Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceFeaturesTest	19	717	23	1.0100%	Show methods

Class SequenceFeaturesTest

Class SequenceFeaturesTest	Line # 19	Total Statements 717	Complexity 23	TOTAL Coverage 1.0100%
testConstructor() : void   testConstructor() : void	2121	20.020	1.01	1.0 1.0100%
testGetPositionalFeatures() : void   testGetPositionalFeatures() : void	5252	48.048	1.01	1.0 1.0100%
testGetContactFeatures() : void   testGetContactFeatures() : void	132132	27.027	1.01	1.0 1.0100%
testGetNonPositionalFeatures() : void   testGetNonPositionalFeatures() : void	184184	30.030	1.01	1.0 1.0100%
addFeature(SequenceFeaturesI,String,int,int) : SequenceFeature   addFeature(SequenceFeaturesI,String,int,int) : SequenceFeature	250250	3.03	1.01	1.0 1.0100%
testFindFeatures() : void   testFindFeatures() : void	260260	47.047	1.01	1.0 1.0100%
testDelete() : void   testDelete() : void	321321	8.08	1.01	1.0 1.0100%
testHasFeatures() : void   testHasFeatures() : void	335335	6.06	1.01	1.0 1.0100%
testGetFeatureGroups() : void   testGetFeatureGroups() : void	352352	60.060	1.01	1.0 1.0100%
testGetFeatureTypesForGroups() : void   testGetFeatureTypesForGroups() : void	450450	47.047	1.01	1.0 1.0100%
testGetFeatureTypes() : void   testGetFeatureTypes() : void	535535	36.036	1.01	1.0 1.0100%
testGetFeatureCount() : void   testGetFeatureCount() : void	604604	36.036	1.01	1.0 1.0100%
testGetAllFeatures() : void   testGetAllFeatures() : void	680680	44.044	1.01	1.0 1.0100%
testGetTotalFeatureLength() : void   testGetTotalFeatureLength() : void	761761	26.026	1.01	1.0 1.0100%
testGetMinimumScore_getMaximumScore() : void   testGetMinimumScore_getMaximumScore() : void	818818	44.044	1.01	1.0 1.0100%
testVarargsToTypes() : void   testVarargsToTypes() : void	880880	44.044	1.01	1.0 1.0100%
testGetFeatureTypes_byOntology() : void   testGetFeatureTypes_byOntology() : void	962962	20.020	1.01	1.0 1.0100%
testGetFeaturesByOntology() : void   testGetFeaturesByOntology() : void	998998	24.024	1.01	1.0 1.0100%
testSortFeatures() : void   testSortFeatures() : void	10501050	23.023	1.01	1.0 1.0100%
testGetFeaturesForGroup() : void   testGetFeaturesForGroup() : void	10941094	50.050	1.01	1.0 1.0100%
testShiftFeatures() : void   testShiftFeatures() : void	11761176	57.057	1.01	1.0 1.0100%
testIsOntologyTerm() : void   testIsOntologyTerm() : void	12681268	8.08	1.01	1.0 1.0100%
testDeleteAll() : void   testDeleteAll() : void	12811281	9.09	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.082432434	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureGroupsjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureGroups	1PASS
	0.07837838	jalview.datamodel.features.SequenceFeaturesTest.testShiftFeaturesjalview.datamodel.features.SequenceFeaturesTest.testShiftFeatures	1PASS
	0.07027027	jalview.datamodel.features.SequenceFeaturesTest.testFindFeaturesjalview.datamodel.features.SequenceFeaturesTest.testFindFeatures	1PASS
	0.06891892	jalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesForGroupjalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesForGroup	1PASS
	0.066216215	jalview.datamodel.features.SequenceFeaturesTest.testGetPositionalFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetPositionalFeatures	1PASS
	0.06486487	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesForGroupsjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesForGroups	1PASS
	0.06081081	jalview.datamodel.features.SequenceFeaturesTest.testGetAllFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetAllFeatures	1PASS
	0.06081081	jalview.datamodel.features.SequenceFeaturesTest.testVarargsToTypesjalview.datamodel.features.SequenceFeaturesTest.testVarargsToTypes	1PASS
	0.06081081	jalview.datamodel.features.SequenceFeaturesTest.testGetMinimumScore_getMaximumScorejalview.datamodel.features.SequenceFeaturesTest.testGetMinimumScore_getMaximumScore	1PASS
	0.05	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes	1PASS
	0.05	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureCountjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureCount	1PASS
	0.04189189	jalview.datamodel.features.SequenceFeaturesTest.testGetNonPositionalFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetNonPositionalFeatures	1PASS
	0.037837837	jalview.datamodel.features.SequenceFeaturesTest.testGetContactFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetContactFeatures	1PASS
	0.036486488	jalview.datamodel.features.SequenceFeaturesTest.testGetTotalFeatureLengthjalview.datamodel.features.SequenceFeaturesTest.testGetTotalFeatureLength	1PASS
	0.033783782	jalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesByOntologyjalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesByOntology	1PASS
	0.032432433	jalview.datamodel.features.SequenceFeaturesTest.testSortFeaturesjalview.datamodel.features.SequenceFeaturesTest.testSortFeatures	1PASS
	0.028378379	jalview.datamodel.features.SequenceFeaturesTest.testConstructorjalview.datamodel.features.SequenceFeaturesTest.testConstructor	1PASS
	0.028378379	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes_byOntologyjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes_byOntology	1PASS
	0.017567568	jalview.datamodel.features.SequenceFeaturesTest.testDeletejalview.datamodel.features.SequenceFeaturesTest.testDelete	1PASS
	0.014864865	jalview.datamodel.features.SequenceFeaturesTest.testHasFeaturesjalview.datamodel.features.SequenceFeaturesTest.testHasFeatures	1PASS
	0.013513514	jalview.datamodel.features.SequenceFeaturesTest.testDeleteAlljalview.datamodel.features.SequenceFeaturesTest.testDeleteAll	1PASS
	0.012162162	jalview.datamodel.features.SequenceFeaturesTest.testIsOntologyTermjalview.datamodel.features.SequenceFeaturesTest.testIsOntologyTerm	1PASS

 

Source view

1		package jalview.datamodel.features;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertFalse;
5		import static org.testng.Assert.assertSame;
6		import static org.testng.Assert.assertTrue;
7
8		import java.util.ArrayList;
9		import java.util.Iterator;
10		import java.util.List;
11		import java.util.Map;
12		import java.util.Set;
13
14		import org.testng.annotations.Test;
15
16		import jalview.datamodel.SequenceFeature;
17		import junit.extensions.PA;
18
		100% Uncovered Elements: 0 (740) Complexity: 23 Complexity Density: 0.03
19		public class SequenceFeaturesTest
20		{
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
21	1	@Test(groups = "Functional")...
