X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreJSTest.java;fp=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreJSTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=12b6c74fc42cb9d4e350deec29fda8fbad555dd2;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/test/jalview/datamodel/features/FeatureStoreJSTest.java b/test/jalview/datamodel/features/FeatureStoreJSTest.java deleted file mode 100644 index 12b6c74..0000000 --- a/test/jalview/datamodel/features/FeatureStoreJSTest.java +++ /dev/null @@ -1,891 +0,0 @@ -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.List; -import java.util.Set; - -import org.testng.annotations.Test; - -public class FeatureStoreJSTest -{ - - @Test(groups = "Functional") - public void testFindFeatures_nonNested() - { - FeatureStoreI fs = newFeatureStore(); - fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN, - null)); - // same range different description - fs.addFeature(new SequenceFeature("", "desc", 10, 20, Float.NaN, null)); - fs.addFeature(new SequenceFeature("", "", 15, 25, Float.NaN, null)); - fs.addFeature(new SequenceFeature("", "", 20, 35, Float.NaN, null)); - - List overlaps = fs.findOverlappingFeatures(1, 9); - assertTrue(overlaps.isEmpty()); - - overlaps = fs.findOverlappingFeatures(8, 10); - assertEquals(overlaps.size(), 2); - assertEquals(overlaps.get(0).getEnd(), 20); - assertEquals(overlaps.get(1).getEnd(), 20); - - overlaps = fs.findOverlappingFeatures(12, 16); - assertEquals(overlaps.size(), 3); - assertEquals(overlaps.get(0).getEnd(), 20); - assertEquals(overlaps.get(1).getEnd(), 20); - assertEquals(overlaps.get(2).getEnd(), 25); - - overlaps = fs.findOverlappingFeatures(33, 33); - assertEquals(overlaps.size(), 1); - assertEquals(overlaps.get(0).getEnd(), 35); - } - - private FeatureStoreI newFeatureStore() - { - return new FeatureStoreJS(); - // return new FeatureStoreImpl(); - } - - @Test(groups = "Functional") - public void testFindFeatures_nested() - { - FeatureStoreI fs = newFeatureStore(); - SequenceFeature sf1 = addFeature(fs, 10, 50); - SequenceFeature sf2 = addFeature(fs, 10, 40); - SequenceFeature sf3 = addFeature(fs, 20, 30); - // fudge feature at same location but different group (so is added) - SequenceFeature sf4 = new SequenceFeature("", "", 20, 30, Float.NaN, - "different group"); - fs.addFeature(sf4); - SequenceFeature sf5 = addFeature(fs, 35, 36); - - List overlaps = fs.findOverlappingFeatures(1, 9); - assertTrue(overlaps.isEmpty()); - - overlaps = fs.findOverlappingFeatures(10, 15); - assertEquals(overlaps.size(), 2); - assertTrue(overlaps.contains(sf1)); - assertTrue(overlaps.contains(sf2)); - - overlaps = fs.findOverlappingFeatures(45, 60); - assertEquals(overlaps.size(), 1); - assertTrue(overlaps.contains(sf1)); - - overlaps = fs.findOverlappingFeatures(32, 38); - assertEquals(overlaps.size(), 3); - assertTrue(overlaps.contains(sf1)); - assertTrue(overlaps.contains(sf2)); - assertTrue(overlaps.contains(sf5)); - - overlaps = fs.findOverlappingFeatures(15, 25); - assertEquals(overlaps.size(), 4); - assertTrue(overlaps.contains(sf1)); - assertTrue(overlaps.contains(sf2)); - assertTrue(overlaps.contains(sf3)); - assertTrue(overlaps.contains(sf4)); - } - - @Test(groups = "Functional") - public void testFindFeatures_mixed() - { - FeatureStoreI fs = newFeatureStore(); - SequenceFeature sf1 = addFeature(fs, 10, 50); - SequenceFeature sf2 = addFeature(fs, 1, 15); - SequenceFeature sf3 = addFeature(fs, 20, 30); - SequenceFeature sf4 = addFeature(fs, 40, 100); - SequenceFeature sf5 = addFeature(fs, 60, 100); - SequenceFeature sf6 = addFeature(fs, 70, 70); - - List overlaps = fs.findOverlappingFeatures(200, 200); - assertTrue(overlaps.isEmpty()); - - overlaps = fs.findOverlappingFeatures(1, 