import jalview.datamodel.SequenceFeature;
+import java.util.ArrayList;
import java.util.List;
+import java.util.Set;
import org.testng.annotations.Test;
}
@Test(groups = "Functional")
- public void testGetFeatures()
+ public void testGetPositionalFeatures()
{
FeatureStore store = new FeatureStore();
SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
18, 45, Float.NaN, null);
store.addFeature(sf7);
- List<SequenceFeature> features = store.getFeatures();
- assertEquals(features.size(), 7);
+ List<SequenceFeature> features = store.getPositionalFeatures();
+ assertEquals(features.size(), 6);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf4));
assertTrue(features.contains(sf5));
- assertTrue(features.contains(sf6));
+ assertFalse(features.contains(sf6));
assertTrue(features.contains(sf7));
+
+ features = store.getNonPositionalFeatures();
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf6));
}
@Test(groups = "Functional")
{
FeatureStore store = new FeatureStore();
SequenceFeature sf1 = addFeature(store, 10, 20);
- assertTrue(store.getFeatures().contains(sf1));
+ assertTrue(store.getPositionalFeatures().contains(sf1));
/*
* simple deletion
*/
assertTrue(store.delete(sf1));
- assertTrue(store.getFeatures().isEmpty());
+ assertTrue(store.getPositionalFeatures().isEmpty());
/*
* non-positional feature deletion
*/
SequenceFeature sf2 = addFeature(store, 0, 0);
- assertTrue(store.getFeatures().contains(sf2));
+ assertFalse(store.getPositionalFeatures().contains(sf2));
+ assertTrue(store.getNonPositionalFeatures().contains(sf2));
assertTrue(store.delete(sf2));
- assertTrue(store.getFeatures().isEmpty());
+ assertTrue(store.getNonPositionalFeatures().isEmpty());
/*
* contact feature deletion
SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11,
23, Float.NaN, null);
store.addFeature(sf3);
- assertEquals(store.getFeatures().size(), 1);
- assertTrue(store.getFeatures().contains(sf3));
+ assertEquals(store.getPositionalFeatures().size(), 1);
+ assertTrue(store.getPositionalFeatures().contains(sf3));
assertTrue(store.delete(sf3));
- assertTrue(store.getFeatures().isEmpty());
+ assertTrue(store.getPositionalFeatures().isEmpty());
/*
* nested feature deletion
SequenceFeature sf7 = addFeature(store, 25, 25); // sibling of sf6
SequenceFeature sf8 = addFeature(store, 24, 24); // child of sf6
SequenceFeature sf9 = addFeature(store, 23, 23); // child of sf6
- assertEquals(store.getFeatures().size(), 6);
+ assertEquals(store.getPositionalFeatures().size(), 6);
// delete a node with children - they take its place
assertTrue(store.delete(sf6)); // sf8, sf9 should become children of sf5
- assertEquals(store.getFeatures().size(), 5);
- assertFalse(store.getFeatures().contains(sf6));
+ assertEquals(store.getPositionalFeatures().size(), 5);
+ assertFalse(store.getPositionalFeatures().contains(sf6));
// delete a node with no children
assertTrue(store.delete(sf7));
- assertEquals(store.getFeatures().size(), 4);
- assertFalse(store.getFeatures().contains(sf7));
+ assertEquals(store.getPositionalFeatures().size(), 4);
+ assertFalse(store.getPositionalFeatures().contains(sf7));
// delete root of NCList
assertTrue(store.delete(sf5));
- assertEquals(store.getFeatures().size(), 3);
- assertFalse(store.getFeatures().contains(sf5));
+ assertEquals(store.getPositionalFeatures().size(), 3);
+ assertFalse(store.getPositionalFeatures().contains(sf5));
// continue the killing fields
assertTrue(store.delete(sf4));
- assertEquals(store.getFeatures().size(), 2);
- assertFalse(store.getFeatures().contains(sf4));
+ assertEquals(store.getPositionalFeatures().size(), 2);
+ assertFalse(store.getPositionalFeatures().contains(sf4));
assertTrue(store.delete(sf9));
- assertEquals(store.getFeatures().size(), 1);
- assertFalse(store.getFeatures().contains(sf9));
+ assertEquals(store.getPositionalFeatures().size(), 1);
+ assertFalse(store.getPositionalFeatures().contains(sf9));
assertTrue(store.delete(sf8));
- assertTrue(store.getFeatures().isEmpty());
+ assertTrue(store.getPositionalFeatures().isEmpty());
}
@Test(groups = "Functional")
Float.NaN, null);
assertTrue(fs.addFeature(sf1));
+ assertEquals(fs.getFeatureCount(true), 1); // positional
+ assertEquals(fs.getFeatureCount(false), 0); // non-positional
/*
* re-adding the same or an identical feature should fail
*/
assertFalse(fs.addFeature(sf1));
+ assertEquals(fs.getFeatureCount(true), 1);
assertFalse(fs.addFeature(sf2));
+ assertEquals(fs.getFeatureCount(true), 1);
+
+ /*
+ * add non-positional
+ */
+ SequenceFeature sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
+ null);
+ assertTrue(fs.addFeature(sf3));
+ assertEquals(fs.getFeatureCount(true), 1); // positional
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+ SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