22		public void testConstructor()
23		{
24	1	SequenceFeaturesI store = new SequenceFeatures();
25	1	assertFalse(store.hasFeatures());
26
27	1	store = new SequenceFeatures((List<SequenceFeature>) null);
28	1	assertFalse(store.hasFeatures());
29
30	1	List<SequenceFeature> features = new ArrayList<>();
31	1	store = new SequenceFeatures(features);
32	1	assertFalse(store.hasFeatures());
33
34	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
35		Float.NaN, null);
36	1	features.add(sf1);
37	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 15, 18,
38		Float.NaN, null);
39	1	features.add(sf2); // nested
40	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc2", 0, 0,
41		Float.NaN, null); // non-positional
42	1	features.add(sf3);
43	1	store = new SequenceFeatures(features);
44	1	assertTrue(store.hasFeatures());
45	1	assertEquals(2, store.getFeatureCount(true)); // positional
46	1	assertEquals(1, store.getFeatureCount(false)); // non-positional
47	1	assertFalse(store.add(sf1)); // already contained
48	1	assertFalse(store.add(sf2)); // already contained
49	1	assertFalse(store.add(sf3)); // already contained
50		}
51
		100% Uncovered Elements: 0 (48) Complexity: 1 Complexity Density: 0.02 1PASS
52	1	@Test(groups = "Functional")...
53		public void testGetPositionalFeatures()
54		{
55	1	SequenceFeaturesI store = new SequenceFeatures();
56	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
57		Float.NaN, null);
58	1	store.add(sf1);
59		// same range, different description
60	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20,
61		Float.NaN, null);
62	1	store.add(sf2);
63		// discontiguous range
64	1	SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 30, 40,
65		Float.NaN, null);
66	1	store.add(sf3);
67		// overlapping range
68	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 15, 35,
69		Float.NaN, null);
70	1	store.add(sf4);
71		// enclosing range
72	1	SequenceFeature sf5 = new SequenceFeature("Metal", "desc", 5, 50,
73		Float.NaN, null);
74	1	store.add(sf5);
75		// non-positional feature
76	1	SequenceFeature sf6 = new SequenceFeature("Metal", "desc", 0, 0,
77		Float.NaN, null);
78	1	store.add(sf6);
79		// contact feature
80	1	SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
81		18, 45, Float.NaN, null);
82	1	store.add(sf7);
83		// different feature type
84	1	SequenceFeature sf8 = new SequenceFeature("Pfam", "desc", 30, 40,
85		Float.NaN, null);
86	1	store.add(sf8);
87	1	SequenceFeature sf9 = new SequenceFeature("Pfam", "desc", 15, 35,
88		Float.NaN, null);
89	1	store.add(sf9);
90
91		/*
92		* get all positional features
93		*/
94	1	List<SequenceFeature> features = store.getPositionalFeatures();
95	1	assertEquals(features.size(), 8);
96	1	assertTrue(features.contains(sf1));
97	1	assertTrue(features.contains(sf2));
98	1	assertTrue(features.contains(sf3));
99	1	assertTrue(features.contains(sf4));
100	1	assertTrue(features.contains(sf5));
101	1	assertFalse(features.contains(sf6)); // non-positional
102	1	assertTrue(features.contains(sf7));
103	1	assertTrue(features.contains(sf8));
104	1	assertTrue(features.contains(sf9));
105
106		/*
107		* get features by type
108		*/
109	1	assertTrue(store.getPositionalFeatures((String) null).isEmpty());
110	1	assertTrue(store.getPositionalFeatures("Cath").isEmpty());
111	1	assertTrue(store.getPositionalFeatures("METAL").isEmpty());
112
113	1	features = store.getPositionalFeatures("Metal");
114	1	assertEquals(features.size(), 5);
115	1	assertTrue(features.contains(sf1));
116	1	assertTrue(features.contains(sf2));
117	1	assertTrue(features.contains(sf3));
118	1	assertTrue(features.contains(sf4));
119	1	assertTrue(features.contains(sf5));
120	1	assertFalse(features.contains(sf6));
121
122	1	features = store.getPositionalFeatures("Disulphide bond");
123	1	assertEquals(features.size(), 1);
124	1	assertTrue(features.contains(sf7));
125
126	1	features = store.getPositionalFeatures("Pfam");
127	1	assertEquals(features.size(), 2);
128	1	assertTrue(features.contains(sf8));
129	1	assertTrue(features.contains(sf9));
130		}
131
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
132	1	@Test(groups = "Functional")...
133		public void testGetContactFeatures()
134		{
135	1	SequenceFeaturesI store = new SequenceFeatures();
136		// non-contact
137	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
138		Float.NaN, null);
139	1	store.add(sf1);
140		// non-positional
141	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
142		Float.NaN, null);
143	1	store.add(sf2);
144		// contact feature
145	1	SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
146		18, 45, Float.NaN, null);
147	1	store.add(sf3);
148		// repeat for different feature type
149	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
150		Float.NaN, null);
151	1	store.add(sf4);
152	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
153		Float.NaN, null);
154	1	store.add(sf5);
155	1	SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
156		45, Float.NaN, null);
157	1	store.add(sf6);
158
159		/*
160		* get all contact features
161		*/
162	1	List<SequenceFeature> features = store.getContactFeatures();
163	1	assertEquals(features.size(), 2);
164	1	assertTrue(features.contains(sf3));
165	1	assertTrue(features.contains(sf6));
166
167		/*
168		* get contact features by type
169		*/
170	1	assertTrue(store.getContactFeatures((String) null).isEmpty());
171	1	assertTrue(store.getContactFeatures("Cath").isEmpty());
172	1	assertTrue(store.getContactFeatures("Pfam").isEmpty());
173	1	assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
174
175	1	features = store.getContactFeatures("Disulphide bond");
176	1	assertEquals(features.size(), 1);
177	1	assertTrue(features.contains(sf3));
178
179	1	features = store.getContactFeatures("Disulfide bond");
180	1	assertEquals(features.size(), 1);
181	1	assertTrue(features.contains(sf6));
182		}
183
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
184	1	@Test(groups = "Functional")...
185		public void testGetNonPositionalFeatures()
186		{
187	1	SequenceFeaturesI store = new SequenceFeatures();
188		// positional
189	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
190		Float.NaN, null);
191	1	store.add(sf1);
192		// non-positional
193	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
194		Float.NaN, null);
195	1	store.add(sf2);
196		// contact feature
197	1	SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
198		18, 45, Float.NaN, null);
199	1	store.add(sf3);
200		// repeat for different feature type
201	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
202		Float.NaN, null);
203	1	store.add(sf4);
204	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
205		Float.NaN, null);
206	1	store.add(sf5);
207	1	SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
208		45, Float.NaN, null);
209	1	store.add(sf6);
210		// one more non-positional, different description
211	1	SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0,
212		Float.NaN, null);
213	1	store.add(sf7);
214
215		/*
216		* get all non-positional features
217		*/
218	1	List<SequenceFeature> features = store.getNonPositionalFeatures();
219	1	assertEquals(features.size(), 3);
220	1	assertTrue(features.contains(sf2));
221	1	assertTrue(features.contains(sf5));
222	1	assertTrue(features.contains(sf7));
223
224		/*
225		* get non-positional features by type
226		*/
227	1	assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
228	1	assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
229	1	assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
230
231	1	features = store.getNonPositionalFeatures("Metal");
232	1	assertEquals(features.size(), 1);
233	1	assertTrue(features.contains(sf2));
234
235	1	features = store.getNonPositionalFeatures("Pfam");
236	1	assertEquals(features.size(), 2);
237	1	assertTrue(features.contains(sf5));
238	1	assertTrue(features.contains(sf7));
239		}
240
241		/**
242		* Helper method to add a feature of no particular type
243		*
244		* @param sf
245		* @param type
246		* @param from
247		* @param to
248		* @return
249		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
250	14	SequenceFeature addFeature(SequenceFeaturesI sf, String type, int from,...
