X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreTest.java;h=db0fabf6567bd4eb3626ed9f8bc27b66a0428e65;hb=0058ae87ea065cb53e5f4b8c19a188fad88ff6ad;hp=e4bf122d00d0f470789186ca5b8fffeda915c682;hpb=6a2fd9a13d79f316acdd4fcff066b8cfaaefa939;p=jalview.git diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java index e4bf122..db0fabf 100644 --- a/test/jalview/datamodel/features/FeatureStoreTest.java +++ b/test/jalview/datamodel/features/FeatureStoreTest.java @@ -2,22 +2,32 @@ 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 static org.testng.Assert.fail; import jalview.datamodel.SequenceFeature; +import java.util.ArrayList; +import java.util.Collection; import java.util.List; import java.util.Set; import org.testng.annotations.Test; +import junit.extensions.PA; + public class FeatureStoreTest { + private FeatureStore newFeatureStore() + { + return new FeatureStore(); + } @Test(groups = "Functional") public void testFindFeatures_nonNested() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN, null)); // same range different description @@ -25,21 +35,21 @@ public class FeatureStoreTest fs.addFeature(new SequenceFeature("", "", 15, 25, Float.NaN, null)); fs.addFeature(new SequenceFeature("", "", 20, 35, Float.NaN, null)); - List overlaps = fs.findOverlappingFeatures(1, 9); + List overlaps = fs.findFeatures(1, 9); assertTrue(overlaps.isEmpty()); - overlaps = fs.findOverlappingFeatures(8, 10); + overlaps = fs.findFeatures(8, 10); assertEquals(overlaps.size(), 2); assertEquals(overlaps.get(0).getEnd(), 20); assertEquals(overlaps.get(1).getEnd(), 20); - overlaps = fs.findOverlappingFeatures(12, 16); + overlaps = fs.findFeatures(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); + overlaps = fs.findFeatures(33, 33); assertEquals(overlaps.size(), 1); assertEquals(overlaps.get(0).getEnd(), 35); } @@ -47,7 +57,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testFindFeatures_nested() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); SequenceFeature sf1 = addFeature(fs, 10, 50); SequenceFeature sf2 = addFeature(fs, 10, 40); SequenceFeature sf3 = addFeature(fs, 20, 30); @@ -57,25 +67,25 @@ public class FeatureStoreTest fs.addFeature(sf4); SequenceFeature sf5 = addFeature(fs, 35, 36); - List overlaps = fs.findOverlappingFeatures(1, 9); + List overlaps = fs.findFeatures(1, 9); assertTrue(overlaps.isEmpty()); - overlaps = fs.findOverlappingFeatures(10, 15); + overlaps = fs.findFeatures(10, 15); assertEquals(overlaps.size(), 2); assertTrue(overlaps.contains(sf1)); assertTrue(overlaps.contains(sf2)); - overlaps = fs.findOverlappingFeatures(45, 60); + overlaps = fs.findFeatures(45, 60); assertEquals(overlaps.size(), 1); assertTrue(overlaps.contains(sf1)); - overlaps = fs.findOverlappingFeatures(32, 38); + overlaps = fs.findFeatures(32, 38); assertEquals(overlaps.size(), 3); assertTrue(overlaps.contains(sf1)); assertTrue(overlaps.contains(sf2)); assertTrue(overlaps.contains(sf5)); - overlaps = fs.findOverlappingFeatures(15, 25); + overlaps = fs.findFeatures(15, 25); assertEquals(overlaps.size(), 4); assertTrue(overlaps.contains(sf1)); assertTrue(overlaps.contains(sf2)); @@ -86,7 +96,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testFindFeatures_mixed() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); SequenceFeature sf1 = addFeature(fs, 10, 50); SequenceFeature sf2 = addFeature(fs, 1, 15); SequenceFeature sf3 = addFeature(fs, 20, 30); @@ -94,30 +104,30 @@ public class FeatureStoreTest SequenceFeature sf5 = addFeature(fs, 60, 100); SequenceFeature sf6 = addFeature(fs, 70, 70); - List overlaps = fs.findOverlappingFeatures(200, 200); + List overlaps = fs.findFeatures(200, 200); assertTrue(overlaps.isEmpty()); - overlaps = fs.findOverlappingFeatures(1, 9); + overlaps = fs.findFeatures(1, 9); assertEquals(overlaps.size(), 1); assertTrue(overlaps.contains(sf2)); - overlaps = fs.findOverlappingFeatures(5, 18); + overlaps = fs.findFeatures(5, 18); assertEquals(overlaps.size(), 2); assertTrue(overlaps.contains(sf1)); assertTrue(overlaps.contains(sf2)); - overlaps = fs.findOverlappingFeatures(30, 40); + overlaps = fs.findFeatures(30, 40); assertEquals(overlaps.size(), 3); assertTrue(overlaps.contains(sf1)); assertTrue(overlaps.contains(sf3)); assertTrue(overlaps.contains(sf4)); - overlaps = fs.findOverlappingFeatures(80, 90); + overlaps = fs.findFeatures(80, 90); assertEquals(overlaps.size(), 2); assertTrue(overlaps.contains(sf4)); assertTrue(overlaps.contains(sf5)); - overlaps = fs.findOverlappingFeatures(68, 70); + overlaps = fs.findFeatures(68, 70); assertEquals(overlaps.size(), 3); assertTrue(overlaps.contains(sf4)); assertTrue(overlaps.contains(sf5)); @@ -143,7 +153,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testFindFeatures_contactFeatures() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); SequenceFeature sf = new SequenceFeature("disulphide bond", "bond", 10, 20, Float.NaN, null); @@ -152,93 +162,135 @@ public class FeatureStoreTest /* * neither contact point in range */ - List overlaps = fs.findOverlappingFeatures(1, 9); + List overlaps = fs.findFeatures(1, 9); assertTrue(overlaps.isEmpty()); /* * neither contact point in range */ - overlaps = fs.findOverlappingFeatures(11, 19); + overlaps = fs.findFeatures(11, 19); assertTrue(overlaps.isEmpty()); /* * first contact point in range */ - overlaps = fs.findOverlappingFeatures(5, 15); + overlaps = fs.findFeatures(5, 15); assertEquals(overlaps.size(), 1); assertTrue(overlaps.contains(sf)); /* * second contact point in range */ - overlaps = fs.findOverlappingFeatures(15, 25); + overlaps = fs.findFeatures(15, 25); assertEquals(overlaps.size(), 1); assertTrue(overlaps.contains(sf)); /* * both contact points in range */ - overlaps = fs.findOverlappingFeatures(5, 25); + overlaps = fs.findFeatures(5, 25); assertEquals(overlaps.size(), 1); assertTrue(overlaps.contains(sf)); } - /** - * Tests for the method that returns false for an attempt to add a feature - * that would enclose, or be enclosed by, another feature - */ @Test(groups = "Functional") - public void testAddNonNestedFeature() + public void testGetPositionalFeatures_withResultList() { - FeatureStore fs = new FeatureStore(); - - String type = "Domain"; - SequenceFeature sf1 = new SequenceFeature(type, type, 10, 20, + FeatureStore store = newFeatureStore(); + SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20, Float.NaN, null); - assertTrue(fs.addNonNestedFeature(sf1)); + store.addFeature(sf1); + // contact feature + SequenceFeature sf2 = new SequenceFeature("Disulphide bond", "desc", 18, + 45, Float.NaN, null); + store.addFeature(sf2); - // co-located feature is ok - SequenceFeature sf2 = new SequenceFeature(type, type, 10, 20, - Float.NaN, null); - assertTrue(fs.addNonNestedFeature(sf2)); + List features = new ArrayList<>(); + store.getPositionalFeatures(features); + assertEquals(features.size(), 2); + assertTrue(features.contains(sf1)); + assertTrue(features.contains(sf2)); - // overlap left is ok - SequenceFeature sf3 = new SequenceFeature(type, type, 5, 15, Float.NaN, - null); - assertTrue(fs.addNonNestedFeature(sf3)); + /* + * no check for duplicates + */ + features.remove(sf1); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf2)); + store.getPositionalFeatures(features); + assertEquals(features.size(), 3); + assertTrue(features.contains(sf1)); + assertTrue(features.contains(sf2)); // two copies now + features.remove(sf2); + assertTrue(features.contains(sf2)); // one copy left + assertEquals(features.size(), 2); - // overlap right is ok - SequenceFeature sf4 = new SequenceFeature(type, type, 15, 25, - Float.NaN, null); - assertTrue(fs.addNonNestedFeature(sf4)); + /* + * null argument throws exception + */ + try + { + store.getPositionalFeatures(null); + fail("expected exception"); + } catch (NullPointerException e) + { + // expected + } + } - // add enclosing feature is not ok - SequenceFeature sf5 = new SequenceFeature(type, type, 10, 21, - Float.NaN, null); - assertFalse(fs.addNonNestedFeature(sf5)); - SequenceFeature sf6 = new SequenceFeature(type, type, 4, 15, Float.NaN, - null); - assertFalse(fs.addNonNestedFeature(sf6)); - SequenceFeature sf7 = new SequenceFeature(type, type, 1, 50, Float.NaN, - null); - assertFalse(fs.addNonNestedFeature(sf7)); + @Test(groups = "Functional") + public void testGetNonPositionalFeatures() + { + FeatureStore store = newFeatureStore(); + List features = store.getNonPositionalFeatures(); + assertTrue(features.isEmpty()); - // add enclosed feature is not ok - SequenceFeature sf8 = new SequenceFeature(type, type, 10, 19, + SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20, Float.NaN, null); - assertFalse(fs.addNonNestedFeature(sf8)); - SequenceFeature sf9 = new SequenceFeature(type, type, 16, 25, + store.addFeature(sf1); + assertTrue(features.isEmpty()); + + SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0, Float.NaN, null); - assertFalse(fs.addNonNestedFeature(sf9)); - SequenceFeature sf10 = new SequenceFeature(type, type, 7, 7, Float.NaN, - null); - assertFalse(fs.addNonNestedFeature(sf10)); + store.addFeature(sf2); + features = store.getNonPositionalFeatures(); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf2)); + + /* + * with result list argument + */ + features.clear(); + store.getNonPositionalFeatures(features); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf2)); + + /* + * no check for duplicates + */ + store.getNonPositionalFeatures(features); + assertEquals(features.size(), 