@Test(groups = "Functional")
public void testGetPositionalFeatures()
{
- SequenceFeatures store = new SequenceFeatures();
+ SequenceFeaturesI store = new SequenceFeatures();
SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
Float.NaN, null);
store.add(sf1);
/*
* get features by type
*/
- assertTrue(store.getPositionalFeatures(null).isEmpty());
+ assertTrue(store.getPositionalFeatures((String) null).isEmpty());
assertTrue(store.getPositionalFeatures("Cath").isEmpty());
assertTrue(store.getPositionalFeatures("METAL").isEmpty());
@Test(groups = "Functional")
public void testGetContactFeatures()
{
- SequenceFeatures store = new SequenceFeatures();
+ SequenceFeaturesI store = new SequenceFeatures();
// non-contact
SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
Float.NaN, null);
/*
* get contact features by type
*/
- assertTrue(store.getContactFeatures(null).isEmpty());
+ assertTrue(store.getContactFeatures((String) null).isEmpty());
assertTrue(store.getContactFeatures("Cath").isEmpty());
assertTrue(store.getContactFeatures("Pfam").isEmpty());
assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
@Test(groups = "Functional")
public void testGetNonPositionalFeatures()
{
- SequenceFeatures store = new SequenceFeatures();
+ SequenceFeaturesI store = new SequenceFeatures();
// positional
SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
Float.NaN, null);
/*
* get non-positional features by type
*/
- assertTrue(store.getNonPositionalFeatures(null).isEmpty());
+ assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
* @param to
* @return
*/
- SequenceFeature addFeature(SequenceFeatures sf, String type, int from,
+ SequenceFeature addFeature(SequenceFeaturesI sf, String type, int from,
int to)
{
SequenceFeature sf1 = new SequenceFeature(type, "", from, to,
@Test(groups = "Functional")
public void testFindFeatures()
{
- SequenceFeatures sf = new SequenceFeatures();
+ SequenceFeaturesI sf = new SequenceFeatures();
SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
SequenceFeature sf2 = addFeature(sf, "Pfam", 1, 15);
SequenceFeature sf3 = addFeature(sf, "Pfam", 20, 30);
// null type is weird but possible:
SequenceFeature sf13 = addFeature(sf, null, 5, 12);
- List<SequenceFeature> overlaps = sf.findFeatures("Pfam", 200, 200);
+ List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
assertTrue(overlaps.isEmpty());
- overlaps = sf.findFeatures("Pfam", 1, 9);
+ overlaps = sf.findFeatures( 1, 9, "Pfam");
assertEquals(overlaps.size(), 1);
assertTrue(overlaps.contains(sf2));
- overlaps = sf.findFeatures("Pfam", 5, 18);
+ overlaps = sf.findFeatures( 5, 18, "Pfam");
assertEquals(overlaps.size(), 2);
assertTrue(overlaps.contains(sf1));
assertTrue(overlaps.contains(sf2));
- overlaps = sf.findFeatures("Pfam", 30, 40);
+ overlaps = sf.findFeatures(30, 40, "Pfam");
assertEquals(overlaps.size(), 3);
assertTrue(overlaps.contains(sf1));
assertTrue(overlaps.contains(sf3));
assertTrue(overlaps.contains(sf4));
- overlaps = sf.findFeatures("Pfam", 80, 90);
+ overlaps = sf.findFeatures( 80, 90, "Pfam");
assertEquals(overlaps.size(), 2);
assertTrue(overlaps.contains(sf4));
assertTrue(overlaps.contains(sf5));
- overlaps = sf.findFeatures("Pfam", 68, 70);
+ overlaps = sf.findFeatures( 68, 70, "Pfam");
assertEquals(overlaps.size(), 3);
assertTrue(overlaps.contains(sf4));
assertTrue(overlaps.contains(sf5));
assertTrue(overlaps.contains(sf6));
- overlaps = sf.findFeatures("Cath", 16, 69);
+ overlaps = sf.findFeatures(16, 69, "Cath");
assertEquals(overlaps.size(), 4);
assertTrue(overlaps.contains(sf7));
assertFalse(overlaps.contains(sf8));
assertTrue(overlaps.contains(sf11));
assertFalse(overlaps.contains(sf12));
- assertTrue(sf.findFeatures("Metal", 0, 1000).isEmpty());
+ assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());
- overlaps = sf.findFeatures(null, 7, 7);
+ overlaps = sf.findFeatures(7, 7, (String) null);
assertEquals(overlaps.size(), 1);
assertTrue(overlaps.contains(sf13));
}
@Test(groups = "Functional")
public void testDelete()
{
- SequenceFeatures sf = new SequenceFeatures();
+ SequenceFeaturesI sf = new SequenceFeatures();
SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
assertTrue(sf.getPositionalFeatures().contains(sf1));
@Test(groups = "Functional")
public void testHasFeatures()
{
- SequenceFeatures sf = new SequenceFeatures();
+ SequenceFeaturesI sf = new SequenceFeatures();
assertFalse(sf.hasFeatures());
SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
@Test(groups = "Functional")
public void testGetFeatureGroups()
{
- SequenceFeatures sf = new SequenceFeatures();
+ SequenceFeaturesI sf = new SequenceFeatures();
assertTrue(sf.getFeatureGroups(true).isEmpty());
assertTrue(sf.getFeatureGroups(false).isEmpty());
@Test(groups = "Functional")
public void testGetFeatureTypesForGroups()
{
- SequenceFeatures sf = new SequenceFeatures();
+ SequenceFeaturesI sf = new SequenceFeatures();
assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
/*
assertTrue(groups.contains("turn"));
assertTrue(groups.contains("strand"));
}
+
+ @Test(groups = "Functional")
+ public void testGetFeatureTypes()
+ {
+ SequenceFeaturesI store = new SequenceFeatures();
+ Set<String> types = store.getFeatureTypes();
+ assertTrue(types.isEmpty());
+
+ SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf1);
+ types = store.getFeatureTypes();
+ assertEquals(types.size(), 1);
+ assertTrue(types.contains("Metal"));
+
+ // null type is possible...
+ SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf2);
+ types = store.getFeatureTypes();
+ assertEquals(types.size(), 2);
+ assertTrue(types.contains(null));
+ assertTrue(types.contains("Metal"));
+
+ /*
+ * add non-positional feature
+ */
+ SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
+ Float.NaN, null);
+ store.add(sf3);
+ types = store.getFeatureTypes();
+ assertEquals(types.size(), 3);
+ assertTrue(types.contains("Pfam"));
+
+ /*
+ * add contact feature
+ */
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
+ 10, 20, Float.NaN, null);
+ store.add(sf4);
+ types = store.getFeatureTypes();
+ assertEquals(types.size(), 4);
+ assertTrue(types.contains("Disulphide Bond"));
+
+ /*
+ * add another Pfam
+ */
+ SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf5);
+ types = store.getFeatureTypes();
+ assertEquals(types.size(), 4); // unchanged
+
+ /*
+ * delete first Pfam - still have one
+ */
+ assertTrue(store.delete(sf3));
+ types = store.getFeatureTypes();
+ assertEquals(types.size(), 4);
+ assertTrue(types.contains("Pfam"));
+
+ /*
+ * delete second Pfam - no longer have one
+ */
+ assertTrue(store.delete(sf5));
+ types = store.getFeatureTypes();
+ assertEquals(types.size(), 3);
+ assertFalse(types.contains("Pfam"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetFeatureCount()
+ {
+ SequenceFeaturesI store = new SequenceFeatures();
+ assertEquals(store.getFeatureCount(true), 0);
+ assertEquals(store.getFeatureCount(false), 0);
+
+ /*
+ * add positional
+ */
+ SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf1);
+ assertEquals(store.getFeatureCount(true), 1);
+ assertEquals(store.getFeatureCount(false), 0);
+
+ /*
+ * another positional
+ */
+ SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf2);
+ assertEquals(store.getFeatureCount(true), 2);
+ assertEquals(store.getFeatureCount(false), 0);
+
+ /*
+ * add non-positional feature
+ */
+ SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