251		int to)
252		{
253	14	SequenceFeature sf1 = new SequenceFeature(type, "", from, to,
254		Float.NaN,
255		null);
256	14	sf.add(sf1);
257	14	return sf1;
258		}
259
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
260	1	@Test(groups = "Functional")...
261		public void testFindFeatures()
262		{
263	1	SequenceFeaturesI sf = new SequenceFeatures();
264	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
265	1	SequenceFeature sf2 = addFeature(sf, "Pfam", 1, 15);
266	1	SequenceFeature sf3 = addFeature(sf, "Pfam", 20, 30);
267	1	SequenceFeature sf4 = addFeature(sf, "Pfam", 40, 100);
268	1	SequenceFeature sf5 = addFeature(sf, "Pfam", 60, 100);
269	1	SequenceFeature sf6 = addFeature(sf, "Pfam", 70, 70);
270	1	SequenceFeature sf7 = addFeature(sf, "Cath", 10, 50);
271	1	SequenceFeature sf8 = addFeature(sf, "Cath", 1, 15);
272	1	SequenceFeature sf9 = addFeature(sf, "Cath", 20, 30);
273	1	SequenceFeature sf10 = addFeature(sf, "Cath", 40, 100);
274	1	SequenceFeature sf11 = addFeature(sf, "Cath", 60, 100);
275	1	SequenceFeature sf12 = addFeature(sf, "Cath", 70, 70);
276
277	1	List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
278	1	assertTrue(overlaps.isEmpty());
279
280	1	overlaps = sf.findFeatures( 1, 9, "Pfam");
281	1	assertEquals(overlaps.size(), 1);
282	1	assertTrue(overlaps.contains(sf2));
283
284	1	overlaps = sf.findFeatures( 5, 18, "Pfam");
285	1	assertEquals(overlaps.size(), 2);
286	1	assertTrue(overlaps.contains(sf1));
287	1	assertTrue(overlaps.contains(sf2));
288
289	1	overlaps = sf.findFeatures(30, 40, "Pfam");
290	1	assertEquals(overlaps.size(), 3);
291	1	assertTrue(overlaps.contains(sf1));
292	1	assertTrue(overlaps.contains(sf3));
293	1	assertTrue(overlaps.contains(sf4));
294
295	1	overlaps = sf.findFeatures( 80, 90, "Pfam");
296	1	assertEquals(overlaps.size(), 2);
297	1	assertTrue(overlaps.contains(sf4));
298	1	assertTrue(overlaps.contains(sf5));
299
300	1	overlaps = sf.findFeatures( 68, 70, "Pfam");
301	1	assertEquals(overlaps.size(), 3);
302	1	assertTrue(overlaps.contains(sf4));
303	1	assertTrue(overlaps.contains(sf5));
304	1	assertTrue(overlaps.contains(sf6));
305
306	1	overlaps = sf.findFeatures(16, 69, "Cath");
307	1	assertEquals(overlaps.size(), 4);
308	1	assertTrue(overlaps.contains(sf7));
309	1	assertFalse(overlaps.contains(sf8));
310	1	assertTrue(overlaps.contains(sf9));
311	1	assertTrue(overlaps.contains(sf10));
312	1	assertTrue(overlaps.contains(sf11));
313	1	assertFalse(overlaps.contains(sf12));
314
315	1	assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());
316
317	1	overlaps = sf.findFeatures(7, 7, (String) null);
318	1	assertTrue(overlaps.isEmpty());
319		}
320
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
321	1	@Test(groups = "Functional")...
322		public void testDelete()
323		{
324	1	SequenceFeaturesI sf = new SequenceFeatures();
325	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
326	1	assertTrue(sf.getPositionalFeatures().contains(sf1));
327
328	1	assertFalse(sf.delete(null));
329	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 15, 0f, null);
330	1	assertFalse(sf.delete(sf2)); // not added, can't delete it
331	1	assertTrue(sf.delete(sf1));
332	1	assertTrue(sf.getPositionalFeatures().isEmpty());
333		}
334
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
335	1	@Test(groups = "Functional")...
336		public void testHasFeatures()
337		{
338	1	SequenceFeaturesI sf = new SequenceFeatures();
339	1	assertFalse(sf.hasFeatures());
340
341	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
342	1	assertTrue(sf.hasFeatures());
343
344	1	sf.delete(sf1);
345	1	assertFalse(sf.hasFeatures());
346		}
347
348		/**
349		* Tests for the method that gets feature groups for positional or
350		* non-positional features
351		*/
		100% Uncovered Elements: 0 (60) Complexity: 1 Complexity Density: 0.02 1PASS
352	1	@Test(groups = "Functional")...
353		public void testGetFeatureGroups()
354		{
355	1	SequenceFeaturesI sf = new SequenceFeatures();
356	1	assertTrue(sf.getFeatureGroups(true).isEmpty());
357	1	assertTrue(sf.getFeatureGroups(false).isEmpty());
358
359		/*
360		* add a non-positional feature (begin/end = 0/0)
361		*/
362	1	SequenceFeature sfx = new SequenceFeature("AType", "Desc", 0, 0, 0f,
363		"AGroup");
364	1	sf.add(sfx);
365	1	Set<String> groups = sf.getFeatureGroups(true); // for positional
366	1	assertTrue(groups.isEmpty());
367	1	groups = sf.getFeatureGroups(false); // for non-positional
368	1	assertEquals(groups.size(), 1);
369	1	assertTrue(groups.contains("AGroup"));
370	1	groups = sf.getFeatureGroups(false, "AType");
371	1	assertEquals(groups.size(), 1);
372	1	assertTrue(groups.contains("AGroup"));
373	1	groups = sf.getFeatureGroups(true, "AnotherType");
374	1	assertTrue(groups.isEmpty());
375
376		/*
377		* add, then delete, more non-positional features of different types
378		*/
379	1	SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0,
380		0f,
381		"AnotherGroup");
382	1	sf.add(sfy);
383	1	SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0,
384		0f,
385		null);
386	1	sf.add(sfz);
387	1	groups = sf.getFeatureGroups(false);
388	1	assertEquals(groups.size(), 3);
389	1	assertTrue(groups.contains("AGroup"));
390	1	assertTrue(groups.contains("AnotherGroup"));
391	1	assertTrue(groups.contains(null)); // null is a possible group
392	1	sf.delete(sfz);
393	1	sf.delete(sfy);
394	1	groups = sf.getFeatureGroups(false);
395	1	assertEquals(groups.size(), 1);
396	1	assertTrue(groups.contains("AGroup"));
397
398		/*
399		* add positional features
400		*/
401	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "Desc", 10, 50, 0f,
402		"PfamGroup");
403	1	sf.add(sf1);
404	1	groups = sf.getFeatureGroups(true);
405	1	assertEquals(groups.size(), 1);
406	1	assertTrue(groups.contains("PfamGroup"));
407	1	groups = sf.getFeatureGroups(false); // non-positional unchanged
408	1	assertEquals(groups.size(), 1);
409	1	assertTrue(groups.contains("AGroup"));
410
411	1	SequenceFeature sf2 = new SequenceFeature("Cath", "Desc", 10, 50, 0f,
412		null);
413	1	sf.add(sf2);
414	1	groups = sf.getFeatureGroups(true);
415	1	assertEquals(groups.size(), 2);
416	1	assertTrue(groups.contains("PfamGroup"));
417	1	assertTrue(groups.contains(null));
418
419	1	sf.delete(sf1);
420	1	sf.delete(sf2);
421	1	assertTrue(sf.getFeatureGroups(true).isEmpty());
422
423	1	SequenceFeature sf3 = new SequenceFeature("CDS", "", 10, 50, 0f,
424		"Ensembl");
425	1	sf.add(sf3);
426	1	SequenceFeature sf4 = new SequenceFeature("exon", "", 10, 50, 0f,
427		"Ensembl");
428	1	sf.add(sf4);
429	1	groups = sf.getFeatureGroups(true);
430	1	assertEquals(groups.size(), 1);
431	1	assertTrue(groups.contains("Ensembl"));
432
433		/*
434		* delete last Ensembl group feature from CDS features
435		* but still have one in exon features
436		*/
437	1	sf.delete(sf3);
438	1	groups = sf.getFeatureGroups(true);
439	1	assertEquals(groups.size(), 1);
440	1	assertTrue(groups.contains("Ensembl"));
441
442		/*
443		* delete the last non-positional feature
444		*/
445	1	sf.delete(sfx);
446	1	groups = sf.getFeatureGroups(false);
447	1	assertTrue(groups.isEmpty());
448		}
449
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
450	1	@Test(groups = "Functional")...
