X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesTest.java;h=7dde97b6006b5db39bf4b91115963de7efa3f37c;hb=HEAD;hp=eaa527625256a3ebdb97dee865b36f88300ee37d;hpb=1ec8fc3e8bc982115e5ba1b16a101d239a2df591;p=jalview.git diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java index eaa5276..7dde97b 100644 --- a/test/jalview/datamodel/features/SequenceFeaturesTest.java +++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel.features; import static org.testng.Assert.assertEquals; @@ -5,18 +25,51 @@ 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.Iterator; import java.util.List; +import java.util.Map; import java.util.Set; import org.testng.annotations.Test; +import jalview.datamodel.SequenceFeature; +import junit.extensions.PA; + public class SequenceFeaturesTest { @Test(groups = "Functional") + public void testConstructor() + { + SequenceFeaturesI store = new SequenceFeatures(); + assertFalse(store.hasFeatures()); + + store = new SequenceFeatures((List) null); + assertFalse(store.hasFeatures()); + + List features = new ArrayList<>(); + store = new SequenceFeatures(features); + assertFalse(store.hasFeatures()); + + SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20, + Float.NaN, null); + features.add(sf1); + SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 15, 18, + Float.NaN, null); + features.add(sf2); // nested + SequenceFeature sf3 = new SequenceFeature("Pfam", "desc2", 0, 0, + Float.NaN, null); // non-positional + features.add(sf3); + store = new SequenceFeatures(features); + assertTrue(store.hasFeatures()); + assertEquals(2, store.getFeatureCount(true)); // positional + assertEquals(1, store.getFeatureCount(false)); // non-positional + assertFalse(store.add(sf1)); // already contained + assertFalse(store.add(sf2)); // already contained + assertFalse(store.add(sf3)); // already contained + } + + @Test(groups = "Functional") public void testGetPositionalFeatures() { SequenceFeaturesI store = new SequenceFeatures(); @@ -44,8 +97,8 @@ public class SequenceFeaturesTest Float.NaN, null); store.add(sf6); // contact feature - SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", - 18, 45, Float.NaN, null); + SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", 18, + 45, Float.NaN, null); store.add(sf7); // different feature type SequenceFeature sf8 = new SequenceFeature("Pfam", "desc", 30, 40, @@ -109,8 +162,8 @@ public class SequenceFeaturesTest Float.NaN, null); store.add(sf2); // contact feature - SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", - 18, 45, Float.NaN, null); + SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 18, + 45, Float.NaN, null); store.add(sf3); // repeat for different feature type SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20, @@ -122,7 +175,7 @@ public class SequenceFeaturesTest SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18, 45, Float.NaN, null); store.add(sf6); - + /* * get all contact features */ @@ -130,7 +183,7 @@ public class SequenceFeaturesTest assertEquals(features.size(), 2); assertTrue(features.contains(sf3)); assertTrue(features.contains(sf6)); - + /* * get contact features by type */ @@ -138,11 +191,11 @@ public class SequenceFeaturesTest assertTrue(store.getContactFeatures("Cath").isEmpty()); assertTrue(store.getContactFeatures("Pfam").isEmpty()); assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty()); - + features = store.getContactFeatures("Disulphide bond"); assertEquals(features.size(), 1); assertTrue(features.contains(sf3)); - + features = store.getContactFeatures("Disulfide bond"); assertEquals(features.size(), 1); assertTrue(features.contains(sf6)); @@ -161,8 +214,8 @@ public class SequenceFeaturesTest Float.NaN, null); store.add(sf2); // contact feature - SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", - 18, 45, Float.NaN, null); + SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 18, + 45, Float.NaN, null); store.add(sf3); // repeat for different feature type SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20, @@ -178,7 +231,7 @@ public class SequenceFeaturesTest SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0, Float.NaN, null); store.add(sf7); - + /* * get all