+ null);
+ assertFalse(fs.addFeature(sf4)); // already stored
+ assertEquals(fs.getFeatureCount(true), 1); // positional
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+
+ /*
+ * add contact
+ */
+ SequenceFeature sf5 = new SequenceFeature("Disulfide bond", "", 0, 0,
+ Float.NaN, null);
+ assertTrue(fs.addFeature(sf5));
+ assertEquals(fs.getFeatureCount(true), 2); // positional - add 1 for contact
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+ SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "", 0, 0,
+ Float.NaN, null);
+ assertFalse(fs.addFeature(sf6)); // already stored
+ assertEquals(fs.getFeatureCount(true), 2); // no change
+ assertEquals(fs.getFeatureCount(false), 1); // no change
}
@Test(groups = "Functional")
{
FeatureStore fs = new FeatureStore();
assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 0);
/*
* non-nested feature
Float.NaN, null);
fs.addFeature(sf1);
assertFalse(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 1);
fs.delete(sf1);
assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 0);
/*
* non-positional feature
sf1 = new SequenceFeature("Cath", "", 0, 0, Float.NaN, null);
fs.addFeature(sf1);
assertFalse(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+ assertEquals(fs.getFeatureCount(true), 0); // positional
fs.delete(sf1);
assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(false), 0);
/*
* contact feature
sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN, null);
fs.addFeature(sf1);
assertFalse(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 1);
fs.delete(sf1);
assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 0);
/*
* sf2, sf3 added as nested features
fs.addFeature(sf1);
fs.addFeature(sf2);
fs.addFeature(sf3);
+ assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
+ assertEquals(fs.getFeatureCount(true), 2);
// FeatureStore should now only contain features in the NCList
- assertEquals(fs.nonNestedFeatures.size(), 0);
+ assertTrue(fs.nonNestedFeatures.isEmpty());
assertEquals(fs.nestedFeatures.size(), 2);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
+ assertEquals(fs.getFeatureCount(true), 1);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf3));
+ assertEquals(fs.getFeatureCount(true), 0);
assertTrue(fs.isEmpty()); // all gone
}
+
+ @Test(groups = "Functional")
+ public void testGetFeatureGroups()
+ {
+ FeatureStore fs = new FeatureStore();
+ assertTrue(fs.getFeatureGroups(true).isEmpty());
+ assertTrue(fs.getFeatureGroups(false).isEmpty());
+
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ fs.addFeature(sf1);
+ Set<String> groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("group1"));
+
+ /*
+ * add another feature of the same group, delete one, delete both
+ */
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group1");
+ fs.addFeature(sf2);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("group1"));
+ fs.delete(sf2);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("group1"));
+ fs.delete(sf1);
+ groups = fs.getFeatureGroups(true);
+ assertTrue(fs.getFeatureGroups(true).isEmpty());
+
+ SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group2");
+ fs.addFeature(sf3);
+ SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "Group2");
+ fs.addFeature(sf4);
+ SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f, null);
+ fs.addFeature(sf5);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 3);
+ assertTrue(groups.contains("group2"));
+ assertTrue(groups.contains("Group2")); // case sensitive
+ assertTrue(groups.contains(null)); // null allowed
+ assertTrue(fs.getFeatureGroups(false).isEmpty()); // non-positional
+
+ fs.delete(sf3);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 2);
+ assertFalse(groups.contains("group2"));
+ fs.delete(sf4);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertFalse(groups.contains("Group2"));
+ fs.delete(sf5);
+ groups = fs.getFeatureGroups(true);
+ assertTrue(groups.isEmpty());
+
+ /*
+ * add non-positional feature
+ */
+ SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, 1f,
+ "CathGroup");
+ fs.addFeature(sf6);
+ groups = fs.getFeatureGroups(false);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("CathGroup"));
+ assertTrue(fs.delete(sf6));
+ assertTrue(fs.getFeatureGroups(false).isEmpty());
+ }
+
+ @Test(groups = "Functional")
+ public void testGetTotalFeatureLength()
+ {
+ FeatureStore fs = new FeatureStore();
+ assertEquals(fs.getTotalFeatureLength(), 0);
+
+ addFeature(fs, 10, 20); // 11
+ assertEquals(fs.getTotalFeatureLength(), 11);
+ addFeature(fs, 17, 37); // 21
+ SequenceFeature sf1 = addFeature(fs, 14, 74); // 61
+ assertEquals(fs.getTotalFeatureLength(), 93);
+
+ // non-positional features don't count
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 0, 0, 1f,
+ "group1");
+ fs.addFeature(sf2);
