1 package jalview.datamodel.features;
3 import static org.testng.Assert.assertEquals;
4 import static org.testng.Assert.assertFalse;
5 import static org.testng.Assert.assertTrue;
7 import jalview.datamodel.SequenceFeature;
12 import org.testng.annotations.Test;
14 public class SequenceFeaturesTest
16 @Test(groups = "Functional")
17 public void testGetPositionalFeatures()
19 SequenceFeatures store = new SequenceFeatures();
20 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
23 // same range, different description
24 SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20,
27 // discontiguous range
28 SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 30, 40,
32 SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 15, 35,
36 SequenceFeature sf5 = new SequenceFeature("Metal", "desc", 5, 50,
39 // non-positional feature
40 SequenceFeature sf6 = new SequenceFeature("Metal", "desc", 0, 0,
44 SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
45 18, 45, Float.NaN, null);
47 // different feature type
48 SequenceFeature sf8 = new SequenceFeature("Pfam", "desc", 30, 40,
51 SequenceFeature sf9 = new SequenceFeature("Pfam", "desc", 15, 35,
56 * get all positional features
58 List<SequenceFeature> features = store.getPositionalFeatures();
59 assertEquals(features.size(), 8);
60 assertTrue(features.contains(sf1));
61 assertTrue(features.contains(sf2));
62 assertTrue(features.contains(sf3));
63 assertTrue(features.contains(sf4));
64 assertTrue(features.contains(sf5));
65 assertFalse(features.contains(sf6)); // non-positional
66 assertTrue(features.contains(sf7));
67 assertTrue(features.contains(sf8));
68 assertTrue(features.contains(sf9));
71 * get features by type
73 assertTrue(store.getPositionalFeatures((String) null).isEmpty());
74 assertTrue(store.getPositionalFeatures("Cath").isEmpty());
75 assertTrue(store.getPositionalFeatures("METAL").isEmpty());
77 features = store.getPositionalFeatures("Metal");
78 assertEquals(features.size(), 5);
79 assertTrue(features.contains(sf1));
80 assertTrue(features.contains(sf2));
81 assertTrue(features.contains(sf3));
82 assertTrue(features.contains(sf4));
83 assertTrue(features.contains(sf5));
84 assertFalse(features.contains(sf6));
86 features = store.getPositionalFeatures("Disulphide bond");
87 assertEquals(features.size(), 1);
88 assertTrue(features.contains(sf7));
90 features = store.getPositionalFeatures("Pfam");
91 assertEquals(features.size(), 2);
92 assertTrue(features.contains(sf8));
93 assertTrue(features.contains(sf9));
96 @Test(groups = "Functional")
97 public void testGetContactFeatures()
99 SequenceFeatures store = new SequenceFeatures();
101 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
105 SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
109 SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
110 18, 45, Float.NaN, null);
112 // repeat for different feature type
113 SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
116 SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
119 SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
120 45, Float.NaN, null);
124 * get all contact features
126 List<SequenceFeature> features = store.getContactFeatures();
127 assertEquals(features.size(), 2);
128 assertTrue(features.contains(sf3));
129 assertTrue(features.contains(sf6));
132 * get contact features by type
134 assertTrue(store.getContactFeatures((String) null).isEmpty());
135 assertTrue(store.getContactFeatures("Cath").isEmpty());
136 assertTrue(store.getContactFeatures("Pfam").isEmpty());
137 assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
139 features = store.getContactFeatures("Disulphide bond");
140 assertEquals(features.size(), 1);
141 assertTrue(features.contains(sf3));
143 features = store.getContactFeatures("Disulfide bond");
144 assertEquals(features.size(), 1);
145 assertTrue(features.contains(sf6));
148 @Test(groups = "Functional")
149 public void testGetNonPositionalFeatures()
151 SequenceFeatures store = new SequenceFeatures();
153 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
157 SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
161 SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
162 18, 45, Float.NaN, null);
164 // repeat for different feature type
165 SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
168 SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
171 SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
172 45, Float.NaN, null);
174 // one more non-positional, different description
175 SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0,
180 * get all non-positional features
