Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
SequenceFeaturesTest	20	682	22	0	1.0100%	Show methods

Class SequenceFeaturesTest

Class SequenceFeaturesTest	Line # 20	Total Statements 682	Complexity 22	Uncovered Elements 0	TOTAL Coverage 1.0100%
testConstructor() : void   testConstructor() : void	2222	20.020	1.01	0.00	1.0 1.0100%
testGetPositionalFeatures() : void   testGetPositionalFeatures() : void	5353	48.048	1.01	0.00	1.0 1.0100%
testGetContactFeatures() : void   testGetContactFeatures() : void	133133	27.027	1.01	0.00	1.0 1.0100%
testGetNonPositionalFeatures() : void   testGetNonPositionalFeatures() : void	185185	30.030	1.01	0.00	1.0 1.0100%
addFeature(SequenceFeaturesI,String,int,int) : SequenceFeature   addFeature(SequenceFeaturesI,String,int,int) : SequenceFeature	251251	3.03	1.01	0.00	1.0 1.0100%
testFindFeatures() : void   testFindFeatures() : void	261261	47.047	1.01	0.00	1.0 1.0100%
testDelete() : void   testDelete() : void	322322	8.08	1.01	0.00	1.0 1.0100%
testHasFeatures() : void   testHasFeatures() : void	336336	6.06	1.01	0.00	1.0 1.0100%
testGetFeatureGroups() : void   testGetFeatureGroups() : void	353353	60.060	1.01	0.00	1.0 1.0100%
testGetFeatureTypesForGroups() : void   testGetFeatureTypesForGroups() : void	451451	47.047	1.01	0.00	1.0 1.0100%
testGetFeatureTypes() : void   testGetFeatureTypes() : void	536536	36.036	1.01	0.00	1.0 1.0100%
testGetFeatureCount() : void   testGetFeatureCount() : void	605605	36.036	1.01	0.00	1.0 1.0100%
testGetAllFeatures() : void   testGetAllFeatures() : void	681681	44.044	1.01	0.00	1.0 1.0100%
testGetTotalFeatureLength() : void   testGetTotalFeatureLength() : void	762762	26.026	1.01	0.00	1.0 1.0100%
testGetMinimumScore_getMaximumScore() : void   testGetMinimumScore_getMaximumScore() : void	819819	44.044	1.01	0.00	1.0 1.0100%
testVarargsToTypes() : void   testVarargsToTypes() : void	881881	44.044	1.01	0.00	1.0 1.0100%
testGetFeatureTypes_byOntology() : void   testGetFeatureTypes_byOntology() : void	963963	20.020	1.01	0.00	1.0 1.0100%
testGetFeaturesByOntology() : void   testGetFeaturesByOntology() : void	999999	24.024	1.01	0.00	1.0 1.0100%
testSortFeatures() : void   testSortFeatures() : void	10401040	15.015	1.01	0.00	1.0 1.0100%
testGetFeaturesForGroup() : void   testGetFeaturesForGroup() : void	10671067	50.050	1.01	0.00	1.0 1.0100%
testShiftFeatures() : void   testShiftFeatures() : void	11491149	39.039	1.01	0.00	1.0 1.0100%
testIsOntologyTerm() : void   testIsOntologyTerm() : void	12121212	8.08	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.08664773	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureGroupsjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureGroups	1PASS
	0.07386363	jalview.datamodel.features.SequenceFeaturesTest.testFindFeaturesjalview.datamodel.features.SequenceFeaturesTest.testFindFeatures	1PASS
	0.07244318	jalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesForGroupjalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesForGroup	1PASS
	0.06960227	jalview.datamodel.features.SequenceFeaturesTest.testGetPositionalFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetPositionalFeatures	1PASS
	0.06818182	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesForGroupsjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesForGroups	1PASS
	0.06392045	jalview.datamodel.features.SequenceFeaturesTest.testGetMinimumScore_getMaximumScorejalview.datamodel.features.SequenceFeaturesTest.testGetMinimumScore_getMaximumScore	1PASS
	0.06392045	jalview.datamodel.features.SequenceFeaturesTest.testGetAllFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetAllFeatures	1PASS