+ Float.NaN, null);
+ store.add(sf3);
+ assertEquals(store.getFeatureCount(true), 2);
+ assertEquals(store.getFeatureCount(false), 1);
+
+ /*
+ * add contact feature (counts as 1)
+ */
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
+ 10, 20, Float.NaN, null);
+ store.add(sf4);
+ assertEquals(store.getFeatureCount(true), 3);
+ assertEquals(store.getFeatureCount(false), 1);
+
+ /*
+ * add another Pfam
+ */
+ SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf5);
+ assertEquals(store.getFeatureCount(true), 4);
+ assertEquals(store.getFeatureCount(false), 1);
+ assertEquals(store.getFeatureCount(true, "Pfam"), 1);
+ assertEquals(store.getFeatureCount(false, "Pfam"), 1);
+ // search for type==null
+ assertEquals(store.getFeatureCount(true, (String) null), 1);
+ // search with no type specified
+ assertEquals(store.getFeatureCount(true, (String[]) null), 4);
+ assertEquals(store.getFeatureCount(true, "Metal", "Cath"), 1);
+ assertEquals(store.getFeatureCount(true, "Disulphide Bond"), 1);
+ assertEquals(store.getFeatureCount(true, "Metal", "Pfam", null), 3);
+
+ /*
+ * delete first Pfam (non-positional)
+ */
+ assertTrue(store.delete(sf3));
+ assertEquals(store.getFeatureCount(true), 4);
+ assertEquals(store.getFeatureCount(false), 0);
+
+ /*
+ * delete second Pfam (positional)
+ */
+ assertTrue(store.delete(sf5));
+ assertEquals(store.getFeatureCount(true), 3);
+ assertEquals(store.getFeatureCount(false), 0);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAllFeatures()
+ {
+ SequenceFeaturesI store = new SequenceFeatures();
+ List<SequenceFeature> features = store.getAllFeatures();
+ assertTrue(features.isEmpty());
+
+ SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf1);
+ features = store.getAllFeatures();
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf1));
+
+ SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf2);
+ features = store.getAllFeatures();
+ assertEquals(features.size(), 2);
+ assertTrue(features.contains(sf2));
+
+ /*
+ * add non-positional feature
+ */
+ SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
+ Float.NaN, null);
+ store.add(sf3);
+ features = store.getAllFeatures();
+ assertEquals(features.size(), 3);
+ assertTrue(features.contains(sf3));
+
+ /*
+ * add contact feature
+ */
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
+ 10, 20, Float.NaN, null);
+ store.add(sf4);
+ features = store.getAllFeatures();
+ assertEquals(features.size(), 4);
+ assertTrue(features.contains(sf4));
+
+ /*
+ * add another Pfam
+ */
+ SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf5);
+ features = store.getAllFeatures();
+ assertEquals(features.size(), 5);
+ assertTrue(features.contains(sf5));
+ features = store.getAllFeatures("Cath");
+ assertTrue(features.isEmpty());
+ features = store.getAllFeatures("Pfam", "Cath", "Metal");
+ assertEquals(features.size(), 3);
+ assertTrue(features.contains(sf1));
+ assertTrue(features.contains(sf3));
+ assertTrue(features.contains(sf5));
+
+ /*
+ * delete first Pfam
+ */
+ assertTrue(store.delete(sf3));
+ features = store.getAllFeatures();
+ assertEquals(features.size(), 4);
+ assertFalse(features.contains(sf3));
+
+ /*
+ * delete second Pfam
+ */
+ assertTrue(store.delete(sf5));
+ features = store.getAllFeatures();
+ assertEquals(features.size(), 3);
+ assertFalse(features.contains(sf3));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetTotalFeatureLength()
+ {
+ SequenceFeaturesI store = new SequenceFeatures();
+ assertEquals(store.getTotalFeatureLength(), 0);
+
+ SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+ Float.NaN, null);
+ assertTrue(store.add(sf1));
+ assertEquals(store.getTotalFeatureLength(), 11);
+
+ // re-add does nothing!
