import jalview.datamodel.SequenceFeature;
import java.util.List;
+import java.util.Set;
import org.testng.annotations.Test;
public class SequenceFeaturesTest
{
@Test(groups = "Functional")
- public void testGetFeatures()
+ public void testGetPositionalFeatures()
{
SequenceFeatures store = new SequenceFeatures();
SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
Float.NaN, null);
store.add(sf1);
- // same range
- SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 10, 20,
+ // same range, different description
+ SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20,
Float.NaN, null);
store.add(sf2);
// discontiguous range
store.add(sf9);
/*
- * get all features
+ * get all positional features
*/
- List<SequenceFeature> features = store.getFeatures();
- assertEquals(features.size(), 9);
+ List<SequenceFeature> features = store.getPositionalFeatures();
+ assertEquals(features.size(), 8);
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)); // non-positional
assertTrue(features.contains(sf7));
assertTrue(features.contains(sf8));
assertTrue(features.contains(sf9));
/*
* get features by type
*/
- assertTrue(store.getFeatures(null).isEmpty());
- assertTrue(store.getFeatures("Cath").isEmpty());
- assertTrue(store.getFeatures("METAL").isEmpty());
+ assertTrue(store.getPositionalFeatures((String) null).isEmpty());
+ assertTrue(store.getPositionalFeatures("Cath").isEmpty());
+ assertTrue(store.getPositionalFeatures("METAL").isEmpty());
- features = store.getFeatures("Metal");
- assertEquals(features.size(), 6);
+ features = store.getPositionalFeatures("Metal");
+ assertEquals(features.size(), 5);
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));
- features = store.getFeatures("Disulphide bond");
+ features = store.getPositionalFeatures("Disulphide bond");
assertEquals(features.size(), 1);
assertTrue(features.contains(sf7));
- features = store.getFeatures("Pfam");
+ features = store.getPositionalFeatures("Pfam");
assertEquals(features.size(), 2);
assertTrue(features.contains(sf8));
assertTrue(features.contains(sf9));
/*
* 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());
SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
45, Float.NaN, null);
store.add(sf6);
- // on more non-positional
- SequenceFeature sf7 = new SequenceFeature("Pfam", "desc", 0, 0,
+ // one more non-positional, different description
+ SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0,
Float.NaN, null);
store.add(sf7);
/*
* 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());
// 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();
+ SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
+ assertTrue(sf.getPositionalFeatures().contains(sf1));
+
+ assertFalse(sf.delete(null));
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 15, 0f, null);
+ assertFalse(sf.delete(sf2)); // not added, can't delete it
+ assertTrue(sf.delete(sf1));
+ assertTrue(sf.getPositionalFeatures().isEmpty());
+ }
+
+ @Test(groups = "Functional")
+ public void testHasFeatures()
+ {
+ SequenceFeatures sf = new SequenceFeatures();
+ assertFalse(sf.hasFeatures());
+
+ SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
+ assertTrue(sf.hasFeatures());
+
+ sf.delete(sf1);
+ assertFalse(sf.hasFeatures());
+ }
+
+ /**
+ * Tests for the method that gets feature groups for positional or
+ * non-positional features
+ */
+ @Test(groups = "Functional")
+ public void testGetFeatureGroups()
+ {
+ SequenceFeatures sf = new SequenceFeatures();
+ assertTrue(sf.getFeatureGroups(true).isEmpty());
+ assertTrue(sf.getFeatureGroups(false).isEmpty());
+
+ /*
+ * add a non-positional feature (begin/end = 0/0)
+ */
+ SequenceFeature sfx = new SequenceFeature("AType", "Desc", 0, 0, 0f,
+ "AGroup");
+ sf.add(sfx);
+ Set<String> groups = sf.getFeatureGroups(true); // for positional
+ assertTrue(groups.isEmpty());
+ groups = sf.getFeatureGroups(false); // for non-positional
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("AGroup"));
+
+ /*
+ * add, then delete, more non-positional features of different types
+ */
+ SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0,
+ 0f,
+ "AnotherGroup");
+ sf.add(sfy);
+ SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0,
+ 0f,
+ null);
+ sf.add(sfz);
+ groups = sf.getFeatureGroups(false);
+ assertEquals(groups.size(), 3);
+ assertTrue(groups.contains("AGroup"));