451		public void testGetFeatureTypesForGroups()
452		{
453	1	SequenceFeaturesI sf = new SequenceFeatures();
454	1	assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
455
456		/*
457		* add feature with group = "Uniprot", type = "helix"
458		*/
459	1	String groupUniprot = "Uniprot";
460	1	SequenceFeature sf1 = new SequenceFeature("helix", "Desc", 10, 50, 0f,
461		groupUniprot);
462	1	sf.add(sf1);
463	1	Set<String> groups = sf.getFeatureTypesForGroups(true, groupUniprot);
464	1	assertEquals(groups.size(), 1);
465	1	assertTrue(groups.contains("helix"));
466	1	assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
467
468		/*
469		* add feature with group = "Uniprot", type = "strand"
470		*/
471	1	SequenceFeature sf2 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
472		groupUniprot);
473	1	sf.add(sf2);
474	1	groups = sf.getFeatureTypesForGroups(true, groupUniprot);
475	1	assertEquals(groups.size(), 2);
476	1	assertTrue(groups.contains("helix"));
477	1	assertTrue(groups.contains("strand"));
478
479		/*
480		* delete the "strand" Uniprot feature - still have "helix"
481		*/
482	1	sf.delete(sf2);
483	1	groups = sf.getFeatureTypesForGroups(true, groupUniprot);
484	1	assertEquals(groups.size(), 1);
485	1	assertTrue(groups.contains("helix"));
486
487		/*
488		* delete the "helix" Uniprot feature - none left
489		*/
490	1	sf.delete(sf1);
491	1	assertTrue(sf.getFeatureTypesForGroups(true, groupUniprot).isEmpty());
492
493		/*
494		* add some null group features
495		*/
496	1	SequenceFeature sf3 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
497		null);
498	1	sf.add(sf3);
499	1	SequenceFeature sf4 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
500		null);
501	1	sf.add(sf4);
502	1	groups = sf.getFeatureTypesForGroups(true, (String) null);
503	1	assertEquals(groups.size(), 2);
504	1	assertTrue(groups.contains("strand"));
505	1	assertTrue(groups.contains("turn"));
506
507		/*
508		* add strand/Cath and turn/Scop and query for one or both groups
509		* (find feature types for groups selected in Feature Settings)
510		*/
511	1	SequenceFeature sf5 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
512		"Cath");
513	1	sf.add(sf5);
514	1	SequenceFeature sf6 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
515		"Scop");
516	1	sf.add(sf6);
517	1	groups = sf.getFeatureTypesForGroups(true, "Cath");
518	1	assertEquals(groups.size(), 1);
519	1	assertTrue(groups.contains("strand"));
520	1	groups = sf.getFeatureTypesForGroups(true, "Scop");
521	1	assertEquals(groups.size(), 1);
522	1	assertTrue(groups.contains("turn"));
523	1	groups = sf.getFeatureTypesForGroups(true, "Cath", "Scop");
524	1	assertEquals(groups.size(), 2);
525	1	assertTrue(groups.contains("turn"));
526	1	assertTrue(groups.contains("strand"));
527		// alternative vararg syntax
528	1	groups = sf.getFeatureTypesForGroups(true, new String[] { "Cath",
529		"Scop" });
530	1	assertEquals(groups.size(), 2);
531	1	assertTrue(groups.contains("turn"));
532	1	assertTrue(groups.contains("strand"));
533		}
534
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
535	1	@Test(groups = "Functional")...
536		public void testGetFeatureTypes()
537		{
538	1	SequenceFeaturesI store = new SequenceFeatures();
539	1	Set<String> types = store.getFeatureTypes();
540	1	assertTrue(types.isEmpty());
541
542	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
543		Float.NaN, null);
544	1	store.add(sf1);
545	1	types = store.getFeatureTypes();
546	1	assertEquals(types.size(), 1);
547	1	assertTrue(types.contains("Metal"));
548
549		// null type is rejected...
550	1	SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
551		Float.NaN, null);
552	1	assertFalse(store.add(sf2));
553	1	types = store.getFeatureTypes();
554	1	assertEquals(types.size(), 1);
555	1	assertFalse(types.contains(null));
556	1	assertTrue(types.contains("Metal"));
557
558		/*
559		* add non-positional feature
560		*/
561	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
562		Float.NaN, null);
563	1	store.add(sf3);
564	1	types = store.getFeatureTypes();
565	1	assertEquals(types.size(), 2);
566	1	assertTrue(types.contains("Pfam"));
567
568		/*
569		* add contact feature
570		*/
571	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
572		10, 20, Float.NaN, null);
573	1	store.add(sf4);
574	1	types = store.getFeatureTypes();
575	1	assertEquals(types.size(), 3);
576	1	assertTrue(types.contains("Disulphide Bond"));
577
578		/*
579		* add another Pfam
580		*/
581	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
582		Float.NaN, null);
583	1	store.add(sf5);
584	1	types = store.getFeatureTypes();
585	1	assertEquals(types.size(), 3); // unchanged
586
587		/*
588		* delete first Pfam - still have one
589		*/
590	1	assertTrue(store.delete(sf3));
591	1	types = store.getFeatureTypes();
592	1	assertEquals(types.size(), 3);
593	1	assertTrue(types.contains("Pfam"));
594
595		/*
596		* delete second Pfam - no longer have one
597		*/
598	1	assertTrue(store.delete(sf5));
599	1	types = store.getFeatureTypes();
600	1	assertEquals(types.size(), 2);
601	1	assertFalse(types.contains("Pfam"));
602		}
603
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
604	1	@Test(groups = "Functional")...