	0.06392045	jalview.datamodel.features.SequenceFeaturesTest.testVarargsToTypesjalview.datamodel.features.SequenceFeaturesTest.testVarargsToTypes	1PASS
	0.056818184	jalview.datamodel.features.SequenceFeaturesTest.testShiftFeaturesjalview.datamodel.features.SequenceFeaturesTest.testShiftFeatures	1PASS
	0.052556816	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes	1PASS
	0.052556816	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureCountjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureCount	1PASS
	0.04403409	jalview.datamodel.features.SequenceFeaturesTest.testGetNonPositionalFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetNonPositionalFeatures	1PASS
	0.039772727	jalview.datamodel.features.SequenceFeaturesTest.testGetContactFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetContactFeatures	1PASS
	0.038352273	jalview.datamodel.features.SequenceFeaturesTest.testGetTotalFeatureLengthjalview.datamodel.features.SequenceFeaturesTest.testGetTotalFeatureLength	1PASS
	0.035511363	jalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesByOntologyjalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesByOntology	1PASS
	0.029829545	jalview.datamodel.features.SequenceFeaturesTest.testConstructorjalview.datamodel.features.SequenceFeaturesTest.testConstructor	1PASS
	0.029829545	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes_byOntologyjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes_byOntology	1PASS
	0.022727273	jalview.datamodel.features.SequenceFeaturesTest.testSortFeaturesjalview.datamodel.features.SequenceFeaturesTest.testSortFeatures	1PASS
	0.018465908	jalview.datamodel.features.SequenceFeaturesTest.testDeletejalview.datamodel.features.SequenceFeaturesTest.testDelete	1PASS
	0.015625	jalview.datamodel.features.SequenceFeaturesTest.testHasFeaturesjalview.datamodel.features.SequenceFeaturesTest.testHasFeatures	1PASS
	0.012784091	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 jalview.datamodel.SequenceFeature;
9
10		import java.util.ArrayList;
11		import java.util.Iterator;
12		import java.util.List;
13		import java.util.Map;
14		import java.util.Set;
15
16		import junit.extensions.PA;
17
18		import org.testng.annotations.Test;
19
		100% Uncovered Elements: 0 (704) Complexity: 22 Complexity Density: 0.03
20		public class SequenceFeaturesTest
21		{
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
22	1	@Test(groups = "Functional")...
23		public void testConstructor()
24		{
25	1	SequenceFeaturesI store = new SequenceFeatures();
26	1	assertFalse(store.hasFeatures());
27
28	1	store = new SequenceFeatures((List<SequenceFeature>) null);
29	1	assertFalse(store.hasFeatures());
30
31	1	List<SequenceFeature> features = new ArrayList<>();
32	1	store = new SequenceFeatures(features);
33	1	assertFalse(store.hasFeatures());
34
35	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
36		Float.NaN, null);
37	1	features.add(sf1);
38	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 15, 18,
39		Float.NaN, null);
40	1	features.add(sf2); // nested
41	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc2", 0, 0,
42		Float.NaN, null); // non-positional
43	1	features.add(sf3);
44	1	store = new SequenceFeatures(features);
45	1	assertTrue(store.hasFeatures());
46	1	assertEquals(2, store.getFeatureCount(true)); // positional
47	1	assertEquals(1, store.getFeatureCount(false)); // non-positional
48	1	assertFalse(store.add(sf1)); // already contained
49	1	assertFalse(store.add(sf2)); // already contained
50	1	assertFalse(store.add(sf3)); // already contained
51		}
52
		100% Uncovered Elements: 0 (48) Complexity: 1 Complexity Density: 0.02 1PASS
53	1	@Test(groups = "Functional")...
