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 SequenceFeaturesI 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 SequenceFeaturesI 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 SequenceFeaturesI 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(SequenceFeaturesI sf, String type, int from,
217 SequenceFeature sf1 = new SequenceFeature(type, "", from, to,
224 @Test(groups = "Functional")
225 public void testFindFeatures()
227 SequenceFeaturesI 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 SequenceFeaturesI 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 SequenceFeaturesI 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 SequenceFeaturesI 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 SequenceFeaturesI 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"));
497 @Test(groups = "Functional")
498 public void testGetFeatureTypes()
500 SequenceFeaturesI store = new SequenceFeatures();
501 Set<String> types = store.getFeatureTypes();
502 assertTrue(types.isEmpty());
504 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
507 types = store.getFeatureTypes();
508 assertEquals(types.size(), 1);
509 assertTrue(types.contains("Metal"));
511 // null type is possible...
512 SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
515 types = store.getFeatureTypes();
516 assertEquals(types.size(), 2);
517 assertTrue(types.contains(null));
518 assertTrue(types.contains("Metal"));
521 * add non-positional feature
523 SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
526 types = store.getFeatureTypes();
527 assertEquals(types.size(), 3);
528 assertTrue(types.contains("Pfam"));
531 * add contact feature
533 SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
534 10, 20, Float.NaN, null);
536 types = store.getFeatureTypes();
537 assertEquals(types.size(), 4);
538 assertTrue(types.contains("Disulphide Bond"));
543 SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
546 types = store.getFeatureTypes();
547 assertEquals(types.size(), 4); // unchanged
550 * delete first Pfam - still have one
552 assertTrue(store.delete(sf3));
553 types = store.getFeatureTypes();
554 assertEquals(types.size(), 4);
555 assertTrue(types.contains("Pfam"));
558 * delete second Pfam - no longer have one
560 assertTrue(store.delete(sf5));
561 types = store.getFeatureTypes();
562 assertEquals(types.size(), 3);
563 assertFalse(types.contains("Pfam"));
566 @Test(groups = "Functional")
567 public void testGetFeatureCount()
569 SequenceFeaturesI store = new SequenceFeatures();
570 assertEquals(store.getFeatureCount(true), 0);
571 assertEquals(store.getFeatureCount(false), 0);
576 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
579 assertEquals(store.getFeatureCount(true), 1);
580 assertEquals(store.getFeatureCount(false), 0);
585 SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
588 assertEquals(store.getFeatureCount(true), 2);
589 assertEquals(store.getFeatureCount(false), 0);
592 * add non-positional feature
594 SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
597 assertEquals(store.getFeatureCount(true), 2);
598 assertEquals(store.getFeatureCount(false), 1);
601 * add contact feature (counts as 1)
603 SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
604 10, 20, Float.NaN, null);
606 assertEquals(store.getFeatureCount(true), 3);
607 assertEquals(store.getFeatureCount(false), 1);
612 SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
615 assertEquals(store.getFeatureCount(true), 4);
616 assertEquals(store.getFeatureCount(false), 1);
617 assertEquals(store.getFeatureCount(true, "Pfam"), 1);
618 assertEquals(store.getFeatureCount(false, "Pfam"), 1);
619 // search for type==null
620 assertEquals(store.getFeatureCount(true, (String) null), 1);
621 // search with no type specified
622 assertEquals(store.getFeatureCount(true, (String[]) null), 4);
623 assertEquals(store.getFeatureCount(true, "Metal", "Cath"), 1);
624 assertEquals(store.getFeatureCount(true, "Disulphide Bond"), 1);
625 assertEquals(store.getFeatureCount(true, "Metal", "Pfam", null), 3);
628 * delete first Pfam (non-positional)
630 assertTrue(store.delete(sf3));
631 assertEquals(store.getFeatureCount(true), 4);
632 assertEquals(store.getFeatureCount(false), 0);
635 * delete second Pfam (positional)
637 assertTrue(store.delete(sf5));
638 assertEquals(store.getFeatureCount(true), 3);
639 assertEquals(store.getFeatureCount(false), 0);
642 @Test(groups = "Functional")
643 public void testGetAllFeatures()
645 SequenceFeaturesI store = new SequenceFeatures();
646 List<SequenceFeature> features = store.getAllFeatures();
647 assertTrue(features.isEmpty());
649 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
652 features = store.getAllFeatures();
653 assertEquals(features.size(), 1);
654 assertTrue(features.contains(sf1));
656 SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
659 features = store.getAllFeatures();
