+
+ @Test(groups = "Functional")
+ public void testVarargsToTypes()
+ {
+ SequenceFeatures sf = new SequenceFeatures();
+ sf.add(new SequenceFeature("Metal", "desc", 0, 0, Float.NaN, "group"));
+ sf.add(new SequenceFeature("Cath", "desc", 10, 20, Float.NaN, "group"));
+
+ /*
+ * no type specified - get all types stored
+ * they are returned in keyset (alphabetical) order
+ */
+ Iterable<String> types = sf.varargToTypes();
+ Iterator<String> iterator = types.iterator();
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Cath");
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
+ assertFalse(iterator.hasNext());
+
+ /*
+ * empty array is the same as no vararg parameter supplied
+ * so treated as all stored types
+ */
+ types = sf.varargToTypes(new String[] {});
+ iterator = types.iterator();
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Cath");
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
+ assertFalse(iterator.hasNext());
+
+ /*
+ * null type specified; this is passed as vararg
+ * String[1] {null}
+ */
+ types = sf.varargToTypes((String) null);
+ assertFalse(types.iterator().hasNext());
+
+ /*
+ * null types array specified; this is passed as vararg null
+ */
+ types = sf.varargToTypes((String[]) null);
+ iterator = types.iterator();
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Cath");
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
+ assertFalse(iterator.hasNext());
+
+ /*
+ * one type specified
+ */
+ types = sf.varargToTypes("Metal");
+ iterator = types.iterator();
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
+ assertFalse(iterator.hasNext());
+
+ /*
+ * two types specified - get sorted alphabetically
+ */
+ types = sf.varargToTypes("Metal", "Helix");
+ iterator = types.iterator();
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Helix");
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
+ assertFalse(iterator.hasNext());
+
+ /*
+ * null type included - should get removed
+ */
+ types = sf.varargToTypes("Metal", null, "Helix");
+ iterator = types.iterator();
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Helix");
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
+ 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);
+ }