+ assertTrue(groups.contains("AnotherGroup"));
+ assertTrue(groups.contains(null)); // null is a possible group
+ sf.delete(sfz);
+ sf.delete(sfy);
+ groups = sf.getFeatureGroups(false);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("AGroup"));
+
+ /*
+ * add positional features
+ */
+ SequenceFeature sf1 = new SequenceFeature("Pfam", "Desc", 10, 50, 0f,
+ "PfamGroup");
+ sf.add(sf1);
+ groups = sf.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("PfamGroup"));
+ groups = sf.getFeatureGroups(false); // non-positional unchanged
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("AGroup"));
+
+ SequenceFeature sf2 = new SequenceFeature("Cath", "Desc", 10, 50, 0f,
+ null);
+ sf.add(sf2);
+ groups = sf.getFeatureGroups(true);
+ assertEquals(groups.size(), 2);
+ assertTrue(groups.contains("PfamGroup"));
+ assertTrue(groups.contains(null));
+
+ sf.delete(sf1);
+ sf.delete(sf2);
+ assertTrue(sf.getFeatureGroups(true).isEmpty());
+
+ SequenceFeature sf3 = new SequenceFeature("CDS", "", 10, 50, 0f,
+ "Ensembl");
+ sf.add(sf3);
+ SequenceFeature sf4 = new SequenceFeature("exon", "", 10, 50, 0f,
+ "Ensembl");
+ sf.add(sf4);
+ groups = sf.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("Ensembl"));
+
+ /*
+ * delete last Ensembl group feature from CDS features
+ * but still have one in exon features
+ */
+ sf.delete(sf3);
+ groups = sf.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("Ensembl"));
+
+ /*
+ * delete the last non-positional feature
+ */
+ sf.delete(sfx);
+ groups = sf.getFeatureGroups(false);
+ assertTrue(groups.isEmpty());
+ }
+
+ @Test(groups = "Functional")
+ public void testGetFeatureTypesForGroups()
+ {
+ SequenceFeatures sf = new SequenceFeatures();
+ assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
+
+ /*
+ * add feature with group = "Uniprot", type = "helix"
+ */
+ String groupUniprot = "Uniprot";
+ SequenceFeature sf1 = new SequenceFeature("helix", "Desc", 10, 50, 0f,
+ groupUniprot);
+ sf.add(sf1);
+ Set<String> groups = sf.getFeatureTypesForGroups(true, groupUniprot);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("helix"));
+ assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
+
+ /*
+ * add feature with group = "Uniprot", type = "strand"
+ */
+ SequenceFeature sf2 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
+ groupUniprot);
+ sf.add(sf2);
+ groups = sf.getFeatureTypesForGroups(true, groupUniprot);
+ assertEquals(groups.size(), 2);
+ assertTrue(groups.contains("helix"));
+ assertTrue(groups.contains("strand"));
+
+ /*
+ * delete the "strand" Uniprot feature - still have "helix"
+ */
+ sf.delete(sf2);
+ groups = sf.getFeatureTypesForGroups(true, groupUniprot);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("helix"));
+
+ /*
+ * delete the "helix" Uniprot feature - none left
+ */
+ sf.delete(sf1);
+ assertTrue(sf.getFeatureTypesForGroups(true, groupUniprot).isEmpty());
+
+ /*
+ * add some null group features
+ */
+ SequenceFeature sf3 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
+ null);
+ sf.add(sf3);
+ SequenceFeature sf4 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
+ null);
+ sf.add(sf4);
+ groups = sf.getFeatureTypesForGroups(true, (String) null);
+ assertEquals(groups.size(), 2);
+ assertTrue(groups.contains("strand"));
+ assertTrue(groups.contains("turn"));
+
+ /*
+ * add strand/Cath and turn/Scop and query for one or both groups
+ * (find feature types for groups selected in Feature Settings)
+ */
+ SequenceFeature sf5 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
+ "Cath");
+ sf.add(sf5);
+ SequenceFeature sf6 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
+ "Scop");
+ sf.add(sf6);
+ groups = sf.getFeatureTypesForGroups(true, "Cath");
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("strand"));
+ groups = sf.getFeatureTypesForGroups(true, "Scop");
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("turn"));
+ groups = sf.getFeatureTypesForGroups(true, "Cath", "Scop");
+ assertEquals(groups.size(), 2);
+ assertTrue(groups.contains("turn"));
+ assertTrue(groups.contains("strand"));
+ // alternative vararg syntax
+ groups = sf.getFeatureTypesForGroups(true, new String[] { "Cath",
+ "Scop" });
+ assertEquals(groups.size(), 2);
+ assertTrue(groups.contains("turn"));
+ assertTrue(groups.contains("strand"));
+ }
}
git://source.jalview.org / jalview.git / blobdiff