54		public void testGetPositionalFeatures()
55		{
56	1	SequenceFeaturesI store = new SequenceFeatures();
57	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
58		Float.NaN, null);
59	1	store.add(sf1);
60		// same range, different description
61	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20,
62		Float.NaN, null);
63	1	store.add(sf2);
64		// discontiguous range
65	1	SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 30, 40,
66		Float.NaN, null);
67	1	store.add(sf3);
68		// overlapping range
69	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 15, 35,
70		Float.NaN, null);
71	1	store.add(sf4);
72		// enclosing range
73	1	SequenceFeature sf5 = new SequenceFeature("Metal", "desc", 5, 50,
74		Float.NaN, null);
75	1	store.add(sf5);
76		// non-positional feature
77	1	SequenceFeature sf6 = new SequenceFeature("Metal", "desc", 0, 0,
78		Float.NaN, null);
79	1	store.add(sf6);
80		// contact feature
81	1	SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
82		18, 45, Float.NaN, null);
83	1	store.add(sf7);
84		// different feature type
85	1	SequenceFeature sf8 = new SequenceFeature("Pfam", "desc", 30, 40,
86		Float.NaN, null);
87	1	store.add(sf8);
88	1	SequenceFeature sf9 = new SequenceFeature("Pfam", "desc", 15, 35,
89		Float.NaN, null);
90	1	store.add(sf9);
91
92		/*
93		* get all positional features
94		*/
95	1	List<SequenceFeature> features = store.getPositionalFeatures();
96	1	assertEquals(features.size(), 8);
97	1	assertTrue(features.contains(sf1));
98	1	assertTrue(features.contains(sf2));
99	1	assertTrue(features.contains(sf3));
100	1	assertTrue(features.contains(sf4));
101	1	assertTrue(features.contains(sf5));
102	1	assertFalse(features.contains(sf6)); // non-positional
103	1	assertTrue(features.contains(sf7));
104	1	assertTrue(features.contains(sf8));
105	1	assertTrue(features.contains(sf9));
106
107		/*
108		* get features by type
109		*/
110	1	assertTrue(store.getPositionalFeatures((String) null).isEmpty());
111	1	assertTrue(store.getPositionalFeatures("Cath").isEmpty());
112	1	assertTrue(store.getPositionalFeatures("METAL").isEmpty());
113
114	1	features = store.getPositionalFeatures("Metal");
115	1	assertEquals(features.size(), 5);
116	1	assertTrue(features.contains(sf1));
117	1	assertTrue(features.contains(sf2));
118	1	assertTrue(features.contains(sf3));
119	1	assertTrue(features.contains(sf4));
120	1	assertTrue(features.contains(sf5));
121	1	assertFalse(features.contains(sf6));
122
123	1	features = store.getPositionalFeatures("Disulphide bond");
124	1	assertEquals(features.size(), 1);
125	1	assertTrue(features.contains(sf7));
126
127	1	features = store.getPositionalFeatures("Pfam");
128	1	assertEquals(features.size(), 2);
129	1	assertTrue(features.contains(sf8));
130	1	assertTrue(features.contains(sf9));
131		}
132
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
133	1	@Test(groups = "Functional")...
134		public void testGetContactFeatures()
135		{
136	1	SequenceFeaturesI store = new SequenceFeatures();
137		// non-contact
138	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
139		Float.NaN, null);
140	1	store.add(sf1);
141		// non-positional
142	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
143		Float.NaN, null);
144	1	store.add(sf2);
145		// contact feature
146	1	SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
147		18, 45, Float.NaN, null);
148	1	store.add(sf3);
149		// repeat for different feature type
150	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
151		Float.NaN, null);
152	1	store.add(sf4);
153	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
154		Float.NaN, null);
155	1	store.add(sf5);
156	1	SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
157		45, Float.NaN, null);
158	1	store.add(sf6);
159
160		/*
161		* get all contact features
162		*/
163	1	List<SequenceFeature> features = store.getContactFeatures();
164	1	assertEquals(features.size(), 2);
165	1	assertTrue(features.contains(sf3));
166	1	assertTrue(features.contains(sf6));
167
168		/*
169		* get contact features by type
170		*/
171	1	assertTrue(store.getContactFeatures((String) null).isEmpty());
172	1	assertTrue(store.getContactFeatures("Cath").isEmpty());
173	1	assertTrue(store.getContactFeatures("Pfam").isEmpty());
174	1	assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
175
176	1	features = store.getContactFeatures("Disulphide bond");
177	1	assertEquals(features.size(), 1);
178	1	assertTrue(features.contains(sf3));
179
180	1	features = store.getContactFeatures("Disulfide bond");
181	1	assertEquals(features.size(), 1);
182	1	assertTrue(features.contains(sf6));
183		}
184
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
185	1	@Test(groups = "Functional")...
