3253-omnibus save

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

diff --git a/test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java b/test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
index 2b9198a..14f0f07 100644 (file)
--- a/test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
@@ -6,26 +6,31 @@ import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.features.FeatureStore.IntervalStoreType;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
+/**
+ * Tests that exercise the 'NC array' implementation of IntervalStore
+ */
 public class FeatureStoreNCListBufferTest
 {
-
-  private FeatureStoreI newFeatureStore()
+  private FeatureStore newFeatureStore()
   {
-    return new FeatureStoreImpl(
-            FeatureStore.INTERVAL_STORE_NCLIST_BUFFER_PRESORT);
+    return new FeatureStore(IntervalStoreType.INTERVAL_STORE_NCARRAY);
   }
 
   @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
@@ -33,21 +38,21 @@ public class FeatureStoreNCListBufferTest
     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);
   }
@@ -55,7 +60,7 @@ public class FeatureStoreNCListBufferTest
   @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);
@@ -65,25 +70,25 @@ public class FeatureStoreNCListBufferTest
     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));
@@ -94,7 +99,7 @@ public class FeatureStoreNCListBufferTest
   @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);
@@ -102,30 +107,30 @@ public class FeatureStoreNCListBufferTest
     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));
@@ -140,7 +145,7 @@ public class FeatureStoreNCListBufferTest
    * @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 +156,7 @@ public class FeatureStoreNCListBufferTest
   @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);
@@ -160,33 +165,33 @@ public class FeatureStoreNCListBufferTest
     /*
      * 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));
   }
@@ -194,7 +199,7 @@ public class FeatureStoreNCListBufferTest
   @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 +246,7 @@ public class FeatureStoreNCListBufferTest
   @Test(groups = "Functional")
   public void testDelete()
   {
-    FeatureStoreI store = newFeatureStore();
+    FeatureStore store = newFeatureStore();
     SequenceFeature sf1 = addFeature(store, 10, 20);
     assertTrue(store.getPositionalFeatures().contains(sf1));
 
@@ -321,7 +326,7 @@ public class FeatureStoreNCListBufferTest
   @Test(groups = "Functional")
   public void testAddFeature()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
             Float.NaN, null);
@@ -372,7 +377,7 @@ public class FeatureStoreNCListBufferTest
   @Test(groups = "Functional")
   public void testIsEmpty()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.isEmpty());
     assertEquals(fs.getFeatureCount(true), 0);
 
@@ -425,7 +430,9 @@ public class FeatureStoreNCListBufferTest
     assertEquals(fs.getFeatureCount(true), 3);
     assertTrue(fs.delete(sf1));
     assertEquals(fs.getFeatureCount(true), 2);
-    assertEquals(fs.getFeatures().size(), 2);
+    Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+            .getValue(fs, "features");
+    assertEquals(intervalStore.size(), 2);
     assertFalse(fs.isEmpty());
     assertTrue(fs.delete(sf2));
     assertEquals(fs.getFeatureCount(true), 1);
@@ -438,7 +445,7 @@ public class FeatureStoreNCListBufferTest
   @Test(groups = "Functional")
   public void testGetFeatureGroups()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.getFeatureGroups(true).isEmpty());
     assertTrue(fs.getFeatureGroups(false).isEmpty());
 
@@ -505,7 +512,7 @@ public class FeatureStoreNCListBufferTest
   @Test(groups = "Functional")
   public void testGetTotalFeatureLength()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertEquals(fs.getTotalFeatureLength(), 0);
 
     addFeature(fs, 10, 20); // 11
@@ -581,7 +588,7 @@ public class FeatureStoreNCListBufferTest
   @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
@@ -653,7 +660,7 @@ public class FeatureStoreNCListBufferTest
   @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));
@@ -677,7 +684,7 @@ public class FeatureStoreNCListBufferTest
   @Test(groups = "Functional")
   public void testGetFeaturesForGroup()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     /*
      * with no features
@@ -735,7 +742,7 @@ public class FeatureStoreNCListBufferTest
   @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);
@@ -822,7 +829,7 @@ public class FeatureStoreNCListBufferTest
     /*
      * 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);
@@ -830,8 +837,10 @@ public class FeatureStoreNCListBufferTest
     assertEquals(features.size(), 2);
     assertTrue(features.contains(sf1));
     assertTrue(features.contains(sf2));
-    assertTrue(store.getFeatures().contains(sf1));
-    assertTrue(store.getFeatures().contains(sf2));
+    Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+            .getValue(store, "features");
+    assertTrue(intervalStore.contains(sf1));
+    assertTrue(intervalStore.contains(sf2));
   
     /*
      * delete the first feature
@@ -853,7 +862,7 @@ public class FeatureStoreNCListBufferTest
   @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,