605		public void testGetFeatureCount()
606		{
607	1	SequenceFeaturesI store = new SequenceFeatures();
608	1	assertEquals(store.getFeatureCount(true), 0);
609	1	assertEquals(store.getFeatureCount(false), 0);
610
611		/*
612		* add positional
613		*/
614	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
615		Float.NaN, null);
616	1	store.add(sf1);
617	1	assertEquals(store.getFeatureCount(true), 1);
618	1	assertEquals(store.getFeatureCount(false), 0);
619
620		/*
621		* null feature type is rejected
622		*/
623	1	SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
624		Float.NaN, null);
625	1	assertFalse(store.add(sf2));
626	1	assertEquals(store.getFeatureCount(true), 1);
627	1	assertEquals(store.getFeatureCount(false), 0);
628
629		/*
630		* add non-positional feature
631		*/
632	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
633		Float.NaN, null);
634	1	store.add(sf3);
635	1	assertEquals(store.getFeatureCount(true), 1);
636	1	assertEquals(store.getFeatureCount(false), 1);
637
638		/*
639		* add contact feature (counts as 1)
640		*/
641	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
642		10, 20, Float.NaN, null);
643	1	store.add(sf4);
644	1	assertEquals(store.getFeatureCount(true), 2);
645	1	assertEquals(store.getFeatureCount(false), 1);
646
647		/*
648		* add another Pfam but this time as a positional feature
649		*/
650	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
651		Float.NaN, null);
652	1	store.add(sf5);
653	1	assertEquals(store.getFeatureCount(true), 3); // sf1, sf4, sf5
654	1	assertEquals(store.getFeatureCount(false), 1); // sf3
655	1	assertEquals(store.getFeatureCount(true, "Pfam"), 1); // positional
656	1	assertEquals(store.getFeatureCount(false, "Pfam"), 1); // non-positional
657		// search for type==null
658	1	assertEquals(store.getFeatureCount(true, (String) null), 0);
659		// search with no type specified
660	1	assertEquals(store.getFeatureCount(true, (String[]) null), 3);
661	1	assertEquals(store.getFeatureCount(true, "Metal", "Cath"), 1);
662	1	assertEquals(store.getFeatureCount(true, "Disulphide Bond"), 1);
663	1	assertEquals(store.getFeatureCount(true, "Metal", "Pfam", null), 2);
664
665		/*
666		* delete first Pfam (non-positional)
667		*/
668	1	assertTrue(store.delete(sf3));
669	1	assertEquals(store.getFeatureCount(true), 3);
670	1	assertEquals(store.getFeatureCount(false), 0);
671
672		/*
673		* delete second Pfam (positional)
674		*/
675	1	assertTrue(store.delete(sf5));
676	1	assertEquals(store.getFeatureCount(true), 2);
677	1	assertEquals(store.getFeatureCount(false), 0);
678		}
679
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
680	1	@Test(groups = "Functional")...
681		public void testGetAllFeatures()
682		{
683	1	SequenceFeaturesI store = new SequenceFeatures();
684	1	List<SequenceFeature> features = store.getAllFeatures();
685	1	assertTrue(features.isEmpty());
686
687	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
688		Float.NaN, null);
689	1	store.add(sf1);
690	1	features = store.getAllFeatures();
691	1	assertEquals(features.size(), 1);
692	1	assertTrue(features.contains(sf1));
693
694	1	SequenceFeature sf2 = new SequenceFeature("Metallic", "desc", 10, 20,
695		Float.NaN, null);
696	1	store.add(sf2);
697	1	features = store.getAllFeatures();
698	1	assertEquals(features.size(), 2);
699	1	assertTrue(features.contains(sf2));
700
701		/*
702		* add non-positional feature
703		*/
704	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
705		Float.NaN, null);
706	1	store.add(sf3);
707	1	features = store.getAllFeatures();
708	1	assertEquals(features.size(), 3);
709	1	assertTrue(features.contains(sf3));
710
711		/*
712		* add contact feature
713		*/
714	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
715		10, 20, Float.NaN, null);
716	1	store.add(sf4);
717	1	features = store.getAllFeatures();
718	1	assertEquals(features.size(), 4);
719	1	assertTrue(features.contains(sf4));
720
721		/*
722		* add another Pfam
723		*/
724	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
725		Float.NaN, null);
726	1	store.add(sf5);
727	1	features = store.getAllFeatures();
728	1	assertEquals(features.size(), 5);
729	1	assertTrue(features.contains(sf5));
730
731		/*
732		* select by type does not apply to non-positional features
733		*/
734	1	features = store.getAllFeatures("Cath");
735	1	assertEquals(features.size(), 1);
736	1	assertTrue(features.contains(sf3));
737
738	1	features = store.getAllFeatures("Pfam", "Cath", "Metal");
739	1	assertEquals(features.size(), 3);
740	1	assertTrue(features.contains(sf1));
741	1	assertTrue(features.contains(sf3));
742	1	assertTrue(features.contains(sf5));
743
744		/*
745		* delete first Pfam
746		*/
747	1	assertTrue(store.delete(sf3));
748	1	features = store.getAllFeatures();
749	1	assertEquals(features.size(), 4);
750	1	assertFalse(features.contains(sf3));
751
752		/*
753		* delete second Pfam
754		*/
755	1	assertTrue(store.delete(sf5));
756	1	features = store.getAllFeatures();
757	1	assertEquals(features.size(), 3);
758	1	assertFalse(features.contains(sf3));
759		}
760
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
761	1	@Test(groups = "Functional")...
762		public void testGetTotalFeatureLength()
763		{
764	1	SequenceFeaturesI store = new SequenceFeatures();
765	1	assertEquals(store.getTotalFeatureLength(), 0);
766
767	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
768		Float.NaN, null);
769	1	assertTrue(store.add(sf1));
770	1	assertEquals(store.getTotalFeatureLength(), 11);
771	1	assertEquals(store.getTotalFeatureLength("Metal"), 11);
772	1	assertEquals(store.getTotalFeatureLength("Plastic"), 0);
773
774		// re-add does nothing!
775	1	assertFalse(store.add(sf1));
776	1	assertEquals(store.getTotalFeatureLength(), 11);
777
778		/*
779		* add non-positional feature
780		*/
781	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
782		Float.NaN, null);
783	1	store.add(sf3);
784	1	assertEquals(store.getTotalFeatureLength(), 11);
785
786		/*
787		* add contact feature - counts 1 to feature length
788		*/
789	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
790		10, 20, Float.NaN, null);
791	1	store.add(sf4);
792	1	assertEquals(store.getTotalFeatureLength(), 12);
793
794		/*
795		* add another Pfam
796		*/
797	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
798		Float.NaN, null);
799	1	store.add(sf5);
800	1	assertEquals(store.getTotalFeatureLength(), 23);
801
802		/*
803		* delete features
804		*/
805	1	assertTrue(store.delete(sf3)); // non-positional
806	1	assertEquals(store.getTotalFeatureLength(), 23); // no change
807
808	1	assertTrue(store.delete(sf5));
809	1	assertEquals(store.getTotalFeatureLength(), 12);
810
811	1	assertTrue(store.delete(sf4)); // contact
812	1	assertEquals(store.getTotalFeatureLength(), 11);
813
814	1	assertTrue(store.delete(sf1));
815	1	assertEquals(store.getTotalFeatureLength(), 0);
816		}
817
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
818	1	@Test(groups = "Functional")...