186		public void testGetNonPositionalFeatures()
187		{
188	1	SequenceFeaturesI store = new SequenceFeatures();
189		// positional
190	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
191		Float.NaN, null);
192	1	store.add(sf1);
193		// non-positional
194	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
195		Float.NaN, null);
196	1	store.add(sf2);
197		// contact feature
198	1	SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
199		18, 45, Float.NaN, null);
200	1	store.add(sf3);
201		// repeat for different feature type
202	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
203		Float.NaN, null);
204	1	store.add(sf4);
205	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
206		Float.NaN, null);
207	1	store.add(sf5);
208	1	SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
209		45, Float.NaN, null);
210	1	store.add(sf6);
211		// one more non-positional, different description
212	1	SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0,
213		Float.NaN, null);
214	1	store.add(sf7);
215
216		/*
217		* get all non-positional features
218		*/
219	1	List<SequenceFeature> features = store.getNonPositionalFeatures();
220	1	assertEquals(features.size(), 3);
221	1	assertTrue(features.contains(sf2));
222	1	assertTrue(features.contains(sf5));
223	1	assertTrue(features.contains(sf7));
224
225		/*
226		* get non-positional features by type
227		*/
228	1	assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
229	1	assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
230	1	assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
231
232	1	features = store.getNonPositionalFeatures("Metal");
233	1	assertEquals(features.size(), 1);
234	1	assertTrue(features.contains(sf2));
235
236	1	features = store.getNonPositionalFeatures("Pfam");
237	1	assertEquals(features.size(), 2);
238	1	assertTrue(features.contains(sf5));
239	1	assertTrue(features.contains(sf7));
240		}
241
242		/**
243		* Helper method to add a feature of no particular type
244		*
245		* @param sf
246		* @param type
247		* @param from
248		* @param to
249		* @return
250		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
251	14	SequenceFeature addFeature(SequenceFeaturesI sf, String type, int from,...
252		int to)
253		{
254	14	SequenceFeature sf1 = new SequenceFeature(type, "", from, to,
255		Float.NaN,
256		null);
257	14	sf.add(sf1);
258	14	return sf1;
259		}
260
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
261	1	@Test(groups = "Functional")...
262		public void testFindFeatures()
263		{
264	1	SequenceFeaturesI sf = new SequenceFeatures();
265	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
266	1	SequenceFeature sf2 = addFeature(sf, "Pfam", 1, 15);
267	1	SequenceFeature sf3 = addFeature(sf, "Pfam", 20, 30);
268	1	SequenceFeature sf4 = addFeature(sf, "Pfam", 40, 100);
269	1	SequenceFeature sf5 = addFeature(sf, "Pfam", 60, 100);
270	1	SequenceFeature sf6 = addFeature(sf, "Pfam", 70, 70);
271	1	SequenceFeature sf7 = addFeature(sf, "Cath", 10, 50);
272	1	SequenceFeature sf8 = addFeature(sf, "Cath", 1, 15);
273	1	SequenceFeature sf9 = addFeature(sf, "Cath", 20, 30);
274	1	SequenceFeature sf10 = addFeature(sf, "Cath", 40, 100);
275	1	SequenceFeature sf11 = addFeature(sf, "Cath", 60, 100);
276	1	SequenceFeature sf12 = addFeature(sf, "Cath", 70, 70);
277
278	1	List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
279	1	assertTrue(overlaps.isEmpty());
280
281	1	overlaps = sf.findFeatures( 1, 9, "Pfam");
282	1	assertEquals(overlaps.size(), 1);
283	1	assertTrue(overlaps.contains(sf2));
284
285	1	overlaps = sf.findFeatures( 5, 18, "Pfam");
286	1	assertEquals(overlaps.size(), 2);
287	1	assertTrue(overlaps.contains(sf1));
288	1	assertTrue(overlaps.contains(sf2));
289
290	1	overlaps = sf.findFeatures(30, 40, "Pfam");
291	1	assertEquals(overlaps.size(), 3);
292	1	assertTrue(overlaps.contains(sf1));
293	1	assertTrue(overlaps.contains(sf3));
294	1	assertTrue(overlaps.contains(sf4));
295
296	1	overlaps = sf.findFeatures( 80, 90, "Pfam");
297	1	assertEquals(overlaps.size(), 2);
298	1	assertTrue(overlaps.contains(sf4));
299	1	assertTrue(overlaps.contains(sf5));
300
301	1	overlaps = sf.findFeatures( 68, 70, "Pfam");
302	1	assertEquals(overlaps.size(), 3);
303	1	assertTrue(overlaps.contains(sf4));
304	1	assertTrue(overlaps.contains(sf5));
305	1	assertTrue(overlaps.contains(sf6));
306
307	1	overlaps = sf.findFeatures(16, 69, "Cath");
308	1	assertEquals(overlaps.size(), 4);
309	1	assertTrue(overlaps.contains(sf7));
310	1	assertFalse(overlaps.contains(sf8));
311	1	assertTrue(overlaps.contains(sf9));
312	1	assertTrue(overlaps.contains(sf10));
313	1	assertTrue(overlaps.contains(sf11));
314	1	assertFalse(overlaps.contains(sf12));
315
316	1	assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());
317
318	1	overlaps = sf.findFeatures(7, 7, (String) null);
319	1	assertTrue(overlaps.isEmpty());
320		}
321
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
322	1	@Test(groups = "Functional")...