660 assertEquals(features.size(), 2);
661 assertTrue(features.contains(sf2));
664 * add non-positional feature
666 SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
669 features = store.getAllFeatures();
670 assertEquals(features.size(), 3);
671 assertTrue(features.contains(sf3));
674 * add contact feature
676 SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
677 10, 20, Float.NaN, null);
679 features = store.getAllFeatures();
680 assertEquals(features.size(), 4);
681 assertTrue(features.contains(sf4));
686 SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
689 features = store.getAllFeatures();
690 assertEquals(features.size(), 5);
691 assertTrue(features.contains(sf5));
692 features = store.getAllFeatures("Cath");
693 assertTrue(features.isEmpty());
694 features = store.getAllFeatures("Pfam", "Cath", "Metal");
695 assertEquals(features.size(), 3);
696 assertTrue(features.contains(sf1));
697 assertTrue(features.contains(sf3));
698 assertTrue(features.contains(sf5));
703 assertTrue(store.delete(sf3));
704 features = store.getAllFeatures();
705 assertEquals(features.size(), 4);
706 assertFalse(features.contains(sf3));
711 assertTrue(store.delete(sf5));
712 features = store.getAllFeatures();
713 assertEquals(features.size(), 3);
714 assertFalse(features.contains(sf3));
717 @Test(groups = "Functional")
718 public void testGetTotalFeatureLength()
720 SequenceFeaturesI store = new SequenceFeatures();
721 assertEquals(store.getTotalFeatureLength(), 0);
723 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
725 assertTrue(store.add(sf1));
726 assertEquals(store.getTotalFeatureLength(), 11);
728 // re-add does nothing!
729 assertFalse(store.add(sf1));
730 assertEquals(store.getTotalFeatureLength(), 11);
733 * add non-positional feature
735 SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
738 assertEquals(store.getTotalFeatureLength(), 11);
741 * add contact feature - counts 1 to feature length
743 SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
744 10, 20, Float.NaN, null);
746 assertEquals(store.getTotalFeatureLength(), 12);
751 SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
754 assertEquals(store.getTotalFeatureLength(), 23);
759 assertTrue(store.delete(sf3)); // non-positional
760 assertEquals(store.getTotalFeatureLength(), 23); // no change
762 assertTrue(store.delete(sf5));
763 assertEquals(store.getTotalFeatureLength(), 12);
765 assertTrue(store.delete(sf4)); // contact
766 assertEquals(store.getTotalFeatureLength(), 11);
768 assertTrue(store.delete(sf1));
769 assertEquals(store.getTotalFeatureLength(), 0);
772 @Test(groups = "Functional")
773 public void testGetMinimumScore_getMaximumScore()
775 SequenceFeatures sf = new SequenceFeatures();
776 SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 0, 0,
777 Float.NaN, "group"); // non-positional, no score
779 SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 10, 20,
780 Float.NaN, "group"); // positional, no score
782 SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 10, 20, 1f,
785 SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 12, 16, 4f,
788 SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 0, 0, 11f,
791 SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, -7f,
795 assertEquals(sf.getMinimumScore("nosuchtype", true), Float.NaN);
796 assertEquals(sf.getMinimumScore("nosuchtype", false), Float.NaN);
797 assertEquals(sf.getMaximumScore("nosuchtype", true), Float.NaN);
798 assertEquals(sf.getMaximumScore("nosuchtype", false), Float.NaN);
800 // positional features min-max:
801 assertEquals(sf.getMinimumScore("Metal", true), 1f);
802 assertEquals(sf.getMaximumScore("Metal", true), 4f);
803 assertEquals(sf.getMinimumScore("Cath", true), Float.NaN);
804 assertEquals(sf.getMaximumScore("Cath", true), Float.NaN);
806 // non-positional features min-max:
807 assertEquals(sf.getMinimumScore("Cath", false), -7f);
808 assertEquals(sf.getMaximumScore("Cath", false), 11f);
809 assertEquals(sf.getMinimumScore("Metal", false), Float.NaN);
810 assertEquals(sf.getMaximumScore("Metal", false), Float.NaN);
812 // delete features; min-max should get recomputed
814 assertEquals(sf.getMinimumScore("Cath", false), 11f);
815 assertEquals(sf.getMaximumScore("Cath", false), 11f);
817 assertEquals(sf.getMinimumScore("Metal", true), 1f);
818 assertEquals(sf.getMaximumScore("Metal", true), 1f);
820 assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
821 assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
823 assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
824 assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
827 assertFalse(sf.hasFeatures());
828 assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
829 assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
830 assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
831 assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);