatures(68, 70);
+    overlaps = fs.findFeatures(68, 70);
     assertEquals(overlaps.size(), 3);
     assertTrue(overlaps.contains(sf4));
     assertTrue(overlaps.contains(sf5));
@@ -161,38 +162,132 @@ public class FeatureStoreTest
     /*
      * neither contact point in range
      */
-    List<SequenceFeature> overlaps = fs.findOverlappingFeatures(1, 9);
+    List<SequenceFeature> overlaps = fs.findFeatures(1, 9);
     assertTrue(overlaps.isEmpty());
 
     /*
      * neither contact point in range
      */
-    overlaps = fs.findOverlappingFeatures(11, 19);
+    overlaps = fs.findFeatures(11, 19);
     assertTrue(overlaps.isEmpty());
 
     /*
      * first contact point in range
      */
-    overlaps = fs.findOverlappingFeatures(5, 15);
+    overlaps = fs.findFeatures(5, 15);
     assertEquals(overlaps.size(), 1);
     assertTrue(overlaps.contains(sf));
 
     /*
      * second contact point in range
      */
-    overlaps = fs.findOverlappingFeatures(15, 25);
+    overlaps = fs.findFeatures(15, 25);
     assertEquals(overlaps.size(), 1);
     assertTrue(overlaps.contains(sf));
 
     /*
      * both contact points in range
      */
-    overlaps = fs.findOverlappingFeatures(5, 25);
+    overlaps = fs.findFeatures(5, 25);
     assertEquals(overlaps.size(), 1);
     assertTrue(overlaps.contains(sf));
   }
 
   @Test(groups = "Functional")
+  public void testGetPositionalFeatures_withResultList()
+  {
+    FeatureStore store = newFeatureStore();
+    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+            Float.NaN, null);
+    store.addFeature(sf1);
+    // contact feature
+    SequenceFeature sf2 = new SequenceFeature("Disulphide bond", "desc", 18,
+            45, Float.NaN, null);
+    store.addFeature(sf2);
+
+    List<SequenceFeature> features = new ArrayList<>();
+    store.getPositionalFeatures(features);
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2));
+
+    /*
+     * no check for duplicates
+     */
+    features.remove(sf1);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+    store.getPositionalFeatures(features);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2)); // two copies now
+    features.remove(sf2);
+    assertTrue(features.contains(sf2)); // one copy left
+    assertEquals(features.size(), 2);
+
+    /*
+     * null argument throws exception
+     */
+    try
+    {
+      store.getPositionalFeatures(null);
+      fail("expected exception");
+    } catch (NullPointerException e)
+    {
+      // expected
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testGetNonPositionalFeatures()
+  {
+    FeatureStore store = newFeatureStore();
+    List<SequenceFeature> features = store.getNonPositionalFeatures();
+    assertTrue(features.isEmpty());
+
+    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+            Float.NaN, null);
+    store.addFeature(sf1);
+    assertTrue(features.isEmpty());
+
+    SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
+            Float.NaN, null);
+    store.addFeature(sf2);
+    features = store.getNonPositionalFeatures();
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+
+    /*
+     * with result list argument
+     */
+    features.clear();
+    store.getNonPositionalFeatures(features);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+
+    /*
+     * no check for duplicates
+     */
+    store.getNonPositionalFeatures(features);
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf2)); // two copies
+    features.remove(sf2);
+    assertTrue(features.contains(sf2));
+
+    /*
+     * null argument throws exception
+     */
+    try
+    {
+      store.getNonPositionalFeatures(null);
+      fail("expected exception");
+    } catch (NullPointerException e)
+    {
+      // expected
+    }
+  }
+
+  @Test(groups = "Functional")
   public void testGetPositionalFeatures()
   {
     FeatureStore store = newFeatureStore();
@@ -902,7 +997,7 @@ public class FeatureStoreTest
     SequenceFeature sf2 = addFeature(fs, 150, 250);
   
     List<SequenceFeature> overlaps = new ArrayList<>();
-    List<SequenceFeature> result = fs.findOverlappingFeatures(200, 200,
+    List<SequenceFeature> result = fs.findFeatures(200, 200,
             overlaps);
     assertSame(result, overlaps);
     assertEquals(result.size(), 1);
@@ -912,7 +1007,7 @@ public class FeatureStoreTest
     /*
      * if no list supplied, method creates one
      */
-    result = fs.findOverlappingFeatures(200, 200, null);
+    result = fs.findFeatures(200, 200, null);
     assertEquals(result.size(), 1);
     assertTrue(result.contains(sf2));
     assertFalse(result.contains(sf1));