323		public void testDelete()
324		{
325	1	SequenceFeaturesI sf = new SequenceFeatures();
326	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
327	1	assertTrue(sf.getPositionalFeatures().contains(sf1));
328
329	1	assertFalse(sf.delete(null));
330	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 15, 0f, null);
331	1	assertFalse(sf.delete(sf2)); // not added, can't delete it
332	1	assertTrue(sf.delete(sf1));
333	1	assertTrue(sf.getPositionalFeatures().isEmpty());
334		}
335
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
336	1	@Test(groups = "Functional")...
337		public void testHasFeatures()
338		{
339	1	SequenceFeaturesI sf = new SequenceFeatures();
340	1	assertFalse(sf.hasFeatures());
341
342	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
343	1	assertTrue(sf.hasFeatures());
344
345	1	sf.delete(sf1);
346	1	assertFalse(sf.hasFeatures());
347		}
348
349		/**
350		* Tests for the method that gets feature groups for positional or
351		* non-positional features
352		*/
		100% Uncovered Elements: 0 (60) Complexity: 1 Complexity Density: 0.02 1PASS
353	1	@Test(groups = "Functional")...
354		public void testGetFeatureGroups()
355		{
356	1	SequenceFeaturesI sf = new SequenceFeatures();
357	1	assertTrue(sf.getFeatureGroups(true).isEmpty());
358	1	assertTrue(sf.getFeatureGroups(false).isEmpty());
359
360		/*
361		* add a non-positional feature (begin/end = 0/0)
362		*/
363	1	SequenceFeature sfx = new SequenceFeature("AType", "Desc", 0, 0, 0f,
364		"AGroup");
365	1	sf.add(sfx);
366	1	Set<String> groups = sf.getFeatureGroups(true); // for positional
367	1	assertTrue(groups.isEmpty());
368	1	groups = sf.getFeatureGroups(false); // for non-positional
369	1	assertEquals(groups.size(), 1);
370	1	assertTrue(groups.contains("AGroup"));
371	1	groups = sf.getFeatureGroups(false, "AType");
372	1	assertEquals(groups.size(), 1);
373	1	assertTrue(groups.contains("AGroup"));
374	1	groups = sf.getFeatureGroups(true, "AnotherType");
375	1	assertTrue(groups.isEmpty());
376
377		/*
378		* add, then delete, more non-positional features of different types
379		*/
380	1	SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0,
381		0f,
382		"AnotherGroup");
383	1	sf.add(sfy);
384	1	SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0,
385		0f,
386		null);
387	1	sf.add(sfz);
388	1	groups = sf.getFeatureGroups(false);
389	1	assertEquals(groups.size(), 3);
390	1	assertTrue(groups.contains("AGroup"));
391	1	assertTrue(groups.contains("AnotherGroup"));
392	1	assertTrue(groups.contains(null)); // null is a possible group
393	1	sf.delete(sfz);
394	1	sf.delete(sfy);
395	1	groups = sf.getFeatureGroups(false);
396	1	assertEquals(groups.size(), 1);
397	1	assertTrue(groups.contains("AGroup"));
398
399		/*
400		* add positional features
401		*/
402	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "Desc", 10, 50, 0f,
403		"PfamGroup");
404	1	sf.add(sf1);
405	1	groups = sf.getFeatureGroups(true);
406	1	assertEquals(groups.size(), 1);
407	1	assertTrue(groups.contains("PfamGroup"));
408	1	groups = sf.getFeatureGroups(false); // non-positional unchanged
409	1	assertEquals(groups.size(), 1);
410	1	assertTrue(groups.contains("AGroup"));
411
412	1	SequenceFeature sf2 = new SequenceFeature("Cath", "Desc", 10, 50, 0f,
413		null);
414	1	sf.add(sf2);
415	1	groups = sf.getFeatureGroups(true);
416	1	assertEquals(groups.size(), 2);
417	1	assertTrue(groups.contains("PfamGroup"));
418	1	assertTrue(groups.contains(null));
419
420	1	sf.delete(sf1);
421	1	sf.delete(sf2);
422	1	assertTrue(sf.getFeatureGroups(true).isEmpty());
423
424	1	SequenceFeature sf3 = new SequenceFeature("CDS", "", 10, 50, 0f,
425		"Ensembl");
426	1	sf.add(sf3);
427	1	SequenceFeature sf4 = new SequenceFeature("exon", "", 10, 50, 0f,
428		"Ensembl");
429	1	sf.add(sf4);