819		public void testGetMinimumScore_getMaximumScore()
820		{
821	1	SequenceFeatures sf = new SequenceFeatures();
822	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 0, 0,
823		Float.NaN, "group"); // non-positional, no score
824	1	sf.add(sf1);
825	1	SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 10, 20,
826		Float.NaN, "group"); // positional, no score
827	1	sf.add(sf2);
828	1	SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 10, 20, 1f,
829		"group");
830	1	sf.add(sf3);
831	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 12, 16, 4f,
832		"group");
833	1	sf.add(sf4);
834	1	SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 0, 0, 11f,
835		"group");
836	1	sf.add(sf5);
837	1	SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, -7f,
838		"group");
839	1	sf.add(sf6);
840
841	1	assertEquals(sf.getMinimumScore("nosuchtype", true), Float.NaN);
842	1	assertEquals(sf.getMinimumScore("nosuchtype", false), Float.NaN);
843	1	assertEquals(sf.getMaximumScore("nosuchtype", true), Float.NaN);
844	1	assertEquals(sf.getMaximumScore("nosuchtype", false), Float.NaN);
845
846		// positional features min-max:
847	1	assertEquals(sf.getMinimumScore("Metal", true), 1f);
848	1	assertEquals(sf.getMaximumScore("Metal", true), 4f);
849	1	assertEquals(sf.getMinimumScore("Cath", true), Float.NaN);
850	1	assertEquals(sf.getMaximumScore("Cath", true), Float.NaN);
851
852		// non-positional features min-max:
853	1	assertEquals(sf.getMinimumScore("Cath", false), -7f);
854	1	assertEquals(sf.getMaximumScore("Cath", false), 11f);
855	1	assertEquals(sf.getMinimumScore("Metal", false), Float.NaN);
856	1	assertEquals(sf.getMaximumScore("Metal", false), Float.NaN);
857
858		// delete features; min-max should get recomputed
859	1	sf.delete(sf6);
860	1	assertEquals(sf.getMinimumScore("Cath", false), 11f);
861	1	assertEquals(sf.getMaximumScore("Cath", false), 11f);
862	1	sf.delete(sf4);
863	1	assertEquals(sf.getMinimumScore("Metal", true), 1f);
864	1	assertEquals(sf.getMaximumScore("Metal", true), 1f);
865	1	sf.delete(sf5);
866	1	assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
867	1	assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
868	1	sf.delete(sf3);
869	1	assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
870	1	assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
871	1	sf.delete(sf1);
872	1	sf.delete(sf2);
873	1	assertFalse(sf.hasFeatures());
874	1	assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
875	1	assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
876	1	assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
877	1	assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
878		}
879
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
880	1	@Test(groups = "Functional")...
881		public void testVarargsToTypes()
882		{
883	1	SequenceFeatures sf = new SequenceFeatures();
884	1	sf.add(new SequenceFeature("Metal", "desc", 0, 0, Float.NaN, "group"));
885	1	sf.add(new SequenceFeature("Cath", "desc", 10, 20, Float.NaN, "group"));
886
887		/*
888		* no type specified - get all types stored
889		* they are returned in keyset (alphabetical) order
890		*/
891	1	Map<String, FeatureStore> featureStores = (Map<String, FeatureStore>) PA
892		.getValue(sf, "featureStore");
893
894	1	Iterable<FeatureStore> types = sf.varargToTypes();
895	1	Iterator<FeatureStore> iterator = types.iterator();
896	1	assertTrue(iterator.hasNext());
897	1	assertSame(iterator.next(), featureStores.get("Cath"));
898	1	assertTrue(iterator.hasNext());
899	1	assertSame(iterator.next(), featureStores.get("Metal"));
900	1	assertFalse(iterator.hasNext());
901
902		/*
903		* empty array is the same as no vararg parameter supplied
904		* so treated as all stored types
905		*/
906	1	types = sf.varargToTypes(new String[] {});
907	1	iterator = types.iterator();
908	1	assertTrue(iterator.hasNext());
909	1	assertSame(iterator.next(), featureStores.get("Cath"));
910	1	assertTrue(iterator.hasNext());
911	1	assertSame(iterator.next(), featureStores.get("Metal"));
912	1	assertFalse(iterator.hasNext());
913
914		/*
915		* null type specified; this is passed as vararg
916		* String[1] {null}
917		*/
918	1	types = sf.varargToTypes((String) null);
919	1	assertFalse(types.iterator().hasNext());
920
921		/*
922		* null types array specified; this is passed as vararg null
923		*/
924	1	types = sf.varargToTypes((String[]) null);
925	1	iterator = types.iterator();
926	1	assertTrue(iterator.hasNext());
927	1	assertSame(iterator.next(), featureStores.get("Cath"));
928	1	assertTrue(iterator.hasNext());
929	1	assertSame(iterator.next(), featureStores.get("Metal"));
930	1	assertFalse(iterator.hasNext());
931
932		/*
933		* one type specified
934		*/
935	1	types = sf.varargToTypes("Metal");
936	1	iterator = types.iterator();
937	1	assertTrue(iterator.hasNext());
938	1	assertSame(iterator.next(), featureStores.get("Metal"));
939	1	assertFalse(iterator.hasNext());
940
941		/*
942		* two types specified - order is preserved
943		*/
944	1	types = sf.varargToTypes("Metal", "Cath");
945	1	iterator = types.iterator();
946	1	assertTrue(iterator.hasNext());
947	1	assertSame(iterator.next(), featureStores.get("Metal"));
948	1	assertTrue(iterator.hasNext());
949	1	assertSame(iterator.next(), featureStores.get("Cath"));
950	1	assertFalse(iterator.hasNext());
951
952		/*
953		* null type included - should be ignored
954		*/
955	1	types = sf.varargToTypes("Metal", null, "Helix");
956	1	iterator = types.iterator();
957	1	assertTrue(iterator.hasNext());
958	1	assertSame(iterator.next(), featureStores.get("Metal"));
959	1	assertFalse(iterator.hasNext());
960		}
961
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
962	1	@Test(groups = "Functional")...