2); + assertTrue(features.contains(sf2)); // two copies + features.remove(sf2); + assertTrue(features.contains(sf2)); + + /* + * null argument throws exception + */ + try + { + store.getNonPositionalFeatures(null); + fail("expected exception"); + } catch (NullPointerException e) + { + // expected + } } @Test(groups = "Functional") public void testGetPositionalFeatures() { - FeatureStore store = new FeatureStore(); + FeatureStore store = newFeatureStore(); SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20, Float.NaN, null); store.addFeature(sf1); @@ -285,7 +337,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testDelete() { - FeatureStore store = new FeatureStore(); + FeatureStore store = newFeatureStore(); SequenceFeature sf1 = addFeature(store, 10, 20); assertTrue(store.getPositionalFeatures().contains(sf1)); @@ -357,7 +409,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testAddFeature() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN, null); @@ -393,12 +445,12 @@ public class FeatureStoreTest /* * add contact */ - SequenceFeature sf5 = new SequenceFeature("Disulfide bond", "", 0, 0, + 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", "", 0, 0, + SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "", 10, 20, Float.NaN, null); assertFalse(fs.addFeature(sf6)); // already stored assertEquals(fs.getFeatureCount(true), 2); // no change @@ -408,7 +460,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testIsEmpty() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); assertTrue(fs.isEmpty()); assertEquals(fs.getFeatureCount(true), 0); @@ -461,9 +513,9 @@ public class FeatureStoreTest assertEquals(fs.getFeatureCount(true), 3); assertTrue(fs.delete(sf1)); assertEquals(fs.getFeatureCount(true), 2); - // FeatureStore should now only contain features in the NCList - assertTrue(fs.nonNestedFeatures.isEmpty()); - assertEquals(fs.nestedFeatures.size(), 2); + Collection intervalStore = (Collection) PA + .getValue(fs, "features"); + assertEquals(intervalStore.size(), 2); assertFalse(fs.isEmpty()); assertTrue(fs.delete(sf2)); assertEquals(fs.getFeatureCount(true), 1); @@ -476,8 +528,9 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testGetFeatureGroups() { - FeatureStore fs = new FeatureStore(); + FeatureStore 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); @@ -512,6 +565,7 @@ public class FeatureStoreTest 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); @@ -524,30 +578,438 @@ public class FeatureStoreTest 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(); + FeatureStore fs = newFeatureStore(); assertEquals(fs.getTotalFeatureLength(), 0); addFeature(fs, 10, 20); // 11 assertEquals(fs.getTotalFeatureLength(), 11); addFeature(fs, 17, 37); // 21 - addFeature(fs, 14, 74); // 61 + SequenceFeature sf1 = addFeature(fs, 14, 74); // 61 assertEquals(fs.getTotalFeatureLength(), 93); // non-positional features don't count - SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 0, 0, 1f, + SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 0, 0, 1f, "group1"); - fs.addFeature(sf1); + fs.addFeature(sf2); assertEquals(fs.getTotalFeatureLength(), 93); // contact features count 1 - SequenceFeature sf2 = new SequenceFeature("disulphide bond", "desc", + SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc", 15, 35, 1f, "group1"); - fs.addFeature(sf2); + 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 = 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() + { + FeatureStore 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() + { + FeatureStore 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() + { + FeatureStore 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 + */ + FeatureStore 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)); + Collection intervalStore = (Collection) PA + .getValue(store, "features"); + assertTrue(intervalStore.contains(sf1)); + assertTrue(intervalStore.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() + { + FeatureStore 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)); + } + + @Test(groups = "Functional") + public void testFindFeatures_withResultList() + { + FeatureStore fs = newFeatureStore(); + SequenceFeature sf1 = addFeature(fs, 10, 50); + SequenceFeature sf2 = addFeature(fs, 150, 250); + + List overlaps = new ArrayList<>(); + List result = fs.findFeatures(200, 200, + overlaps); + assertSame(result, overlaps); + assertEquals(result.size(), 1); + assertTrue(result.contains(sf2)); + assertFalse(result.contains(sf1)); + + /* + * if no list supplied, method creates one + */ + result = fs.findFeatures(200, 200, null); + assertEquals(result.size(), 1); + assertTrue(result.contains(sf2)); + assertFalse(result.contains(sf1)); } }