+ assertFalse(store.add(sf1));
+ assertEquals(store.getTotalFeatureLength(), 11);
+
+ /*
+ * add non-positional feature
+ */
+ SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
+ Float.NaN, null);
+ store.add(sf3);
+ assertEquals(store.getTotalFeatureLength(), 11);
+
+ /*
+ * add contact feature - counts 1 to feature length
+ */
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
+ 10, 20, Float.NaN, null);
+ store.add(sf4);
+ assertEquals(store.getTotalFeatureLength(), 12);
+
+ /*
+ * add another Pfam
+ */
+ SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
+ Float.NaN, null);
+ store.add(sf5);
+ assertEquals(store.getTotalFeatureLength(), 23);
+
+ /*
+ * delete features
+ */
+ assertTrue(store.delete(sf3)); // non-positional
+ assertEquals(store.getTotalFeatureLength(), 23); // no change
+
+ assertTrue(store.delete(sf5));
+ assertEquals(store.getTotalFeatureLength(), 12);
+
+ assertTrue(store.delete(sf4)); // contact
+ assertEquals(store.getTotalFeatureLength(), 11);
+
+ assertTrue(store.delete(sf1));
+ assertEquals(store.getTotalFeatureLength(), 0);
+ }
+
+ @Test
+ public void testGetMinimumScore_getMaximumScore()
+ {
+ SequenceFeatures sf = new SequenceFeatures();
+ SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 0, 0,
+ Float.NaN, "group"); // non-positional, no score
+ sf.add(sf1);
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 10, 20,
+ Float.NaN, "group"); // positional, no score
+ sf.add(sf2);
+ SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 10, 20, 1f,
+ "group");
+ sf.add(sf3);
+ SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 12, 16, 4f,
+ "group");
+ sf.add(sf4);
+ SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 0, 0, 11f,
+ "group");
+ sf.add(sf5);
+ SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, -7f,
+ "group");
+ sf.add(sf6);
+
+ assertEquals(sf.getMinimumScore("nosuchtype", true), Float.NaN);
+ assertEquals(sf.getMinimumScore("nosuchtype", false), Float.NaN);
+ assertEquals(sf.getMaximumScore("nosuchtype", true), Float.NaN);
+ assertEquals(sf.getMaximumScore("nosuchtype", false), Float.NaN);
+
+ // positional features min-max:
+ assertEquals(sf.getMinimumScore("Metal", true), 1f);
+ assertEquals(sf.getMaximumScore("Metal", true), 4f);
+ assertEquals(sf.getMinimumScore("Cath", true), Float.NaN);
+ assertEquals(sf.getMaximumScore("Cath", true), Float.NaN);
+
+ // non-positional features min-max:
+ assertEquals(sf.getMinimumScore("Cath", false), -7f);
+ assertEquals(sf.getMaximumScore("Cath", false), 11f);
+ assertEquals(sf.getMinimumScore("Metal", false), Float.NaN);
+ assertEquals(sf.getMaximumScore("Metal", false), Float.NaN);
+
+ // delete features; min-max should get recomputed
+ sf.delete(sf6);
+ assertEquals(sf.getMinimumScore("Cath", false), 11f);
+ assertEquals(sf.getMaximumScore("Cath", false), 11f);
+ sf.delete(sf4);
+ assertEquals(sf.getMinimumScore("Metal", true), 1f);
+ assertEquals(sf.getMaximumScore("Metal", true), 1f);
+ sf.delete(sf5);
+ assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
+ assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
+ sf.delete(sf3);
+ assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
+ assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
+ sf.delete(sf1);
+ sf.delete(sf2);
+ assertFalse(sf.hasFeatures());
+ assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
+ assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
+ assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
+ assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
+ }
}
git://source.jalview.org / jalview.git / blobdiff