430	1	groups = sf.getFeatureGroups(true);
431	1	assertEquals(groups.size(), 1);
432	1	assertTrue(groups.contains("Ensembl"));
433
434		/*
435		* delete last Ensembl group feature from CDS features
436		* but still have one in exon features
437		*/
438	1	sf.delete(sf3);
439	1	groups = sf.getFeatureGroups(true);
440	1	assertEquals(groups.size(), 1);
441	1	assertTrue(groups.contains("Ensembl"));
442
443		/*
444		* delete the last non-positional feature
445		*/
446	1	sf.delete(sfx);
447	1	groups = sf.getFeatureGroups(false);
448	1	assertTrue(groups.isEmpty());
449		}
450
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
451	1	@Test(groups = "Functional")...
452		public void testGetFeatureTypesForGroups()
453		{
454	1	SequenceFeaturesI sf = new SequenceFeatures();
455	1	assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
456
457		/*
458		* add feature with group = "Uniprot", type = "helix"
459		*/
460	1	String groupUniprot = "Uniprot";
461	1	SequenceFeature sf1 = new SequenceFeature("helix", "Desc", 10, 50, 0f,
462		groupUniprot);
463	1	sf.add(sf1);
464	1	Set<String> groups = sf.getFeatureTypesForGroups(true, groupUniprot);
465	1	assertEquals(groups.size(), 1);
466	1	assertTrue(groups.contains("helix"));
467	1	assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
468
469		/*
470		* add feature with group = "Uniprot", type = "strand"
471		*/
472	1	SequenceFeature sf2 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
473		groupUniprot);
474	1	sf.add(sf2);
475	1	groups = sf.getFeatureTypesForGroups(true, groupUniprot);
476	1	assertEquals(groups.size(), 2);
477	1	assertTrue(groups.contains("helix"));
478	1	assertTrue(groups.contains("strand"));
479
480		/*
481		* delete the "strand" Uniprot feature - still have "helix"
482		*/
483	1	sf.delete(sf2);
484	1	groups = sf.getFeatureTypesForGroups(true, groupUniprot);
485	1	assertEquals(groups.size(), 1);
486	1	assertTrue(groups.contains("helix"));
487
488		/*
489		* delete the "helix" Uniprot feature - none left
490		*/
491	1	sf.delete(sf1);
492	1	assertTrue(sf.getFeatureTypesForGroups(true, groupUniprot).isEmpty());
493
494		/*
495		* add some null group features
496		*/
497	1	SequenceFeature sf3 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
498		null);
499	1	sf.add(sf3);
500	1	SequenceFeature sf4 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
501		null);
502	1	sf.add(sf4);
503	1	groups = sf.getFeatureTypesForGroups(true, (String) null);
504	1	assertEquals(groups.size(), 2);
505	1	assertTrue(groups.contains("strand"));
506	1	assertTrue(groups.contains("turn"));
507
508		/*
509		* add strand/Cath and turn/Scop and query for one or both groups
510		* (find feature types for groups selected in Feature Settings)
511		*/
512	1	SequenceFeature sf5 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
513		"Cath");
514	1	sf.add(sf5);
515	1	SequenceFeature sf6 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
516		"Scop");
517	1	sf.add(sf6);
518	1	groups = sf.getFeatureTypesForGroups(true, "Cath");
519	1	assertEquals(groups.size(), 1);
520	1	assertTrue(groups.contains("strand"));
521	1	groups = sf.getFeatureTypesForGroups(true, "Scop");
522	1	assertEquals(groups.size(), 1);
523	1	assertTrue(groups.contains("turn"));
524	1	groups = sf.getFeatureTypesForGroups(true, "Cath", "Scop");
525	1	assertEquals(groups.size(), 2);
526	1	assertTrue(groups.contains("turn"));
527	1	assertTrue(groups.contains("strand"));
528		// alternative vararg syntax
529	1	groups = sf.getFeatureTypesForGroups(true, new String[] { "Cath",
530		"Scop" });
531	1	assertEquals(groups.size(), 2);
532	1	assertTrue(groups.contains("turn"));
533	1	assertTrue(groups.contains("strand"));
534		}
535
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
536	1	@Test(groups = "Functional")...