non-positional features */ @@ -187,18 +240,18 @@ public class SequenceFeaturesTest assertTrue(features.contains(sf2)); assertTrue(features.contains(sf5)); assertTrue(features.contains(sf7)); - + /* * get non-positional features by type */ assertTrue(store.getNonPositionalFeatures((String) null).isEmpty()); assertTrue(store.getNonPositionalFeatures("Cath").isEmpty()); assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty()); - + features = store.getNonPositionalFeatures("Metal"); assertEquals(features.size(), 1); assertTrue(features.contains(sf2)); - + features = store.getNonPositionalFeatures("Pfam"); assertEquals(features.size(), 2); assertTrue(features.contains(sf5)); @@ -217,8 +270,7 @@ public class SequenceFeaturesTest SequenceFeature addFeature(SequenceFeaturesI sf, String type, int from, int to) { - SequenceFeature sf1 = new SequenceFeature(type, "", from, to, - Float.NaN, + SequenceFeature sf1 = new SequenceFeature(type, "", from, to, Float.NaN, null); sf.add(sf1); return sf1; @@ -240,31 +292,31 @@ public class SequenceFeaturesTest SequenceFeature sf10 = addFeature(sf, "Cath", 40, 100); SequenceFeature sf11 = addFeature(sf, "Cath", 60, 100); SequenceFeature sf12 = addFeature(sf, "Cath", 70, 70); - + List overlaps = sf.findFeatures(200, 200, "Pfam"); assertTrue(overlaps.isEmpty()); - - overlaps = sf.findFeatures( 1, 9, "Pfam"); + + overlaps = sf.findFeatures(1, 9, "Pfam"); assertEquals(overlaps.size(), 1); assertTrue(overlaps.contains(sf2)); - - overlaps = sf.findFeatures( 5, 18, "Pfam"); + + overlaps = sf.findFeatures(5, 18, "Pfam"); assertEquals(overlaps.size(), 2); assertTrue(overlaps.contains(sf1)); assertTrue(overlaps.contains(sf2)); - + 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( 80, 90, "Pfam"); + + overlaps = sf.findFeatures(80, 90, "Pfam"); assertEquals(overlaps.size(), 2); assertTrue(overlaps.contains(sf4)); assertTrue(overlaps.contains(sf5)); - - overlaps = sf.findFeatures( 68, 70, "Pfam"); + + overlaps = sf.findFeatures(68, 70, "Pfam"); assertEquals(overlaps.size(), 3); assertTrue(overlaps.contains(sf4)); assertTrue(overlaps.contains(sf5)); @@ -334,17 +386,20 @@ public class SequenceFeaturesTest groups = sf.getFeatureGroups(false); // for non-positional assertEquals(groups.size(), 1); assertTrue(groups.contains("AGroup")); + groups = sf.getFeatureGroups(false, "AType"); + assertEquals(groups.size(), 1); + assertTrue(groups.contains("AGroup")); + groups = sf.getFeatureGroups(true, "AnotherType"); + assertTrue(groups.isEmpty()); /* * add, then delete, more non-positional features of different types */ SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0, - 0f, - "AnotherGroup"); + 0f, "AnotherGroup"); sf.add(sfy); SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0, - 0f, - null); + 0f, null); sf.add(sfz); groups = sf.getFeatureGroups(false); assertEquals(groups.size(), 3); @@ -414,7 +469,7 @@ public class SequenceFeaturesTest { SequenceFeaturesI sf = new SequenceFeatures(); assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty()); - + /* * add feature with group = "Uniprot", type = "helix" */ @@ -426,7 +481,7 @@ public class SequenceFeaturesTest assertEquals(groups.size(), 1); assertTrue(groups.contains("helix")); assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty()); - + /* * add feature with group = "Uniprot", type = "strand" */ @@ -487,8 +542,9 @@ public class SequenceFeaturesTest assertTrue(groups.contains("turn")); assertTrue(groups.contains("strand")); // alternative vararg syntax - groups = sf.getFeatureTypesForGroups(true, new String[] { "Cath", - "Scop" }); + groups = sf.getFeatureTypesForGroups(true, + new String[] + { "Cath", "Scop" }); assertEquals(groups.size(), 2); assertTrue(groups.contains("turn")); assertTrue(groups.contains("strand")); @@ -530,8 +586,8 @@ public class SequenceFeaturesTest /* * add contact feature */ - SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", - 10, 20, Float.NaN, null); + SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10, + 20, Float.NaN, null); store.add(sf4); types = store.getFeatureTypes(); assertEquals(types.size(), 3); @@ -569,7 +625,7 @@ public class SequenceFeaturesTest SequenceFeaturesI store = new SequenceFeatures(); assertEquals(store.getFeatureCount(true), 0); assertEquals(store.getFeatureCount(false), 0); - + /* * add positional */ @@ -587,7 +643,7 @@ public class SequenceFeaturesTest assertFalse(store.add(sf2)); assertEquals(store.getFeatureCount(true), 1); assertEquals(store.getFeatureCount(false), 0); - + /* * add non-positional feature */ @@ -596,16 +652,16 @@ public class SequenceFeaturesTest store.add(sf3); assertEquals(store.getFeatureCount(true), 1); assertEquals(store.getFeatureCount(false), 1); - + /* * add contact feature (counts as 1) */ - SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", - 10, 20, Float.NaN, null); + SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10, + 20, Float.NaN, null); store.add(sf4); assertEquals(store.getFeatureCount(true), 2); assertEquals(store.getFeatureCount(false), 1); - + /* * add another Pfam but this time as a positional feature */ @@ -630,7 +686,7 @@ public class SequenceFeaturesTest assertTrue(store.delete(sf3)); assertEquals(store.getFeatureCount(true), 3); assertEquals(store.getFeatureCount(false), 0); - + /* * delete second Pfam (positional) */ @@ -645,21 +701,21 @@ public class SequenceFeaturesTest SequenceFeaturesI store = new SequenceFeatures(); List features = store.getAllFeatures(); assertTrue(features.isEmpty()); - + SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20, Float.NaN, null); store.add(sf1); features = store.getAllFeatures(); assertEquals(features.size(), 1); assertTrue(features.contains(sf1)); - + SequenceFeature sf2 = new SequenceFeature("Metallic", "desc", 10, 20, Float.NaN, null); store.add(sf2); features = store.getAllFeatures(); assertEquals(features.size(), 2); assertTrue(features.contains(sf2)); - + /* * add non-positional feature */ @@ -669,17 +725,17 @@ public class SequenceFeaturesTest features = store.getAllFeatures(); assertEquals(features.size(), 3); assertTrue(features.contains(sf3)); - + /* * add contact feature */ - SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", - 10, 20, Float.NaN, null); + SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10, + 20, Float.NaN, null); store.add(sf4); features = store.getAllFeatures(); assertEquals(features.size(), 4); assertTrue(features.contains(sf4)); - + /* * add another Pfam */ @@ -702,7 +758,7 @@ public class SequenceFeaturesTest assertTrue(features.contains(sf1)); assertTrue(features.contains(sf3)); assertTrue(features.contains(sf5)); - + /* * delete first Pfam */ @@ -710,7 +766,7 @@ public class SequenceFeaturesTest features = store.getAllFeatures(); assertEquals(features.size(), 4); assertFalse(features.contains(sf3)); - + /* * delete second Pfam */ @@ -730,6 +786,8 @@ public class SequenceFeaturesTest Float.NaN, null); assertTrue(store.add(sf1)); assertEquals(store.getTotalFeatureLength(), 11); + assertEquals(store.getTotalFeatureLength("Metal"), 11); + assertEquals(store.getTotalFeatureLength("Plastic"), 0); // re-add does nothing! assertFalse(store.add(sf1)); @@ -746,8 +804,8 @@ public class SequenceFeaturesTest /* * add contact feature - counts 1 to feature length */ - SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", - 10, 20, Float.NaN, null); + SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10, + 20, Float.NaN, null); store.add(sf4); assertEquals(store.getTotalFeatureLength(), 12); @@ -848,12 +906,15 @@ public class SequenceFeaturesTest * no type specified - get all types stored * they are returned in keyset (alphabetical) order */ - Iterable types = sf.varargToTypes(); - Iterator iterator = types.iterator(); + Map featureStores = (Map) PA + .getValue(sf, "featureStore"); + + Iterable types = sf.varargToTypes(); + Iterator iterator = types.iterator(); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Cath"); + assertSame(iterator.next(), featureStores.get("Cath")); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Metal"); + assertSame(iterator.next(), featureStores.get("Metal")); assertFalse(iterator.hasNext()); /* @@ -863,9 +924,9 @@ public class SequenceFeaturesTest types = sf.varargToTypes(new String[] {}); iterator = types.iterator(); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Cath"); + assertSame(iterator.next(), featureStores.get("Cath")); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Metal"); + assertSame(iterator.next(), featureStores.get("Metal")); assertFalse(iterator.hasNext()); /* @@ -881,9 +942,9 @@ public class SequenceFeaturesTest types = sf.varargToTypes((String[]) null); iterator = types.iterator(); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Cath"); + assertSame(iterator.next(), featureStores.get("Cath")); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Metal"); + assertSame(iterator.next(), featureStores.get("Metal")); assertFalse(iterator.hasNext()); /* @@ -892,29 +953,27 @@ public class SequenceFeaturesTest types = sf.varargToTypes("Metal"); iterator = types.iterator(); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Metal"); + assertSame(iterator.next(), featureStores.get("Metal")); assertFalse(iterator.hasNext()); /* - * two types specified - get sorted alphabetically + * two types specified - order is preserved */ - types = sf.varargToTypes("Metal", "Helix"); + types = sf.varargToTypes("Metal", "Cath"); iterator = types.iterator(); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Helix"); + assertSame(iterator.next(), featureStores.get("Metal")); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Metal"); + assertSame(iterator.next(), featureStores.get("Cath")); assertFalse(iterator.hasNext()); /* - * null type included - should get removed + * null type included - should be ignored */ types = sf.varargToTypes("Metal", null, "Helix"); iterator = types.iterator(); assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Helix"); - assertTrue(iterator.hasNext()); - assertEquals(iterator.next(), "Metal"); + assertSame(iterator.next(), featureStores.get("Metal")); assertFalse(iterator.hasNext()); } @@ -922,7 +981,7 @@ public class SequenceFeaturesTest public void testGetFeatureTypes_byOntology() { SequenceFeaturesI store = new SequenceFeatures(); - + SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20, Float.NaN, null); store.add(sf1); @@ -962,41 +1021,55 @@ public class SequenceFeaturesTest assertTrue(features.isEmpty()); assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty()); assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty()); - - SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20, - Float.NaN, null); - store.add(sf1); - // mRNA isA transcript; added here 'as if' non-positional - // just to show that non-positional features are included in results - SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 0, 0, - Float.NaN, null); - store.add(sf2); + SequenceFeature transcriptFeature = new SequenceFeature("transcript", + "desc", 10, 20, Float.NaN, null); + store.add(transcriptFeature); - SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 30, 40, + /* + * mRNA is a sub-type of transcript; added here 'as if' non-positional + * just to show that non-positional features are included in results + */ + SequenceFeature mrnaFeature = new SequenceFeature("mRNA", "desc", 0, 0, Float.NaN, null); - store.add(sf3); + store.add(mrnaFeature); + + SequenceFeature pfamFeature = new SequenceFeature("Pfam", "desc", 30, + 40, Float.NaN, null); + store.add(pfamFeature); + /* + * "transcript" matches both itself and the sub-term "mRNA" + */ features = store.getFeaturesByOntology("transcript"); assertEquals(features.size(), 2); - assertTrue(features.contains(sf1)); - assertTrue(features.contains(sf2)); + assertTrue(features.contains(transcriptFeature)); + assertTrue(features.contains(mrnaFeature)); + /* + * "mRNA" matches itself but not parent term "transcript" + */ features = store.getFeaturesByOntology("mRNA"); assertEquals(features.size(), 1); - assertTrue(features.contains(sf2)); + assertTrue(features.contains(mrnaFeature)); + /* + * "pfam" is not an SO term but is included as an exact match + */ features = store.getFeaturesByOntology("mRNA", "Pfam"); assertEquals(features.size(), 2); - assertTrue(features.contains(sf2)); - assertTrue(features.contains(sf3)); + assertTrue(features.contains(mrnaFeature)); + assertTrue(features.contains(pfamFeature)); + + features = store.getFeaturesByOntology("sequence_variant"); + assertTrue(features.isEmpty()); } @Test(groups = "Functional") public void testSortFeatures() { - List sfs = new ArrayList(); - SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80, + List sfs = new ArrayList<>(); + SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 60, Float.NaN, null); sfs.add(sf1); SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50, @@ -1005,17 +1078,235 @@ public class SequenceFeaturesTest SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60, Float.NaN, null); sfs.add(sf3); + SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30, 80, + Float.NaN, null); + sfs.add(sf4); + SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30, 90, + Float.NaN, null); + sfs.add(sf5); - // sort by end position descending + /* + * sort by end position descending, order unchanged if matched + */ SequenceFeatures.sortFeatures(sfs, false); - assertSame(sfs.get(0), sf1); - assertSame(sfs.get(1), sf3); - assertSame(sfs.get(2), sf2); + assertSame(sfs.get(0), sf5); // end 90 + assertSame(sfs.get(1), sf4); // end 80 + assertSame(sfs.get(2), sf1); // end 60, start 50 + assertSame(sfs.get(3), sf3); // end 60, start 30 + assertSame(sfs.get(4), sf2); // end 50 - // sort by start position ascending + /* + * resort {5, 4, 1, 3, 2} by start position ascending, end descending + */ SequenceFeatures.sortFeatures(sfs, true); - assertSame(sfs.get(0), sf1); - assertSame(sfs.get(1), sf2); - assertSame(sfs.get(2), sf3); + assertSame(sfs.get(0), sf5); // start 30, end 90 + assertSame(sfs.get(1), sf4); // start 30, end 80 + assertSame(sfs.get(2), sf1); // start 30, end 60 + assertSame(sfs.get(3), sf2); // start 40 + assertSame(sfs.get(4), sf3); // start 50 + } + + @Test(groups = "Functional") + public void testGetFeaturesForGroup() + { + SequenceFeaturesI store = new SequenceFeatures(); + + List features = store.getFeaturesForGroup(true, null); + assertTrue(features.isEmpty()); + assertTrue(store.getFeaturesForGroup(false, null).isEmpty()); + assertTrue(store.getFeaturesForGroup(true, "Uniprot").isEmpty()); + assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty()); + + SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f, + null); + SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f, + null); + SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f, + "Uniprot"); + SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 0, 0, 0f, + "Rfam"); + SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 5, 15, 0f, + null); + store.add(sf1); + store.add(sf2); + store.add(sf3); + store.add(sf4); + store.add(sf5); + + // positional features for null group, any type + features = store.getFeaturesForGroup(true, null); + assertEquals(features.size(), 2); + assertTrue(features.contains(sf1)); + assertTrue(features.contains(sf5)); + + // positional features for null group, specified type + features = store.getFeaturesForGroup(true, null, + new String[] + { "Pfam", "Xfam" }); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf1)); + features = store.getFeaturesForGroup(true, null, + new String[] + { "Pfam", "Xfam", "Cath" }); + assertEquals(features.size(), 2); + assertTrue(features.contains(sf1)); + assertTrue(features.contains(sf5)); + + // positional features for non-null group, any type + features = store.getFeaturesForGroup(true, "Uniprot"); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf3)); + assertTrue(store.getFeaturesForGroup(true, "Rfam").isEmpty()); + + // positional features for non-null group, specified type + features = store.getFeaturesForGroup(true, "Uniprot", "Pfam", "Xfam", + "Rfam"); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf3)); + assertTrue( + store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty()); + + // non-positional features for null group, any type + features = store.getFeaturesForGroup(false, null); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf2)); + + // non-positional features for null group, specified type + features = store.getFeaturesForGroup(false, null, "Pfam", "Xfam"); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf2)); + assertTrue(store.getFeaturesForGroup(false, null, "Cath").isEmpty()); + + // non-positional features for non-null group, any type + features = store.getFeaturesForGroup(false, "Rfam"); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf4)); + assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty()); + + // non-positional features for non-null group, specified type + features = store.getFeaturesForGroup(false, "Rfam", "Pfam", "Metal"); + assertEquals(features.size(), 1); + assertTrue(features.contains(sf4)); + assertTrue(store.getFeaturesForGroup(false, "Rfam", "Cath", "Pfam") + .isEmpty()); + } + + @Test(groups = "Functional") + public void testShiftFeatures() + { + SequenceFeatures store = new SequenceFeatures(); + assertFalse(store.shiftFeatures(0, 1)); + + SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null); + store.add(sf1); + // nested feature: + SequenceFeature sf2 = new SequenceFeature("Metal", "", 8, 14, 0f, null); + store.add(sf2); + // contact feature: + SequenceFeature sf3 = new SequenceFeature("Disulfide bond", "", 23, 32, + 0f, null); + store.add(sf3); + // non-positional feature: + SequenceFeature sf4 = new SequenceFeature("Pfam", "", 0, 0, 0f, null); + store.add(sf4); + + /* + * shift features right by 5 + */ + assertTrue(store.shiftFeatures(0, 5)); + + // non-positional features untouched: + List nonPos = store.getNonPositionalFeatures(); + assertEquals(nonPos.size(), 1); + assertTrue(nonPos.contains(sf4)); + + // positional features are replaced + List pos = store.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(0).getType(), "Cath"); + assertEquals(pos.get(1).getBegin(), 13); + assertEquals(pos.get(1).getEnd(), 19); + assertEquals(pos.get(1).getType(), "Metal"); + assertEquals(pos.get(2).getBegin(), 28); + assertEquals(pos.get(2).getEnd(), 37); + assertEquals(pos.get(2).getType(), "Disulfide bond"); + + /* + * now shift left by 15 + * feature at [7-10] should be removed + * feature at [13-19] should become [1-4] + */ + assertTrue(store.shiftFeatures(0, -15)); + pos = store.getPositionalFeatures(); + assertEquals(pos.size(), 2); + SequenceFeatures.sortFeatures(pos, true); + assertEquals(pos.get(0).getBegin(), 1); + assertEquals(pos.get(0).getEnd(), 4); + assertEquals(pos.get(0).getType(), "Metal"); + assertEquals(pos.get(1).getBegin(), 13); + assertEquals(pos.get(1).getEnd(), 22); + assertEquals(pos.get(1).getType(), "Disulfide bond"); + + /* + * shift right by 4 from column 2 + * feature at [1-4] should be unchanged + * feature at [13-22] should become [17-26] + */ + assertTrue(store.shiftFeatures(2, 4)); + pos = store.getPositionalFeatures(); + assertEquals(pos.size(), 2); + SequenceFeatures.sortFeatures(pos, true); + assertEquals(pos.get(0).getBegin(), 1); + assertEquals(pos.get(0).getEnd(), 4); + assertEquals(pos.get(0).getType(), "Metal"); + assertEquals(pos.get(1).getBegin(), 17); + assertEquals(pos.get(1).getEnd(), 26); + assertEquals(pos.get(1).getType(), "Disulfide bond"); + + /* + * shift right from column 18 + * should be no updates + */ + SequenceFeature f1 = pos.get(0); + SequenceFeature f2 = pos.get(1); + assertFalse(store.shiftFeatures(18, 6)); + pos = store.getPositionalFeatures(); + assertEquals(pos.size(), 2); + SequenceFeatures.sortFeatures(pos, true); + assertSame(pos.get(0), f1); + assertSame(pos.get(1), f2); + } + + @Test(groups = "Functional") + public void testIsOntologyTerm() + { + SequenceFeatures store = new SequenceFeatures(); + assertTrue(store.isOntologyTerm("gobbledygook")); + assertTrue(store.isOntologyTerm("transcript", "transcript")); + assertTrue(store.isOntologyTerm("mRNA", "transcript")); + assertFalse(store.isOntologyTerm("transcript", "mRNA")); + assertTrue(store.isOntologyTerm("junk", "transcript", "junk")); + assertTrue(store.isOntologyTerm("junk", new String[] {})); + assertTrue(store.isOntologyTerm("junk", (String[]) null)); + } + + @Test(groups = "Functional") + public void testDeleteAll() + { + SequenceFeaturesI store = new SequenceFeatures(); + assertFalse(store.hasFeatures()); + store.deleteAll(); + assertFalse(store.hasFeatures()); + store.add(new SequenceFeature("Cath", "Desc", 12, 20, 0f, "Group")); + store.add(new SequenceFeature("Pfam", "Desc", 6, 12, 2f, "Group2")); + assertTrue(store.hasFeatures()); + store.deleteAll(); + assertFalse(store.hasFeatures()); } }