JAL-3383 tests and fixes for overloaded SequenceFeatures.findFeatures

[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 a1593eb..8342018 100644 (file)
--- a/test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreTest.java
@@ -15,11 +15,15 @@ import org.testng.annotations.Test;
 
 public class FeatureStoreTest
 {
+  private FeatureStore newFeatureStore()
+  {
+    return new FeatureStore();
+  }
 
   @Test(groups = "Functional")
   public void testFindFeatures_nonNested()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN,
             null));
     // same range different description
@@ -46,16 +50,10 @@ public class FeatureStoreTest
     assertEquals(overlaps.get(0).getEnd(), 35);
   }
 
-  private FeatureStoreI newFeatureStore()
-  {
-    // return new FeatureStoreJS();
-    return new FeatureStoreImpl();
-  }
-
   @Test(groups = "Functional")
   public void testFindFeatures_nested()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     SequenceFeature sf1 = addFeature(fs, 10, 50);
     SequenceFeature sf2 = addFeature(fs, 10, 40);
     SequenceFeature sf3 = addFeature(fs, 20, 30);
@@ -94,7 +92,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testFindFeatures_mixed()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     SequenceFeature sf1 = addFeature(fs, 10, 50);
     SequenceFeature sf2 = addFeature(fs, 1, 15);
     SequenceFeature sf3 = addFeature(fs, 20, 30);
@@ -140,7 +138,7 @@ public class FeatureStoreTest
    * @param to
    * @return
    */
-  SequenceFeature addFeature(FeatureStoreI fs, int from, int to)
+  SequenceFeature addFeature(FeatureStore fs, int from, int to)
   {
     SequenceFeature sf1 = new SequenceFeature("", "", from, to, Float.NaN,
             null);
@@ -151,7 +149,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testFindFeatures_contactFeatures()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     SequenceFeature sf = new SequenceFeature("disulphide bond", "bond", 10,
             20, Float.NaN, null);
@@ -194,7 +192,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetPositionalFeatures()
   {
-    FeatureStoreI store = newFeatureStore();
+    FeatureStore store = newFeatureStore();
     SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
             Float.NaN, null);
     store.addFeature(sf1);
@@ -241,7 +239,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testDelete()
   {
-    FeatureStoreI store = newFeatureStore();
+    FeatureStore store = newFeatureStore();
     SequenceFeature sf1 = addFeature(store, 10, 20);
     assertTrue(store.getPositionalFeatures().contains(sf1));
 
@@ -313,7 +311,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testAddFeature()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
             Float.NaN, null);
@@ -364,7 +362,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testIsEmpty()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.isEmpty());
     assertEquals(fs.getFeatureCount(true), 0);
 
@@ -430,7 +428,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetFeatureGroups()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.getFeatureGroups(true).isEmpty());
     assertTrue(fs.getFeatureGroups(false).isEmpty());
 
@@ -497,7 +495,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetTotalFeatureLength()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertEquals(fs.getTotalFeatureLength(), 0);
 
     addFeature(fs, 10, 20); // 11
@@ -573,7 +571,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetMinimumScore_getMaximumScore()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertEquals(fs.getMinimumScore(true), Float.NaN); // positional
     assertEquals(fs.getMaximumScore(true), Float.NaN);
     assertEquals(fs.getMinimumScore(false), Float.NaN); // non-positional
@@ -645,7 +643,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testListContains()
   {
-    FeatureStoreI featureStore = newFeatureStore();
+    FeatureStore featureStore = newFeatureStore();
     assertFalse(featureStore.listContains(null, null));
     List<SequenceFeature> features = new ArrayList<>();
     assertFalse(featureStore.listContains(features, null));
@@ -669,7 +667,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetFeaturesForGroup()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     /*
      * with no features
@@ -727,7 +725,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testShiftFeatures()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
@@ -814,7 +812,7 @@ public class FeatureStoreTest
     /*
      * add a feature and a nested feature
      */
-    FeatureStoreI store = newFeatureStore();
+    FeatureStore store = newFeatureStore();
     SequenceFeature sf1 = addFeature(store, 10, 20);
     // sf2 is nested in sf1 so will be stored in nestedFeatures
     SequenceFeature sf2 = addFeature(store, 12, 14);
@@ -845,7 +843,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testContains()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
             Float.NaN, "group1");
     SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
@@ -888,4 +886,28 @@ public class FeatureStoreTest
     assertFalse(fs.contains(sf1));
     assertTrue(fs.contains(sf7));
   }
+
+  @Test(groups = "Functional")
+  public void testFindFeatures_withResultList()
+  {
+    FeatureStore fs = newFeatureStore();
+    SequenceFeature sf1 = addFeature(fs, 10, 50);
+    SequenceFeature sf2 = addFeature(fs, 150, 250);
+  
+    List<SequenceFeature> overlaps = new ArrayList<>();
+    List<SequenceFeature> result = fs.findOverlappingFeatures(200, 200,
+            overlaps);
+    assertSame(result, overlaps);
+    assertEquals(result.size(), 1);
+    assertTrue(result.contains(sf2));
+    assertFalse(result.contains(sf1));
+
+    /*
+     * if no list supplied, method creates one
+     */
+    result = fs.findOverlappingFeatures(200, 200, null);
+    assertEquals(result.size(), 1);
+    assertTrue(result.contains(sf2));
+    assertFalse(result.contains(sf1));
+  }
 }