JAL-3453

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

diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index 3f0eb9a..e979f51 100644 (file)
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -13,10 +13,10 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceFeaturesTest
 {
   @Test(groups = "Functional")
@@ -1005,39 +1005,53 @@ public class SequenceFeaturesTest
     assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty());
     assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty());
   
-    SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
+    SequenceFeature transcriptFeature = new SequenceFeature("transcript", "desc", 10, 20,
             Float.NaN, null);
-    store.add(sf1);
+    store.add(transcriptFeature);
 
-    // mRNA isA transcript; added here 'as if' non-positional
-    // just to show that non-positional features are included in results
-    SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 0, 0,
+    /*
+     * mRNA is a sub-type of transcript; added here 'as if' non-positional
+     * just to show that non-positional features are included in results
+     */
+    SequenceFeature mrnaFeature = new SequenceFeature("mRNA", "desc", 0, 0,
             Float.NaN, null);
-    store.add(sf2);
+    store.add(mrnaFeature);
 
-    SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 30, 40,
+    SequenceFeature pfamFeature = new SequenceFeature("Pfam", "desc", 30, 40,
             Float.NaN, null);
-    store.add(sf3);
+    store.add(pfamFeature);
 
+    /*
+     * "transcript" matches both itself and the sub-term "mRNA"
+     */
     features = store.getFeaturesByOntology("transcript");
     assertEquals(features.size(), 2);
-    assertTrue(features.contains(sf1));
-    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(transcriptFeature));
+    assertTrue(features.contains(mrnaFeature));
 
+    /*
+     * "mRNA" matches itself but not parent term "transcript"
+     */
     features = store.getFeaturesByOntology("mRNA");
     assertEquals(features.size(), 1);
-    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(mrnaFeature));
 
+    /*
+     * "pfam" is not an SO term but is included as an exact match
+     */
     features = store.getFeaturesByOntology("mRNA", "Pfam");
     assertEquals(features.size(), 2);
-    assertTrue(features.contains(sf2));
-    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(mrnaFeature));
+    assertTrue(features.contains(pfamFeature));
+
+    features = store.getFeaturesByOntology("sequence_variant");
+    assertTrue(features.isEmpty());
   }
 
   @Test(groups = "Functional")
   public void testSortFeatures()
   {
-    List<SequenceFeature> sfs = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> sfs = new ArrayList<>();
     SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80,
             Float.NaN, null);
     sfs.add(sf1);
@@ -1247,4 +1261,87 @@ public class SequenceFeaturesTest
     assertTrue(store.isOntologyTerm("junk", new String[] {}));
     assertTrue(store.isOntologyTerm("junk", (String[]) null));
   }
+
+  @Test(groups = "Functional")
+  public void testDeleteAll()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+    assertFalse(store.hasFeatures());
+    store.deleteAll();
+    assertFalse(store.hasFeatures());
+    store.add(new SequenceFeature("Cath", "Desc", 12, 20, 0f, "Group"));
+    store.add(new SequenceFeature("Pfam", "Desc", 6, 12, 2f, "Group2"));
+    assertTrue(store.hasFeatures());
+    store.deleteAll();
+    assertFalse(store.hasFeatures());
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatures_withResultList()
+  {
+    SequenceFeaturesI sf = new SequenceFeatures();
+    SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
+    SequenceFeature sf2 = addFeature(sf, "Pfam", 150, 250);
+  
+    /*
+     * findFeatures with result list to append to
+     */
+    List<SequenceFeature> overlaps = new ArrayList<>();
+    List<SequenceFeature> result = sf.findFeatures(200, "Pfam", overlaps);
+    assertSame(result, overlaps);
+    assertEquals(result.size(), 1);
+    assertTrue(result.contains(sf2));
+    assertFalse(result.contains(sf1));
+
+    /*
+     * with no result list - method creates one
+     */
+    result = sf.findFeatures(200, "Pfam", null);
+    assertEquals(result.size(), 1);
+    assertTrue(result.contains(sf2));
+    assertFalse(result.contains(sf1));
+
+    /*
+     * verify the created list is extendable (is not immutable)
+     * notice it may contain duplicates
+     */
+    result = sf.findFeatures(220, "Pfam", result);
+    assertEquals(result.size(), 2);
+    assertSame(result.get(0), sf2); // in input list
+    assertSame(result.get(1), sf2); // duplicate added
+
+    /*
+     * no feature of requested type - with result list
+     */
+    overlaps.clear();
+    result = sf.findFeatures(200, "Rfam", overlaps);
+    assertTrue(result.isEmpty());
+
+    /*
+     * no feature of requested type - with no result list
+     */
+    result = sf.findFeatures(200, "Rfam", null);
+    assertTrue(result.isEmpty());
+
+    /*
+     * verify the created list is extendable (is not immutable)
+     */
+    result = sf.findFeatures(210, "Pfam", result);
+    assertEquals(result.size(), 1);
+    assertTrue(result.contains(sf2));
+    assertFalse(result.contains(sf1));
+  }
+
+  @Test(groups = "Functional")
+  public void testHasFeatures_ofType()
+  {
+    SequenceFeaturesI sf = new SequenceFeatures();
+    assertFalse(sf.hasFeatures("Pfam"));
+  
+    SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
+    assertTrue(sf.hasFeatures("Pfam"));
+  
+    sf.delete(sf1);
+    assertFalse(sf.hasFeatures("Pfam"));
+  }
 }