182 List<SequenceFeature> features = store.getNonPositionalFeatures();
183 assertEquals(features.size(), 3);
184 assertTrue(features.contains(sf2));
185 assertTrue(features.contains(sf5));
186 assertTrue(features.contains(sf7));
189 * get non-positional features by type
191 assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
192 assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
193 assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
195 features = store.getNonPositionalFeatures("Metal");
196 assertEquals(features.size(), 1);
197 assertTrue(features.contains(sf2));
199 features = store.getNonPositionalFeatures("Pfam");
200 assertEquals(features.size(), 2);
201 assertTrue(features.contains(sf5));
202 assertTrue(features.contains(sf7));
206 * Helper method to add a feature of no particular type
214 SequenceFeature addFeature(SequenceFeatures sf, String type, int from,
217 SequenceFeature sf1 = new SequenceFeature(type, "", from, to,
224 @Test(groups = "Functional")
225 public void testFindFeatures()
227 SequenceFeatures sf = new SequenceFeatures();
228 SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
229 SequenceFeature sf2 = addFeature(sf, "Pfam", 1, 15);
230 SequenceFeature sf3 = addFeature(sf, "Pfam", 20, 30);
231 SequenceFeature sf4 = addFeature(sf, "Pfam", 40, 100);
232 SequenceFeature sf5 = addFeature(sf, "Pfam", 60, 100);
233 SequenceFeature sf6 = addFeature(sf, "Pfam", 70, 70);
234 SequenceFeature sf7 = addFeature(sf, "Cath", 10, 50);
235 SequenceFeature sf8 = addFeature(sf, "Cath", 1, 15);
236 SequenceFeature sf9 = addFeature(sf, "Cath", 20, 30);
237 SequenceFeature sf10 = addFeature(sf, "Cath", 40, 100);
238 SequenceFeature sf11 = addFeature(sf, "Cath", 60, 100);
239 SequenceFeature sf12 = addFeature(sf, "Cath", 70, 70);
240 // null type is weird but possible:
241 SequenceFeature sf13 = addFeature(sf, null, 5, 12);
243 List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
244 assertTrue(overlaps.isEmpty());
246 overlaps = sf.findFeatures( 1, 9, "Pfam");
247 assertEquals(overlaps.size(), 1);
248 assertTrue(overlaps.contains(sf2));
250 overlaps = sf.findFeatures( 5, 18, "Pfam");
251 assertEquals(overlaps.size(), 2);
252 assertTrue(overlaps.contains(sf1));
253 assertTrue(overlaps.contains(sf2));
255 overlaps = sf.findFeatures(30, 40, "Pfam");
256 assertEquals(overlaps.size(), 3);
257 assertTrue(overlaps.contains(sf1));
258 assertTrue(overlaps.contains(sf3));
259 assertTrue(overlaps.contains(sf4));
261 overlaps = sf.findFeatures( 80, 90, "Pfam");
262 assertEquals(overlaps.size(), 2);
263 assertTrue(overlaps.contains(sf4));
264 assertTrue(overlaps.contains(sf5));
266 overlaps = sf.findFeatures( 68, 70, "Pfam");
267 assertEquals(overlaps.size(), 3);
268 assertTrue(overlaps.contains(sf4));
269 assertTrue(overlaps.contains(sf5));
270 assertTrue(overlaps.contains(sf6));
272 overlaps = sf.findFeatures(16, 69, "Cath");
273 assertEquals(overlaps.size(), 4);
274 assertTrue(overlaps.contains(sf7));
275 assertFalse(overlaps.contains(sf8));
276 assertTrue(overlaps.contains(sf9));
277 assertTrue(overlaps.contains(sf10));
278 assertTrue(overlaps.contains(sf11));
279 assertFalse(overlaps.contains(sf12));
281 assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());
283 overlaps = sf.findFeatures(7, 7, (String) null);
284 assertEquals(overlaps.size(), 1);
285 assertTrue(overlaps.contains(sf13));
288 @Test(groups = "Functional")
289 public void testDelete()
291 SequenceFeatures sf = new SequenceFeatures();
292 SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
293 assertTrue(sf.getPositionalFeatures().contains(sf1));
295 assertFalse(sf.delete(null));
296 SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 15, 0f, null);
297 assertFalse(sf.delete(sf2)); // not added, can't delete it
298 assertTrue(sf.delete(sf1));
299 assertTrue(sf.getPositionalFeatures().isEmpty());
302 @Test(groups = "Functional")
303 public void testHasFeatures()
305 SequenceFeatures sf = new SequenceFeatures();
306 assertFalse(sf.hasFeatures());
308 SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
309 assertTrue(sf.hasFeatures());
312 assertFalse(sf.hasFeatures());
316 * Tests for the method that gets feature groups for positional or
317 * non-positional features
319 @Test(groups = "Functional")
320 public void testGetFeatureGroups()
322 SequenceFeatures sf = new SequenceFeatures();
323 assertTrue(sf.getFeatureGroups(true).isEmpty());
324 assertTrue(sf.getFeatureGroups(false).isEmpty());
327 * add a non-positional feature (begin/end = 0/0)
329 SequenceFeature sfx = new SequenceFeature("AType", "Desc", 0, 0, 0f,