+ assertEquals(fs.getTotalFeatureLength(), 93);
+
+ // contact features count 1
+ SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc",
+ 15, 35, 1f, "group1");
+ fs.addFeature(sf3);
+ assertEquals(fs.getTotalFeatureLength(), 94);
+
+ assertTrue(fs.delete(sf1));
+ assertEquals(fs.getTotalFeatureLength(), 33);
+ assertFalse(fs.delete(sf1));
+ assertEquals(fs.getTotalFeatureLength(), 33);
+ assertTrue(fs.delete(sf2));
+ assertEquals(fs.getTotalFeatureLength(), 33);
+ assertTrue(fs.delete(sf3));
+ assertEquals(fs.getTotalFeatureLength(), 32);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetFeatureLength()
+ {
+ /*
+ * positional feature
+ */
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ assertEquals(FeatureStore.getFeatureLength(sf1), 11);
+
+ /*
+ * non-positional feature
+ */
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 0, 0, 1f,
+ "CathGroup");
+ assertEquals(FeatureStore.getFeatureLength(sf2), 0);
+
+ /*
+ * contact feature counts 1
+ */
+ SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc",
+ 14, 28, 1f, "AGroup");
+ assertEquals(FeatureStore.getFeatureLength(sf3), 1);
+ }
+
+ @Test(groups = "Functional")
+ public void testMin()
+ {
+ assertEquals(FeatureStore.min(Float.NaN, Float.NaN), Float.NaN);
+ assertEquals(FeatureStore.min(Float.NaN, 2f), 2f);
+ assertEquals(FeatureStore.min(-2f, Float.NaN), -2f);
+ assertEquals(FeatureStore.min(2f, -3f), -3f);
+ }
+
+ @Test(groups = "Functional")
+ public void testMax()
+ {
+ assertEquals(FeatureStore.max(Float.NaN, Float.NaN), Float.NaN);
+ assertEquals(FeatureStore.max(Float.NaN, 2f), 2f);
+ assertEquals(FeatureStore.max(-2f, Float.NaN), -2f);
+ assertEquals(FeatureStore.max(2f, -3f), 2f);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMinimumScore_getMaximumScore()
+ {
+ FeatureStore fs = new FeatureStore();
+ assertEquals(fs.getMinimumScore(true), Float.NaN); // positional
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN); // non-positional
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // add features with no score
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 0, 0,
+ Float.NaN, "group");
+ fs.addFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("type", "desc", 10, 20,
+ Float.NaN, "group");
+ fs.addFeature(sf2);
+ assertEquals(fs.getMinimumScore(true), Float.NaN);
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // add positional features with score
+ SequenceFeature sf3 = new SequenceFeature("type", "desc", 10, 20, 1f,
+ "group");
+ fs.addFeature(sf3);
+ SequenceFeature sf4 = new SequenceFeature("type", "desc", 12, 16, 4f,
+ "group");
+ fs.addFeature(sf4);
+ assertEquals(fs.getMinimumScore(true), 1f);
+ assertEquals(fs.getMaximumScore(true), 4f);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // add non-positional features with score
+ SequenceFeature sf5 = new SequenceFeature("type", "desc", 0, 0, 11f,
+ "group");
+ fs.addFeature(sf5);
+ SequenceFeature sf6 = new SequenceFeature("type", "desc", 0, 0, -7f,
+ "group");
+ fs.addFeature(sf6);
+ assertEquals(fs.getMinimumScore(true), 1f);
+ assertEquals(fs.getMaximumScore(true), 4f);
+ assertEquals(fs.getMinimumScore(false), -7f);
+ assertEquals(fs.getMaximumScore(false), 11f);
+
+ // delete one positional and one non-positional
+ // min-max should be recomputed
+ assertTrue(fs.delete(sf6));
+ assertTrue(fs.delete(sf3));
+ assertEquals(fs.getMinimumScore(true), 4f);
+ assertEquals(fs.getMaximumScore(true), 4f);
+ assertEquals(fs.getMinimumScore(false), 11f);
+ assertEquals(fs.getMaximumScore(false), 11f);
+
+ // delete remaining features with score
+ assertTrue(fs.delete(sf4));
+ assertTrue(fs.delete(sf5));
+ assertEquals(fs.getMinimumScore(true), Float.NaN);
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // delete all features
+ assertTrue(fs.delete(sf1));
+ assertTrue(fs.delete(sf2));
+ assertTrue(fs.isEmpty());
+ assertEquals(fs.getMinimumScore(true), Float.NaN);
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+ }
+
+ @Test(groups = "Functional")
+ public void testContains()
+ {
+ assertFalse(FeatureStore.contains(null, null));
+ List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ assertFalse(FeatureStore.contains(features, null));
+
+ SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
+ "group1");
+ assertFalse(FeatureStore.contains(null, sf1));
+ assertFalse(FeatureStore.contains(features, sf1));
+
+ features.add(sf1);
+ SequenceFeature sf2 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
+ "group1");
+ SequenceFeature sf3 = new SequenceFeature("type1", "desc1", 20, 40, 3f,
+ "group1");
+
+ // sf2.equals(sf1) so contains should return true
+ assertTrue(FeatureStore.contains(features, sf2));
+ assertFalse(FeatureStore.contains(features, sf3));
+ }
}
git://source.jalview.org / jalview.git / blobdiff