963		public void testGetFeatureTypes_byOntology()
964		{
965	1	SequenceFeaturesI store = new SequenceFeatures();
966
967	1	SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
968		Float.NaN, null);
969	1	store.add(sf1);
970		// mRNA isA mature_transcript isA transcript
971	1	SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 10, 20,
972		Float.NaN, null);
973	1	store.add(sf2);
974		// just to prove non-positional feature types are included
975	1	SequenceFeature sf3 = new SequenceFeature("mRNA", "desc", 0, 0,
976		Float.NaN, null);
977	1	store.add(sf3);
978	1	SequenceFeature sf4 = new SequenceFeature("CDS", "desc", 0, 0,
979		Float.NaN, null);
980	1	store.add(sf4);
981
982	1	Set<String> types = store.getFeatureTypes("transcript");
983	1	assertEquals(types.size(), 2);
984	1	assertTrue(types.contains("transcript"));
985	1	assertTrue(types.contains("mRNA"));
986
987		// matches include arguments whether SO terms or not
988	1	types = store.getFeatureTypes("transcript", "CDS");
989	1	assertEquals(types.size(), 3);
990	1	assertTrue(types.contains("transcript"));
991	1	assertTrue(types.contains("mRNA"));
992	1	assertTrue(types.contains("CDS"));
993
994	1	types = store.getFeatureTypes("exon");
995	1	assertTrue(types.isEmpty());
996		}
997
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
998	1	@Test(groups = "Functional")...
999		public void testGetFeaturesByOntology()
1000		{
1001	1	SequenceFeaturesI store = new SequenceFeatures();
1002	1	List<SequenceFeature> features = store.getFeaturesByOntology();
1003	1	assertTrue(features.isEmpty());
1004	1	assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty());
1005	1	assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty());
1006
1007	1	SequenceFeature transcriptFeature = new SequenceFeature("transcript", "desc", 10, 20,
1008		Float.NaN, null);
1009	1	store.add(transcriptFeature);
1010
1011		/*
1012		* mRNA is a sub-type of transcript; added here 'as if' non-positional
1013		* just to show that non-positional features are included in results
1014		*/
1015	1	SequenceFeature mrnaFeature = new SequenceFeature("mRNA", "desc", 0, 0,
1016		Float.NaN, null);
1017	1	store.add(mrnaFeature);
1018
1019	1	SequenceFeature pfamFeature = new SequenceFeature("Pfam", "desc", 30, 40,
1020		Float.NaN, null);
1021	1	store.add(pfamFeature);
1022
1023		/*
1024		* "transcript" matches both itself and the sub-term "mRNA"
1025		*/
1026	1	features = store.getFeaturesByOntology("transcript");
1027	1	assertEquals(features.size(), 2);
1028	1	assertTrue(features.contains(transcriptFeature));
1029	1	assertTrue(features.contains(mrnaFeature));
1030
1031		/*
1032		* "mRNA" matches itself but not parent term "transcript"
1033		*/
1034	1	features = store.getFeaturesByOntology("mRNA");
1035	1	assertEquals(features.size(), 1);
1036	1	assertTrue(features.contains(mrnaFeature));
1037
1038		/*
1039		* "pfam" is not an SO term but is included as an exact match
1040		*/
1041	1	features = store.getFeaturesByOntology("mRNA", "Pfam");
1042	1	assertEquals(features.size(), 2);
1043	1	assertTrue(features.contains(mrnaFeature));
1044	1	assertTrue(features.contains(pfamFeature));
1045
1046	1	features = store.getFeaturesByOntology("sequence_variant");
1047	1	assertTrue(features.isEmpty());
1048		}
1049
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
1050	1	@Test(groups = "Functional")...
1051		public void testSortFeatures()
1052		{
1053	1	List<SequenceFeature> sfs = new ArrayList<>();
1054	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30,
1055		60,
1056		Float.NaN, null);
1057	1	sfs.add(sf1);
1058	1	SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
1059		Float.NaN, null);
1060	1	sfs.add(sf2);
1061	1	SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
1062		Float.NaN, null);
1063	1	sfs.add(sf3);
1064	1	SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30,
1065		80,
1066		Float.NaN, null);
1067	1	sfs.add(sf4);
1068	1	SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30,
1069		90,
1070		Float.NaN, null);
1071	1	sfs.add(sf5);
1072
1073		/*
1074		* sort by end position descending, order unchanged if matched
1075		*/
1076	1	SequenceFeatures.sortFeatures(sfs, false);
1077	1	assertSame(sfs.get(0), sf5); // end 90
1078	1	assertSame(sfs.get(1), sf4); // end 80
1079	1	assertSame(sfs.get(2), sf1); // end 60, start 50
1080	1	assertSame(sfs.get(3), sf3); // end 60, start 30
1081	1	assertSame(sfs.get(4), sf2); // end 50
1082
1083		/*
1084		* resort {5, 4, 1, 3, 2} by start position ascending, end descending
1085		*/
1086	1	SequenceFeatures.sortFeatures(sfs, true);
1087	1	assertSame(sfs.get(0), sf5); // start 30, end 90
1088	1	assertSame(sfs.get(1), sf4); // start 30, end 80
1089	1	assertSame(sfs.get(2), sf1); // start 30, end 60
1090	1	assertSame(sfs.get(3), sf2); // start 40
1091	1	assertSame(sfs.get(4), sf3); // start 50
1092		}
1093
		100% Uncovered Elements: 0 (50) Complexity: 1 Complexity Density: 0.02 1PASS
1094	1	@Test(groups = "Functional")...
1095		public void testGetFeaturesForGroup()
1096		{
1097	1	SequenceFeaturesI store = new SequenceFeatures();
1098
1099	1	List<SequenceFeature> features = store.getFeaturesForGroup(true, null);
1100	1	assertTrue(features.isEmpty());
1101	1	assertTrue(store.getFeaturesForGroup(false, null).isEmpty());
1102	1	assertTrue(store.getFeaturesForGroup(true, "Uniprot").isEmpty());
1103	1	assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
1104
1105	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
1106		null);
1107	1	SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
1108		null);
1109	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
1110		"Uniprot");
1111	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 0, 0, 0f,
1112		"Rfam");
1113	1	SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 5, 15, 0f,
1114		null);
1115	1	store.add(sf1);
1116	1	store.add(sf2);
1117	1	store.add(sf3);
1118	1	store.add(sf4);
1119	1	store.add(sf5);
1120
1121		// positional features for null group, any type
1122	1	features = store.getFeaturesForGroup(true, null);
1123	1	assertEquals(features.size(), 2);
1124	1	assertTrue(features.contains(sf1));
1125	1	assertTrue(features.contains(sf5));
1126
1127		// positional features for null group, specified type
1128	1	features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
1129		"Xfam" });
1130	1	assertEquals(features.size(), 1);
1131	1	assertTrue(features.contains(sf1));
1132	1	features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
1133		"Xfam", "Cath" });
1134	1	assertEquals(features.size(), 2);
1135	1	assertTrue(features.contains(sf1));
1136	1	assertTrue(features.contains(sf5));
1137
1138		// positional features for non-null group, any type
1139	1	features = store.getFeaturesForGroup(true, "Uniprot");
1140	1	assertEquals(features.size(), 1);
1141	1	assertTrue(features.contains(sf3));
1142	1	assertTrue(store.getFeaturesForGroup(true, "Rfam").isEmpty());
1143
1144		// positional features for non-null group, specified type
1145	1	features = store.getFeaturesForGroup(true, "Uniprot", "Pfam", "Xfam",
1146		"Rfam");
1147	1	assertEquals(features.size(), 1);
1148	1	assertTrue(features.contains(sf3));
1149	1	assertTrue(store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty());
1150
1151		// non-positional features for null group, any type
1152	1	features = store.getFeaturesForGroup(false, null);
1153	1	assertEquals(features.size(), 1);
1154	1	assertTrue(features.contains(sf2));
1155
1156		// non-positional features for null group, specified type
1157	1	features = store.getFeaturesForGroup(false, null, "Pfam", "Xfam");
1158	1	assertEquals(features.size(), 1);
1159	1	assertTrue(features.contains(sf2));
1160	1	assertTrue(store.getFeaturesForGroup(false, null, "Cath").isEmpty());
1161
1162		// non-positional features for non-null group, any type
1163	1	features = store.getFeaturesForGroup(false, "Rfam");
1164	1	assertEquals(features.size(), 1);
1165	1	assertTrue(features.contains(sf4));
1166	1	assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
1167
1168		// non-positional features for non-null group, specified type
1169	1	features = store.getFeaturesForGroup(false, "Rfam", "Pfam", "Metal");
1170	1	assertEquals(features.size(), 1);
1171	1	assertTrue(features.contains(sf4));
1172	1	assertTrue(store.getFeaturesForGroup(false, "Rfam", "Cath", "Pfam")
1173		.isEmpty());
1174		}
1175
		100% Uncovered Elements: 0 (57) Complexity: 1 Complexity Density: 0.02 1PASS
1176	1	@Test(groups = "Functional")...
