X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreJSTest.java;h=489ac38ec7b515ab1e5a40d794b0798359fd0c33;hb=3bc97fb559bcd28299532021c5b62b0ca62d4d3b;hp=12b6c74fc42cb9d4e350deec29fda8fbad555dd2;hpb=99b6c1ca13af92cd8867971986a05664b0cd787c;p=jalview.git

diff --git a/test/jalview/datamodel/features/FeatureStoreJSTest.java b/test/jalview/datamodel/features/FeatureStoreJSTest.java
index 12b6c74..489ac38 100644
--- a/test/jalview/datamodel/features/FeatureStoreJSTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreJSTest.java
@@ -16,10 +16,12 @@ import org.testng.annotations.Test;
 public class FeatureStoreJSTest
 {
 
+  private int intervalStoreOption = FeatureStore.intervalStoreJSOption;
+
   @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
@@ -36,26 +38,26 @@ public class FeatureStoreJSTest
     assertEquals(overlaps.get(1).getEnd(), 20);
 
     overlaps = fs.findOverlappingFeatures(12, 16);
+
     assertEquals(overlaps.size(), 3);
-    assertEquals(overlaps.get(0).getEnd(), 20);
-    assertEquals(overlaps.get(1).getEnd(), 20);
     assertEquals(overlaps.get(2).getEnd(), 25);
+    assertEquals(overlaps.get(1).getEnd(), 20);
+    assertEquals(overlaps.get(0).getEnd(), 20);
 
     overlaps = fs.findOverlappingFeatures(33, 33);
     assertEquals(overlaps.size(), 1);
     assertEquals(overlaps.get(0).getEnd(), 35);
   }
 
-  private FeatureStoreI newFeatureStore()
+  private FeatureStore newFeatureStore()
   {
-    return new FeatureStoreJS();
-    // return new FeatureStoreImpl();
+    return new FeatureStore(intervalStoreOption);
   }
 
   @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);
@@ -91,10 +93,42 @@ public class FeatureStoreJSTest
     assertTrue(overlaps.contains(sf4));
   }
 
+  private void testFind()
+  {
+    FeatureStore fs1 = newFeatureStore();
+
+    SequenceFeature sf = addFeature(fs1, 1, 3000);
+
+    for (int i = 1; i < 1000; i++)
+
+    {
+
+      addFeature(fs1, 1 + i, 1000 + i);
+
+    }
+
+    // 1.......3000
+    // 2....1001
+    // 3....1002
+    // 4....1003
+    // ...
+    // 1000..1999
+
+    List<SequenceFeature> overlaps1 = fs1.findOverlappingFeatures(2000,
+            2001);
+
+    assertEquals(overlaps1.size(), 1);
+
+    assertTrue(overlaps1.contains(sf));
+
+  }
+
   @Test(groups = "Functional")
   public void testFindFeatures_mixed()
   {
-    FeatureStoreI fs = newFeatureStore();
+    testFind();
+
+    FeatureStore fs = newFeatureStore();
     SequenceFeature sf1 = addFeature(fs, 10, 50);
     SequenceFeature sf2 = addFeature(fs, 1, 15);
     SequenceFeature sf3 = addFeature(fs, 20, 30);
@@ -140,7 +174,7 @@ public class FeatureStoreJSTest
    * @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 +185,7 @@ public class FeatureStoreJSTest
   @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 +228,7 @@ public class FeatureStoreJSTest
   @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 +275,7 @@ public class FeatureStoreJSTest
   @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 +347,7 @@ public class FeatureStoreJSTest
   @Test(groups = "Functional")
   public void testAddFeature()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
             Float.NaN, null);
@@ -364,7 +398,7 @@ public class FeatureStoreJSTest
   @Test(groups = "Functional")
   public void testIsEmpty()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.isEmpty());
     assertEquals(fs.getFeatureCount(true), 0);
 
@@ -430,7 +464,7 @@ public class FeatureStoreJSTest
   @Test(groups = "Functional")
   public void testGetFeatureGroups()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.getFeatureGroups(true).isEmpty());
     assertTrue(fs.getFeatureGroups(false).isEmpty());
 
@@ -497,7 +531,7 @@ public class FeatureStoreJSTest
   @Test(groups = "Functional")
   public void testGetTotalFeatureLength()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertEquals(fs.getTotalFeatureLength(), 0);
 
     addFeature(fs, 10, 20); // 11
@@ -573,7 +607,7 @@ public class FeatureStoreJSTest
   @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 +679,7 @@ public class FeatureStoreJSTest
   @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 +703,7 @@ public class FeatureStoreJSTest
   @Test(groups = "Functional")
   public void testGetFeaturesForGroup()
   {
-    FeatureStoreI fs = newFeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     /*
      * with no features
@@ -727,7 +761,7 @@ public class FeatureStoreJSTest
   @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 +848,7 @@ public class FeatureStoreJSTest
     /*
      * 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 +879,7 @@ public class FeatureStoreJSTest
   @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,