X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreTest.java;h=834201818081f1166a796a5c83c081e666156565;hb=7ee36fb2339f8ac0c374262a4335a7d387e81f76;hp=db21c2f5cd3cf8cd0802f613d06ca0dfbbe5c721;hpb=a07949da33a4418114603e5ebf9eea4fe53e9475;p=jalview.git diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java index db21c2f..8342018 100644 --- a/test/jalview/datamodel/features/FeatureStoreTest.java +++ b/test/jalview/datamodel/features/FeatureStoreTest.java @@ -2,6 +2,7 @@ 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; @@ -14,11 +15,15 @@ import org.testng.annotations.Test; 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 @@ -48,7 +53,7 @@ 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); @@ -87,7 +92,7 @@ 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); @@ -144,7 +149,7 @@ 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); @@ -184,62 +189,10 @@ public class FeatureStoreTest 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() - { - FeatureStore fs = new FeatureStore(); - - String type = "Domain"; - SequenceFeature sf1 = new SequenceFeature(type, type, 10, 20, - Float.NaN, null); - assertTrue(fs.addNonNestedFeature(sf1)); - - // co-located feature is ok - SequenceFeature sf2 = new SequenceFeature(type, type, 10, 20, - Float.NaN, null); - assertTrue(fs.addNonNestedFeature(sf2)); - - // overlap left is ok - SequenceFeature sf3 = new SequenceFeature(type, type, 5, 15, Float.NaN, - null); - assertTrue(fs.addNonNestedFeature(sf3)); - - // overlap right is ok - SequenceFeature sf4 = new SequenceFeature(type, type, 15, 25, - Float.NaN, null); - assertTrue(fs.addNonNestedFeature(sf4)); - - // 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)); - - // add enclosed feature is not ok - SequenceFeature sf8 = new SequenceFeature(type, type, 10, 19, - Float.NaN, null); - assertFalse(fs.addNonNestedFeature(sf8)); - SequenceFeature sf9 = new SequenceFeature(type, type, 16, 25, - Float.NaN, null); - assertFalse(fs.addNonNestedFeature(sf9)); - SequenceFeature sf10 = new SequenceFeature(type, type, 7, 7, Float.NaN, - null); - assertFalse(fs.addNonNestedFeature(sf10)); - } - @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 +239,7 @@ 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 +311,7 @@ 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); @@ -409,7 +362,7 @@ 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 +415,7 @@ 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); + assertEquals(fs.getFeatures().size(), 2); assertFalse(fs.isEmpty()); assertTrue(fs.delete(sf2)); assertEquals(fs.getFeatureCount(true), 1); @@ -477,7 +428,7 @@ 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 +495,7 @@ 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 +571,7 @@ 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 @@ -692,14 +643,15 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testListContains() { - assertFalse(FeatureStore.listContains(null, null)); - List features = new ArrayList(); - assertFalse(FeatureStore.listContains(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.listContains(null, sf1)); - assertFalse(FeatureStore.listContains(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 +660,14 @@ public class FeatureStoreTest "group1"); // sf2.equals(sf1) so contains should return true - assertTrue(FeatureStore.listContains(features, sf2)); - assertFalse(FeatureStore.listContains(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 +725,8 @@ 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 +742,9 @@ 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 +770,7 @@ 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); @@ -826,6 +778,32 @@ 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") @@ -834,7 +812,7 @@ public class FeatureStoreTest /* * add a feature and a nested feature */ - FeatureStore store = new FeatureStore(); + 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); @@ -842,8 +820,8 @@ public class FeatureStoreTest assertEquals(features.size(), 2); assertTrue(features.contains(sf1)); assertTrue(features.contains(sf2)); - assertTrue(store.nonNestedFeatures.contains(sf1)); - assertTrue(store.nestedFeatures.contains(sf2)); + assertTrue(store.getFeatures().contains(sf1)); + assertTrue(store.getFeatures().contains(sf2)); /* * delete the first feature @@ -865,7 +843,7 @@ public class FeatureStoreTest @Test(groups = "Functional") public void testContains() { - FeatureStore fs = new FeatureStore(); + FeatureStore fs = newFeatureStore(); SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN, "group1"); SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, @@ -908,4 +886,28 @@ public class FeatureStoreTest 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.findOverlappingFeatures(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.findOverlappingFeatures(200, 200, null); + assertEquals(result.size(), 1); + assertTrue(result.contains(sf2)); + assertFalse(result.contains(sf1)); + } }