537		public void testGetFeatureTypes()
538		{
539	1	SequenceFeaturesI store = new SequenceFeatures();
540	1	Set<String> types = store.getFeatureTypes();
541	1	assertTrue(types.isEmpty());
542
543	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
544		Float.NaN, null);
545	1	store.add(sf1);
546	1	types = store.getFeatureTypes();
547	1	assertEquals(types.size(), 1);
548	1	assertTrue(types.contains("Metal"));
549
550		// null type is rejected...
551	1	SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
552		Float.NaN, null);
553	1	assertFalse(store.add(sf2));
554	1	types = store.getFeatureTypes();
555	1	assertEquals(types.size(), 1);
556	1	assertFalse(types.contains(null));
557	1	assertTrue(types.contains("Metal"));
558
559		/*
560		* add non-positional feature
561		*/
562	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
563		Float.NaN, null);
564	1	store.add(sf3);
565	1	types = store.getFeatureTypes();
566	1	assertEquals(types.size(), 2);
567	1	assertTrue(types.contains("Pfam"));
568
569		/*
570		* add contact feature
571		*/
572	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
573		10, 20, Float.NaN, null);
574	1	store.add(sf4);
575	1	types = store.getFeatureTypes();
576	1	assertEquals(types.size(), 3);
577	1	assertTrue(types.contains("Disulphide Bond"));
578
579		/*
580		* add another Pfam
581		*/
582	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
583		Float.NaN, null);
584	1	store.add(sf5);
585	1	types = store.getFeatureTypes();
586	1	assertEquals(types.size(), 3); // unchanged
587
588		/*
589		* delete first Pfam - still have one
590		*/
591	1	assertTrue(store.delete(sf3));
592	1	types = store.getFeatureTypes();
593	1	assertEquals(types.size(), 3);
594	1	assertTrue(types.contains("Pfam"));
595
596		/*
597		* delete second Pfam - no longer have one
598		*/
599	1	assertTrue(store.delete(sf5));
600	1	types = store.getFeatureTypes();
601	1	assertEquals(types.size(), 2);
602	1	assertFalse(types.contains("Pfam"));
603		}
604
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
605	1	@Test(groups = "Functional")...
606		public void testGetFeatureCount()
607		{
608	1	SequenceFeaturesI store = new SequenceFeatures();
609	1	assertEquals(store.getFeatureCount(true), 0);
610	1	assertEquals(store.getFeatureCount(false), 0);
611
612		/*
613		* add positional
614		*/
615	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
616		Float.NaN, null);
617	1	store.add(sf1);
618	1	assertEquals(store.getFeatureCount(true), 1);
619	1	assertEquals(store.getFeatureCount(false), 0);
620
621		/*
622		* null feature type is rejected
623		*/
624	1	SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
625		Float.NaN, null);
626	1	assertFalse(store.add(sf2));
627	1	assertEquals(store.getFeatureCount(true), 1);
628	1	assertEquals(store.getFeatureCount(false), 0);
629
630		/*
631		* add non-positional feature
632		*/
633	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
634		Float.NaN, null);
635	1	store.add(sf3);
636	1	assertEquals(store.getFeatureCount(true), 1);
637	1	assertEquals(store.getFeatureCount(false), 1);
638
639		/*
640		* add contact feature (counts as 1)
641		*/
642	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
643		10, 20, Float.NaN, null);
644	1	store.add(sf4);
645	1	assertEquals(store.getFeatureCount(true), 2);
646	1	assertEquals(store.getFeatureCount(false), 1);
647
648		/*
649		* add another Pfam but this time as a positional feature
650		*/
651	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
652		Float.NaN, null);
653	1	store.add(sf5);
654	1	assertEquals(store.getFeatureCount(true), 3); // sf1, sf4, sf5
655	1	assertEquals(store.getFeatureCount(false), 1); // sf3
656	1	assertEquals(store.getFeatureCount(true, "Pfam"), 1); // positional
657	1	assertEquals(store.getFeatureCount(false, "Pfam"), 1); // non-positional
658		// search for type==null
659	1	assertEquals(store.getFeatureCount(true, (String) null), 0);
660		// search with no type specified
661	1	assertEquals(store.getFeatureCount(true, (String[]) null), 3);
662	1	assertEquals(store.getFeatureCount(true, "Metal", "Cath"), 1);
663	1	assertEquals(store.getFeatureCount(true, "Disulphide Bond"), 1);
664	1	assertEquals(store.getFeatureCount(true, "Metal", "Pfam", null), 2);
665
666		/*
667		* delete first Pfam (non-positional)
668		*/
669	1	assertTrue(store.delete(sf3));
670	1	assertEquals(store.getFeatureCount(true), 3);
671	1	assertEquals(store.getFeatureCount(false), 0);
672
673		/*
674		* delete second Pfam (positional)
675		*/
676	1	assertTrue(store.delete(sf5));
677	1	assertEquals(store.getFeatureCount(true), 2);
678	1	assertEquals(store.getFeatureCount(false), 0);
679		}
680
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
681	1	@Test(groups = "Functional")...
