X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreTest.java;h=db0fabf6567bd4eb3626ed9f8bc27b66a0428e65;hb=0058ae87ea065cb53e5f4b8c19a188fad88ff6ad;hp=f5be81868a66227f809a1a3baec8cf6e7a738781;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java index f5be818..db0fabf 100644 --- a/test/jalview/datamodel/features/FeatureStoreTest.java +++ b/test/jalview/datamodel/features/FeatureStoreTest.java @@ -2,23 +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 @@ -26,21 +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); } @@ -48,7 +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); @@ -58,25 +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)); @@ -87,7 +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); @@ -95,30 +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)); @@ -144,7 +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); @@ -153,93 +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); @@ -286,7 +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)); @@ -358,7 +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); @@ -394,12 +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 @@ -409,7 +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); @@ -462,9 +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); @@ -477,7 +528,7 @@ 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()); @@ -544,7 +595,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testGetTotalFeatureLength() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); assertEquals(fs.getTotalFeatureLength(), 0); addFeature(fs, 10, 20); // 11 @@ -620,7 +671,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testGetMinimumScore_getMaximumScore() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); assertEquals(fs.getMinimumScore(true), Float.NaN); // positional assertEquals(fs.getMaximumScore(true), Float.NaN); assertEquals(fs.getMinimumScore(false), Float.NaN); // non-positional @@ -690,16 +741,17 @@ public class FeatureStoreTest } @Test(groups = "Functional") - public void testContains() + public void testListContains() { - assertFalse(FeatureStore.contains(null, null)); - List features = new ArrayList(); - assertFalse(FeatureStore.contains(features, null)); + 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.contains(null, sf1)); - assertFalse(FeatureStore.contains(features, sf1)); + assertFalse(featureStore.listContains(null, sf1)); + assertFalse(featureStore.listContains(features, sf1)); features.add(sf1); SequenceFeature sf2 = new SequenceFeature("type1", "desc1", 20, 30, 3f, @@ -708,14 +760,14 @@ public class FeatureStoreTest "group1"); // sf2.equals(sf1) so contains should return true - assertTrue(FeatureStore.contains(features, sf2)); - assertFalse(FeatureStore.contains(features, sf3)); + assertTrue(featureStore.listContains(features, sf2)); + assertFalse(featureStore.listContains(features, sf3)); } @Test(groups = "Functional") public void testGetFeaturesForGroup() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); /* * with no features @@ -773,8 +825,8 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testShiftFeatures() { - FeatureStore fs = new FeatureStore(); - assertFalse(fs.shiftFeatures(1)); + FeatureStore fs = newFeatureStore(); + assertFalse(fs.shiftFeatures(0, 1)); // nothing to do SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null); fs.addFeature(sf1); @@ -790,9 +842,9 @@ public class FeatureStoreTest fs.addFeature(sf4); /* - * shift features right by 5 + * shift all features right by 5 */ - assertTrue(fs.shiftFeatures(5)); + assertTrue(fs.shiftFeatures(0, 5)); // non-positional features untouched: List nonPos = fs.getNonPositionalFeatures(); @@ -818,7 +870,7 @@ public class FeatureStoreTest * feature at [7-10] should be removed * feature at [13-19] should become [1-4] */ - assertTrue(fs.shiftFeatures(-15)); + assertTrue(fs.shiftFeatures(0, -15)); pos = fs.getPositionalFeatures(); assertEquals(pos.size(), 2); SequenceFeatures.sortFeatures(pos, true); @@ -826,5 +878,138 @@ public class FeatureStoreTest 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)); } }