1177		public void testShiftFeatures()
1178		{
1179	1	SequenceFeatures store = new SequenceFeatures();
1180	1	assertFalse(store.shiftFeatures(0, 1));
1181
1182	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
1183	1	store.add(sf1);
1184		// nested feature:
1185	1	SequenceFeature sf2 = new SequenceFeature("Metal", "", 8, 14, 0f, null);
1186	1	store.add(sf2);
1187		// contact feature:
1188	1	SequenceFeature sf3 = new SequenceFeature("Disulfide bond", "", 23, 32,
1189		0f, null);
1190	1	store.add(sf3);
1191		// non-positional feature:
1192	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "", 0, 0, 0f, null);
1193	1	store.add(sf4);
1194
1195		/*
1196		* shift features right by 5
1197		*/
1198	1	assertTrue(store.shiftFeatures(0, 5));
1199
1200		// non-positional features untouched:
1201	1	List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
1202	1	assertEquals(nonPos.size(), 1);
1203	1	assertTrue(nonPos.contains(sf4));
1204
1205		// positional features are replaced
1206	1	List<SequenceFeature> pos = store.getPositionalFeatures();
1207	1	assertEquals(pos.size(), 3);
1208	1	assertFalse(pos.contains(sf1));
1209	1	assertFalse(pos.contains(sf2));
1210	1	assertFalse(pos.contains(sf3));
1211	1	SequenceFeatures.sortFeatures(pos, true); // ascending start pos
1212	1	assertEquals(pos.get(0).getBegin(), 7);
1213	1	assertEquals(pos.get(0).getEnd(), 10);
1214	1	assertEquals(pos.get(0).getType(), "Cath");
1215	1	assertEquals(pos.get(1).getBegin(), 13);
1216	1	assertEquals(pos.get(1).getEnd(), 19);
1217	1	assertEquals(pos.get(1).getType(), "Metal");
1218	1	assertEquals(pos.get(2).getBegin(), 28);
1219	1	assertEquals(pos.get(2).getEnd(), 37);
1220	1	assertEquals(pos.get(2).getType(), "Disulfide bond");
1221
1222		/*
1223		* now shift left by 15
1224		* feature at [7-10] should be removed
1225		* feature at [13-19] should become [1-4]
1226		*/
1227	1	assertTrue(store.shiftFeatures(0, -15));
1228	1	pos = store.getPositionalFeatures();
1229	1	assertEquals(pos.size(), 2);
1230	1	SequenceFeatures.sortFeatures(pos, true);
1231	1	assertEquals(pos.get(0).getBegin(), 1);
1232	1	assertEquals(pos.get(0).getEnd(), 4);
1233	1	assertEquals(pos.get(0).getType(), "Metal");
1234	1	assertEquals(pos.get(1).getBegin(), 13);
1235	1	assertEquals(pos.get(1).getEnd(), 22);
1236	1	assertEquals(pos.get(1).getType(), "Disulfide bond");
1237
1238		/*
1239		* shift right by 4 from column 2
1240		* feature at [1-4] should be unchanged
1241		* feature at [13-22] should become [17-26]
1242		*/
1243	1	assertTrue(store.shiftFeatures(2, 4));
1244	1	pos = store.getPositionalFeatures();
1245	1	assertEquals(pos.size(), 2);
1246	1	SequenceFeatures.sortFeatures(pos, true);
1247	1	assertEquals(pos.get(0).getBegin(), 1);
1248	1	assertEquals(pos.get(0).getEnd(), 4);
1249	1	assertEquals(pos.get(0).getType(), "Metal");
1250	1	assertEquals(pos.get(1).getBegin(), 17);
1251	1	assertEquals(pos.get(1).getEnd(), 26);
1252	1	assertEquals(pos.get(1).getType(), "Disulfide bond");
1253
1254		/*
1255		* shift right from column 18
1256		* should be no updates
1257		*/
1258	1	SequenceFeature f1 = pos.get(0);
1259	1	SequenceFeature f2 = pos.get(1);
1260	1	assertFalse(store.shiftFeatures(18, 6));
1261	1	pos = store.getPositionalFeatures();
1262	1	assertEquals(pos.size(), 2);
1263	1	SequenceFeatures.sortFeatures(pos, true);
1264	1	assertSame(pos.get(0), f1);
1265	1	assertSame(pos.get(1), f2);
1266		}
1267
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
1268	1	@Test(groups = "Functional")...
1269		public void testIsOntologyTerm()
1270		{
1271	1	SequenceFeatures store = new SequenceFeatures();
1272	1	assertTrue(store.isOntologyTerm("gobbledygook"));
1273	1	assertTrue(store.isOntologyTerm("transcript", "transcript"));
1274	1	assertTrue(store.isOntologyTerm("mRNA", "transcript"));
1275	1	assertFalse(store.isOntologyTerm("transcript", "mRNA"));
1276	1	assertTrue(store.isOntologyTerm("junk", "transcript", "junk"));
1277	1	assertTrue(store.isOntologyTerm("junk", new String[] {}));
1278	1	assertTrue(store.isOntologyTerm("junk", (String[]) null));
1279		}
1280
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
1281	1	@Test(groups = "Functional")...
1282		public void testDeleteAll()
1283		{
1284	1	SequenceFeaturesI store = new SequenceFeatures();
1285	1	assertFalse(store.hasFeatures());
1286	1	store.deleteAll();
1287	1	assertFalse(store.hasFeatures());
1288	1	store.add(new SequenceFeature("Cath", "Desc", 12, 20, 0f, "Group"));
1289	1	store.add(new SequenceFeature("Pfam", "Desc", 6, 12, 2f, "Group2"));
1290	1	assertTrue(store.hasFeatures());
1291	1	store.deleteAll();
1292	1	assertFalse(store.hasFeatures());
1293		}
1294		}