9); - assertEquals(overlaps.size(), 1); - assertTrue(overlaps.contains(sf2)); - - overlaps = fs.findOverlappingFeatures(5, 18); - assertEquals(overlaps.size(), 2); - assertTrue(overlaps.contains(sf1)); - assertTrue(overlaps.contains(sf2)); - - overlaps = fs.findOverlappingFeatures(30, 40); - assertEquals(overlaps.size(), 3); - assertTrue(overlaps.contains(sf1)); - assertTrue(overlaps.contains(sf3)); - assertTrue(overlaps.contains(sf4)); - - overlaps = fs.findOverlappingFeatures(80, 90); - assertEquals(overlaps.size(), 2); - assertTrue(overlaps.contains(sf4)); - assertTrue(overlaps.contains(sf5)); - - overlaps = fs.findOverlappingFeatures(68, 70); - assertEquals(overlaps.size(), 3); - assertTrue(overlaps.contains(sf4)); - assertTrue(overlaps.contains(sf5)); - assertTrue(overlaps.contains(sf6)); - } - - /** - * Helper method to add a feature of no particular type - * - * @param fs - * @param from - * @param to - * @return - */ - SequenceFeature addFeature(FeatureStoreI fs, int from, int to) - { - SequenceFeature sf1 = new SequenceFeature("", "", from, to, Float.NaN, - null); - fs.addFeature(sf1); - return sf1; - } - - @Test(groups = "Functional") - public void testFindFeatures_contactFeatures() - { - FeatureStoreI fs = newFeatureStore(); - - SequenceFeature sf = new SequenceFeature("disulphide bond", "bond", 10, - 20, Float.NaN, null); - fs.addFeature(sf); - - /* - * neither contact point in range - */ - List overlaps = fs.findOverlappingFeatures(1, 9); - assertTrue(overlaps.isEmpty()); - - /* - * neither contact point in range - */ - overlaps = fs.findOverlappingFeatures(11, 19); - assertTrue(overlaps.isEmpty()); - - /* - * first contact point in range - */ - overlaps = fs.findOverlappingFeatures(5, 15); - assertEquals(overlaps.size(), 1); - assertTrue(overlaps.contains(sf)); - - /* - * second contact point in range - */ - overlaps = fs.findOverlappingFeatures(15, 25); - assertEquals(overlaps.size(), 1); - assertTrue(overlaps.contains(sf)); - - /* - * both contact points in range - */ - overlaps = fs.findOverlappingFeatures(5, 25); - assertEquals(overlaps.size(), 1); - assertTrue(overlaps.contains(sf)); - } - - @Test(groups = "Functional") - public void testGetPositionalFeatures() - { - FeatureStoreI store = newFeatureStore(); - SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20, - Float.NaN, null); - store.addFeature(sf1); - // same range, different description - SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20, - Float.NaN, null); - store.addFeature(sf2); - // discontiguous range - SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 30, 40, - Float.NaN, null); - store.addFeature(sf3); - // overlapping range - SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 15, 35, - Float.NaN, null); - store.addFeature(sf4); - // enclosing range - SequenceFeature sf5 = new SequenceFeature("Metal", "desc", 5, 50, - Float.NaN, null); - store.addFeature(sf5); - // non-positional feature - SequenceFeature sf6 = new SequenceFeature("Metal", "desc", 0, 0, - Float.NaN, null); - store.addFeature(sf6); - // contact feature - SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", - 18, 45, Float.NaN, null); - store.addFeature(sf7); - - List 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)); - assertFalse(features.contains(sf6)); - assertTrue(features.contains(sf7)); - - features = store.getNonPositionalFeatures(); - assertEquals(features.size(), 1); - assertTrue(features.contains(sf6)); - } - - @Test(groups = "Functional") - public void testDelete() - { - FeatureStoreI store = newFeatureStore(); - SequenceFeature sf1 = addFeature(store, 10, 20); - assertTrue(store.getPositionalFeatures().contains(sf1)); - - /* - * simple deletion - */ - assertTrue(store.delete(sf1)); - assertTrue(store.getPositionalFeatures().isEmpty()); - - /* - * non-positional feature deletion - */ - SequenceFeature sf2 = addFeature(store, 0, 0); - assertFalse(store.getPositionalFeatures().contains(sf2)); - assertTrue(store.getNonPositionalFeatures().contains(sf2)); - assertTrue(store.delete(sf2)); - assertTrue(store.getNonPositionalFeatures().isEmpty()); - - /* - * contact feature deletion - */ - SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11, - 23, Float.NaN, null); - store.addFeature(sf3); - assertEquals(store.getPositionalFeatures().size(), 1); - assertTrue(store.getPositionalFeatures().contains(sf3)); - assertTrue(store.delete(sf3)); - assertTrue(store.getPositionalFeatures().isEmpty()); - - /* - * nested feature deletion - */ - SequenceFeature sf4 = addFeature(store, 20, 30); - SequenceFeature sf5 = addFeature(store, 22, 26); // to NCList - SequenceFeature sf6 = addFeature(store, 23, 24); // child of sf5 - 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.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.getPositionalFeatures().size(), 5); - assertFalse(store.getPositionalFeatures().contains(sf6)); - - // delete a node with no children - assertTrue(store.delete(sf7)); - assertEquals(store.getPositionalFeatures().size(), 4); - assertFalse(store.getPositionalFeatures().contains(sf7)); - - // delete root of NCList - assertTrue(store.delete(sf5)); - assertEquals(store.getPositionalFeatures().size(), 3); - assertFalse(store.getPositionalFeatures().contains(sf5)); - - // continue the killing fields - assertTrue(store.delete(sf4)); - assertEquals(store.getPositionalFeatures().size(), 2); - assertFalse(store.getPositionalFeatures().contains(sf4)); - - assertTrue(store.delete(sf9)); - assertEquals(store.getPositionalFeatures().size(), 1); - assertFalse(store.getPositionalFeatures().contains(sf9)); - - assertTrue(store.delete(sf8)); - assertTrue(store.getPositionalFeatures().isEmpty()); - } - - @Test(groups = "Functional") - public void testAddFeature() - { - FeatureStoreI fs = newFeatureStore(); - - SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, - Float.NaN, null); - SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, - 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", "", 10, 20, - 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", "", 10, 20, - 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") - public void testIsEmpty() - { - FeatureStoreI fs = newFeatureStore(); - assertTrue(fs.isEmpty()); - assertEquals(fs.getFeatureCount(true), 0); - - /* - * non-nested feature - */ - SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, - 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 - */ - sf1 = new SequenceFeature("Cath", "", 19, 49, Float.NaN, null); - SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40, - Float.NaN, null); - SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35, - Float.NaN, null); - fs.addFeature(sf1); - fs.addFeature(sf2); - fs.addFeature(sf3); - assertEquals(fs.getFeatureCount(true), 3); - assertTrue(fs.delete(sf1)); - assertEquals(fs.getFeatureCount(true), 2); - assertEquals(fs.getFeatures().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() - { - FeatureStoreI fs = newFeatureStore(); - assertTrue(fs.getFeatureGroups(true).isEmpty()); - assertTrue(fs.getFeatureGroups(false).isEmpty()); - - SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1"); - fs.addFeature(sf1); - Set 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() - { - FeatureStoreI fs = newFeatureStore(); - 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() - { - FeatureStoreI fs = newFeatureStore(); - 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 testListContains() - { - FeatureStoreI featureStore = newFeatureStore(); - assertFalse(featureStore.listContains(null, null)); - List features = new ArrayList<>(); - assertFalse(featureStore.listContains(features, null)); - - SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f, - "group1"); - assertFalse(featureStore.listContains(null, sf1)); - assertFalse(featureStore.listContains(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.listContains(features, sf2)); - assertFalse(featureStore.listContains(features, sf3)); - } - - @Test(groups = "Functional") - public void testGetFeaturesForGroup() - { - FeatureStoreI fs = newFeatureStore(); - - /* - * with no features - */ - assertTrue(fs.getFeaturesForGroup(true, null).isEmpty()); - assertTrue(fs.getFeaturesForGroup(false, null).isEmpty()); - assertTrue(fs.getFeaturesForGroup(true, "uniprot").isEmpty()); - assertTrue(fs.getFeaturesForGroup(false, "uniprot").isEmpty()); - - /* - * sf1: positional feature in the null group - */ - SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f, - null); - fs.addFeature(sf1); - assertTrue(fs.getFeaturesForGroup(true, "uniprot").isEmpty()); - assertTrue(fs.getFeaturesForGroup(false, "uniprot").isEmpty()); - assertTrue(fs.getFeaturesForGroup(false, null).isEmpty()); - List features = fs.getFeaturesForGroup(true, null); - assertEquals(features.size(), 1); - assertTrue(features.contains(sf1)); - - /* - * sf2: non-positional feature in the null group - * sf3: positional feature in a non-null group - * sf4: non-positional feature in a non-null group - */ - SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f, - null); - SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f, - "Uniprot"); - SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 0, 0, 0f, - "Rfam"); - fs.addFeature(sf2); - fs.addFeature(sf3); - fs.addFeature(sf4); - - features = fs.getFeaturesForGroup(true, null); - assertEquals(features.size(), 1); - assertTrue(features.contains(sf1)); - - features = fs.getFeaturesForGroup(false, null); - assertEquals(features.size(), 1); - assertTrue(features.contains(sf2)); - - features = fs.getFeaturesForGroup(true, "Uniprot"); - assertEquals(features.size(), 1); - assertTrue(features.contains(sf3)); - - features = fs.getFeaturesForGroup(false, "Rfam"); - assertEquals(features.size(), 1); - assertTrue(features.contains(sf4)); - } - - @Test(groups = "Functional") - public void testShiftFeatures() - { - FeatureStoreI fs = newFeatureStore(); - assertFalse(fs.shiftFeatures(0, 1)); // nothing to do - - SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null); - fs.addFeature(sf1); - // nested feature: - SequenceFeature sf2 = new SequenceFeature("Cath", "", 8, 14, 0f, null); - fs.addFeature(sf2); - // contact feature: - SequenceFeature sf3 = new SequenceFeature("Disulfide bond", "", 23, 32, - 0f, null); - fs.addFeature(sf3); - // non-positional feature: - SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f, null); - fs.addFeature(sf4); - - /* - * shift all features right by 5 - */ - assertTrue(fs.shiftFeatures(0, 5)); - - // non-positional features untouched: - List nonPos = fs.getNonPositionalFeatures(); - assertEquals(nonPos.size(), 1); - assertTrue(nonPos.contains(sf4)); - - // positional features are replaced - List pos = fs.getPositionalFeatures(); - assertEquals(pos.size(), 3); - assertFalse(pos.contains(sf1)); - assertFalse(pos.contains(sf2)); - assertFalse(pos.contains(sf3)); - SequenceFeatures.sortFeatures(pos, true); // ascending start pos - assertEquals(pos.get(0).getBegin(), 7); - assertEquals(pos.get(0).getEnd(), 10); - assertEquals(pos.get(1).getBegin(), 13); - assertEquals(pos.get(1).getEnd(), 19); - assertEquals(pos.get(2).getBegin(), 28); - assertEquals(pos.get(2).getEnd(), 37); - - /* - * now shift left by 15 - * feature at [7-10] should be removed - * feature at [13-19] should become [1-4] - */ - assertTrue(fs.shiftFeatures(0, -15)); - pos = fs.getPositionalFeatures(); - assertEquals(pos.size(), 2); - SequenceFeatures.sortFeatures(pos, true); - assertEquals(pos.get(0).getBegin(), 1); - assertEquals(pos.get(0).getEnd(), 4); - assertEquals(pos.get(1).getBegin(), 13); - assertEquals(pos.get(1).getEnd(), 22); - - /* - * shift right by 4 from position 2 onwards - * feature at [1-4] unchanged, feature at [13-22] shifts - */ - assertTrue(fs.shiftFeatures(2, 4)); - pos = fs.getPositionalFeatures(); - assertEquals(pos.size(), 2); - SequenceFeatures.sortFeatures(pos, true); - assertEquals(pos.get(0).getBegin(), 1); - assertEquals(pos.get(0).getEnd(), 4); - assertEquals(pos.get(1).getBegin(), 17); - assertEquals(pos.get(1).getEnd(), 26); - - /* - * shift right by 4 from position 18 onwards - * should be no change - */ - SequenceFeature f1 = pos.get(0); - SequenceFeature f2 = pos.get(1); - assertFalse(fs.shiftFeatures(18, 4)); // no update - pos = fs.getPositionalFeatures(); - assertEquals(pos.size(), 2); - SequenceFeatures.sortFeatures(pos, true); - assertSame(pos.get(0), f1); - assertSame(pos.get(1), f2); - } - - @Test(groups = "Functional") - public void testDelete_readd() - { - /* - * add a feature and a nested feature - */ - FeatureStoreI store = newFeatureStore(); - SequenceFeature sf1 = addFeature(store, 10, 20); - // sf2 is nested in sf1 so will be stored in nestedFeatures - SequenceFeature sf2 = addFeature(store, 12, 14); - List features = store.getPositionalFeatures(); - assertEquals(features.size(), 2); - assertTrue(features.contains(sf1)); - assertTrue(features.contains(sf2)); - assertTrue(store.getFeatures().contains(sf1)); - assertTrue(store.getFeatures().contains(sf2)); - - /* - * delete the first feature - */ - assertTrue(store.delete(sf1)); - features = store.getPositionalFeatures(); - assertFalse(features.contains(sf1)); - assertTrue(features.contains(sf2)); - - /* - * re-add the 'nested' feature; is it now duplicated? - */ - store.addFeature(sf2); - features = store.getPositionalFeatures(); - assertEquals(features.size(), 1); - assertTrue(features.contains(sf2)); - } - - @Test(groups = "Functional") - public void testContains() - { - FeatureStoreI fs = newFeatureStore(); - SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, - Float.NaN, "group1"); - SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, - Float.NaN, "group2"); - SequenceFeature sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN, - "group1"); - SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f, - "group1"); - SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "", 5, 15, - Float.NaN, "group1"); - SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "", 5, 15, - Float.NaN, "group2"); - - fs.addFeature(sf1); - fs.addFeature(sf3); - fs.addFeature(sf5); - assertTrue(fs.contains(sf1)); // positional feature - assertTrue(fs.contains(new SequenceFeature(sf1))); // identical feature - assertFalse(fs.contains(sf2)); // different group - assertTrue(fs.contains(sf3)); // non-positional - assertTrue(fs.contains(new SequenceFeature(sf3))); - assertFalse(fs.contains(sf4)); // different score - assertTrue(fs.contains(sf5)); // contact feature - assertTrue(fs.contains(new SequenceFeature(sf5))); - assertFalse(fs.contains(sf6)); // different group - - /* - * add a nested feature - */ - SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16, - Float.NaN, "group1"); - fs.addFeature(sf7); - assertTrue(fs.contains(sf7)); - assertTrue(fs.contains(new SequenceFeature(sf7))); - - /* - * delete the outer (enclosing, non-nested) feature - */ - fs.delete(sf1); - assertFalse(fs.contains(sf1)); - assertTrue(fs.contains(sf7)); - } -}