JAL-2525 get sequence features for Ontology term(s), tidy feature sort

[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 0d1d89d..5ff2d7b 100644 (file)
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -2,10 +2,12 @@ package jalview.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.SequenceFeature;
 
+import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
@@ -909,4 +911,105 @@ public class SequenceFeaturesTest
     assertEquals(iterator.next(), "Helix");
     assertFalse(iterator.hasNext());
   }
+
+  @Test(groups = "Functional")
+  public void testGetFeatureTypes_byOntology()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+  
+    SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
+            Float.NaN, null);
+    store.add(sf1);
+    // mRNA isA mature_transcript isA transcript
+    SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 10, 20,
+            Float.NaN, null);
+    store.add(sf2);
+    // just to prove non-positional feature types are included
+    SequenceFeature sf3 = new SequenceFeature("mRNA", "desc", 0, 0,
+            Float.NaN, null);
+    store.add(sf3);
+    SequenceFeature sf4 = new SequenceFeature("CDS", "desc", 0, 0,
+            Float.NaN, null);
+    store.add(sf4);
+
+    Set<String> types = store.getFeatureTypes("transcript");
+    assertEquals(types.size(), 2);
+    assertTrue(types.contains("transcript"));
+    assertTrue(types.contains("mRNA"));
+
+    // matches include arguments whether SO terms or not
+    types = store.getFeatureTypes("transcript", "CDS");
+    assertEquals(types.size(), 3);
+    assertTrue(types.contains("transcript"));
+    assertTrue(types.contains("mRNA"));
+    assertTrue(types.contains("CDS"));
+
+    types = store.getFeatureTypes("exon");
+    assertTrue(types.isEmpty());
+  }
+
+  @Test(groups = "Functional")
+  public void testGetFeaturesByOntology()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+    List<SequenceFeature> features = store.getFeaturesByOntology();
+    assertTrue(features.isEmpty());
+    assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty());
+    assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty());
+  
+    SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
+            Float.NaN, null);
+    store.add(sf1);
+
+    // 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,
+            Float.NaN, null);
+    store.add(sf2);
+
+    SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 30, 40,
+            Float.NaN, null);
+    store.add(sf3);
+
+    features = store.getFeaturesByOntology("transcript");
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2));
+
+    features = store.getFeaturesByOntology("mRNA");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+
+    features = store.getFeaturesByOntology("mRNA", "Pfam");
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+  }
+
+  @Test(groups = "Functional")
+  public void testSortFeatures()
+  {
+    List<SequenceFeature> sfs = new ArrayList<SequenceFeature>();
+    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80,
+            Float.NaN, null);
+    sfs.add(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
+            Float.NaN, null);
+    sfs.add(sf2);
+    SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
+            Float.NaN, null);
+    sfs.add(sf3);
+
+    // sort by end position descending
+    SequenceFeatures.sortFeatures(sfs, false);
+    assertSame(sfs.get(0), sf1);
+    assertSame(sfs.get(1), sf3);
+    assertSame(sfs.get(2), sf2);
+
+    // sort by start position ascending
+    SequenceFeatures.sortFeatures(sfs, true);
+    assertSame(sfs.get(0), sf1);
+    assertSame(sfs.get(1), sf2);
+    assertSame(sfs.get(2), sf3);
+  }
 }