332 Set<String> groups = sf.getFeatureGroups(true); // for positional
333 assertTrue(groups.isEmpty());
334 groups = sf.getFeatureGroups(false); // for non-positional
335 assertEquals(groups.size(), 1);
336 assertTrue(groups.contains("AGroup"));
339 * add, then delete, more non-positional features of different types
341 SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0,
345 SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0,
349 groups = sf.getFeatureGroups(false);
350 assertEquals(groups.size(), 3);
351 assertTrue(groups.contains("AGroup"));
352 assertTrue(groups.contains("AnotherGroup"));
353 assertTrue(groups.contains(null)); // null is a possible group
356 groups = sf.getFeatureGroups(false);
357 assertEquals(groups.size(), 1);
358 assertTrue(groups.contains("AGroup"));
361 * add positional features
363 SequenceFeature sf1 = new SequenceFeature("Pfam", "Desc", 10, 50, 0f,
366 groups = sf.getFeatureGroups(true);
367 assertEquals(groups.size(), 1);
368 assertTrue(groups.contains("PfamGroup"));
369 groups = sf.getFeatureGroups(false); // non-positional unchanged
370 assertEquals(groups.size(), 1);
371 assertTrue(groups.contains("AGroup"));
373 SequenceFeature sf2 = new SequenceFeature("Cath", "Desc", 10, 50, 0f,
376 groups = sf.getFeatureGroups(true);
377 assertEquals(groups.size(), 2);
378 assertTrue(groups.contains("PfamGroup"));
379 assertTrue(groups.contains(null));
383 assertTrue(sf.getFeatureGroups(true).isEmpty());
385 SequenceFeature sf3 = new SequenceFeature("CDS", "", 10, 50, 0f,
388 SequenceFeature sf4 = new SequenceFeature("exon", "", 10, 50, 0f,
391 groups = sf.getFeatureGroups(true);
392 assertEquals(groups.size(), 1);
393 assertTrue(groups.contains("Ensembl"));
396 * delete last Ensembl group feature from CDS features
397 * but still have one in exon features
400 groups = sf.getFeatureGroups(true);
401 assertEquals(groups.size(), 1);
402 assertTrue(groups.contains("Ensembl"));
405 * delete the last non-positional feature
408 groups = sf.getFeatureGroups(false);
409 assertTrue(groups.isEmpty());
412 @Test(groups = "Functional")
413 public void testGetFeatureTypesForGroups()
415 SequenceFeatures sf = new SequenceFeatures();
416 assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
419 * add feature with group = "Uniprot", type = "helix"
421 String groupUniprot = "Uniprot";
422 SequenceFeature sf1 = new SequenceFeature("helix", "Desc", 10, 50, 0f,
425 Set<String> groups = sf.getFeatureTypesForGroups(true, groupUniprot);
426 assertEquals(groups.size(), 1);
427 assertTrue(groups.contains("helix"));
428 assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
431 * add feature with group = "Uniprot", type = "strand"
433 SequenceFeature sf2 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
436 groups = sf.getFeatureTypesForGroups(true, groupUniprot);
437 assertEquals(groups.size(), 2);
438 assertTrue(groups.contains("helix"));
439 assertTrue(groups.contains("strand"));
442 * delete the "strand" Uniprot feature - still have "helix"
445 groups = sf.getFeatureTypesForGroups(true, groupUniprot);
446 assertEquals(groups.size(), 1);
447 assertTrue(groups.contains("helix"));
450 * delete the "helix" Uniprot feature - none left
453 assertTrue(sf.getFeatureTypesForGroups(true, groupUniprot).isEmpty());
456 * add some null group features
458 SequenceFeature sf3 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
461 SequenceFeature sf4 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
464 groups = sf.getFeatureTypesForGroups(true, (String) null);
465 assertEquals(groups.size(), 2);
466 assertTrue(groups.contains("strand"));
467 assertTrue(groups.contains("turn"));
470 * add strand/Cath and turn/Scop and query for one or both groups
471 * (find feature types for groups selected in Feature Settings)
473 SequenceFeature sf5 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
476 SequenceFeature sf6 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
479 groups = sf.getFeatureTypesForGroups(true, "Cath");
480 assertEquals(groups.size(), 1);
481 assertTrue(groups.contains("strand"));
482 groups = sf.getFeatureTypesForGroups(true, "Scop");
483 assertEquals(groups.size(), 1);
484 assertTrue(groups.contains("turn"));
485 groups = sf.getFeatureTypesForGroups(true, "Cath", "Scop");
486 assertEquals(groups.size(), 2);
487 assertTrue(groups.contains("turn"));
488 assertTrue(groups.contains("strand"));
489 // alternative vararg syntax
490 groups = sf.getFeatureTypesForGroups(true, new String[] { "Cath",
492 assertEquals(groups.size(), 2);
493 assertTrue(groups.contains("turn"));
494 assertTrue(groups.contains("strand"));