X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreTest.java;h=bc179f69ca6f6857fc29de23415ef4b9817bd8fc;hb=78991c8c3216606a0e7203ec25f59fea4898126c;hp=c38cb1eabfa2de895aa7c2ea7e14ac7388f28c6d;hpb=4a25d1aa51aa9f76efba8eb278bdd976216bb88e;p=jalview.git

diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java
index c38cb1e..bc179f6 100644
--- a/test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreTest.java
@@ -8,18 +8,25 @@ import static org.testng.Assert.assertTrue;
 import jalview.datamodel.SequenceFeature;
 
 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;
+
 public class FeatureStoreTest
 {
+  private FeatureStore newFeatureStore()
+  {
+    return new FeatureStore();
+  }
 
   @Test(groups = "Functional")
   public void testFindFeatures_nonNested()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN,
             null));
     // same range different description
@@ -49,7 +56,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testFindFeatures_nested()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     SequenceFeature sf1 = addFeature(fs, 10, 50);
     SequenceFeature sf2 = addFeature(fs, 10, 40);
     SequenceFeature sf3 = addFeature(fs, 20, 30);
@@ -88,7 +95,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testFindFeatures_mixed()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     SequenceFeature sf1 = addFeature(fs, 10, 50);
     SequenceFeature sf2 = addFeature(fs, 1, 15);
     SequenceFeature sf3 = addFeature(fs, 20, 30);
@@ -145,7 +152,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testFindFeatures_contactFeatures()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     SequenceFeature sf = new SequenceFeature("disulphide bond", "bond", 10,
             20, Float.NaN, null);
@@ -188,7 +195,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetPositionalFeatures()
   {
-    FeatureStore store = new FeatureStore();
+    FeatureStore store = newFeatureStore();
     SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
             Float.NaN, null);
     store.addFeature(sf1);
@@ -235,7 +242,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testDelete()
   {
-    FeatureStore store = new FeatureStore();
+    FeatureStore store = newFeatureStore();
     SequenceFeature sf1 = addFeature(store, 10, 20);
     assertTrue(store.getPositionalFeatures().contains(sf1));
 
@@ -307,7 +314,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testAddFeature()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
             Float.NaN, null);
@@ -358,7 +365,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testIsEmpty()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.isEmpty());
     assertEquals(fs.getFeatureCount(true), 0);
 
@@ -411,7 +418,9 @@ public class FeatureStoreTest
     assertEquals(fs.getFeatureCount(true), 3);
     assertTrue(fs.delete(sf1));
     assertEquals(fs.getFeatureCount(true), 2);
-    assertEquals(fs.features.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);
@@ -424,7 +433,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetFeatureGroups()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertTrue(fs.getFeatureGroups(true).isEmpty());
     assertTrue(fs.getFeatureGroups(false).isEmpty());
 
@@ -491,7 +500,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetTotalFeatureLength()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertEquals(fs.getTotalFeatureLength(), 0);
 
     addFeature(fs, 10, 20); // 11
@@ -567,7 +576,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testGetMinimumScore_getMaximumScore()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertEquals(fs.getMinimumScore(true), Float.NaN); // positional
     assertEquals(fs.getMaximumScore(true), Float.NaN);
     assertEquals(fs.getMinimumScore(false), Float.NaN); // non-positional
@@ -639,14 +648,15 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testListContains()
   {
-    assertFalse(FeatureStore.listContains(null, null));
+    FeatureStore featureStore = newFeatureStore();
+    assertFalse(featureStore.listContains(null, null));
     List<SequenceFeature> features = new ArrayList<>();
-    assertFalse(FeatureStore.listContains(features, null));
+    assertFalse(featureStore.listContains(features, null));
 
     SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
             "group1");
-    assertFalse(FeatureStore.listContains(null, sf1));
-    assertFalse(FeatureStore.listContains(features, sf1));
+    assertFalse(featureStore.listContains(null, sf1));
+    assertFalse(featureStore.listContains(features, sf1));
 
     features.add(sf1);
     SequenceFeature sf2 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
@@ -655,14 +665,14 @@ public class FeatureStoreTest
             "group1");
 
     // sf2.equals(sf1) so contains should return true
-    assertTrue(FeatureStore.listContains(features, sf2));
-    assertFalse(FeatureStore.listContains(features, sf3));
+    assertTrue(featureStore.listContains(features, sf2));
+    assertFalse(featureStore.listContains(features, sf3));
   }
 
   @Test(groups = "Functional")
   public void testGetFeaturesForGroup()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
 
     /*
      * with no features
@@ -720,7 +730,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testShiftFeatures()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
@@ -807,7 +817,7 @@ public class FeatureStoreTest
     /*
      * add a feature and a nested feature
      */
-    FeatureStore store = new FeatureStore();
+    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);
@@ -815,8 +825,10 @@ public class FeatureStoreTest
     assertEquals(features.size(), 2);
     assertTrue(features.contains(sf1));
     assertTrue(features.contains(sf2));
-    assertTrue(store.features.contains(sf1));
-    assertTrue(store.features.contains(sf2));
+    Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+            .getValue(store, "features");
+    assertTrue(intervalStore.contains(sf1));
+    assertTrue(intervalStore.contains(sf2));
   
     /*
      * delete the first feature
@@ -838,7 +850,7 @@ public class FeatureStoreTest
   @Test(groups = "Functional")
   public void testContains()
   {
-    FeatureStore fs = new FeatureStore();
+    FeatureStore fs = newFeatureStore();
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
             Float.NaN, "group1");
     SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
@@ -881,4 +893,28 @@ 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));
+  }
 }