682		public void testGetAllFeatures()
683		{
684	1	SequenceFeaturesI store = new SequenceFeatures();
685	1	List<SequenceFeature> features = store.getAllFeatures();
686	1	assertTrue(features.isEmpty());
687
688	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
689		Float.NaN, null);
690	1	store.add(sf1);
691	1	features = store.getAllFeatures();
692	1	assertEquals(features.size(), 1);
693	1	assertTrue(features.contains(sf1));
694
695	1	SequenceFeature sf2 = new SequenceFeature("Metallic", "desc", 10, 20,
696		Float.NaN, null);
697	1	store.add(sf2);
698	1	features = store.getAllFeatures();
699	1	assertEquals(features.size(), 2);
700	1	assertTrue(features.contains(sf2));
701
702		/*
703		* add non-positional feature
704		*/
705	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
706		Float.NaN, null);
707	1	store.add(sf3);
708	1	features = store.getAllFeatures();
709	1	assertEquals(features.size(), 3);
710	1	assertTrue(features.contains(sf3));
711
712		/*
713		* add contact feature
714		*/
715	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
716		10, 20, Float.NaN, null);
717	1	store.add(sf4);
718	1	features = store.getAllFeatures();
719	1	assertEquals(features.size(), 4);
720	1	assertTrue(features.contains(sf4));
721
722		/*
723		* add another Pfam
724		*/
725	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
726		Float.NaN, null);
727	1	store.add(sf5);
728	1	features = store.getAllFeatures();
729	1	assertEquals(features.size(), 5);
730	1	assertTrue(features.contains(sf5));
731
732		/*
733		* select by type does not apply to non-positional features
734		*/
735	1	features = store.getAllFeatures("Cath");
736	1	assertEquals(features.size(), 1);
737	1	assertTrue(features.contains(sf3));
738
739	1	features = store.getAllFeatures("Pfam", "Cath", "Metal");
740	1	assertEquals(features.size(), 3);
741	1	assertTrue(features.contains(sf1));
742	1	assertTrue(features.contains(sf3));
743	1	assertTrue(features.contains(sf5));
744
745		/*
746		* delete first Pfam
747		*/
748	1	assertTrue(store.delete(sf3));
749	1	features = store.getAllFeatures();
750	1	assertEquals(features.size(), 4);
751	1	assertFalse(features.contains(sf3));
752
753		/*
754		* delete second Pfam
755		*/
756	1	assertTrue(store.delete(sf5));
757	1	features = store.getAllFeatures();
758	1	assertEquals(features.size(), 3);
759	1	assertFalse(features.contains(sf3));
760		}
761
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
762	1	@Test(groups = "Functional")...
763		public void testGetTotalFeatureLength()
764		{
765	1	SequenceFeaturesI store = new SequenceFeatures();
766	1	assertEquals(store.getTotalFeatureLength(), 0);
767
768	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
769		Float.NaN, null);
770	1	assertTrue(store.add(sf1));
771	1	assertEquals(store.getTotalFeatureLength(), 11);
772	1	assertEquals(store.getTotalFeatureLength("Metal"), 11);
773	1	assertEquals(store.getTotalFeatureLength("Plastic"), 0);
774
775		// re-add does nothing!
776	1	assertFalse(store.add(sf1));
777	1	assertEquals(store.getTotalFeatureLength(), 11);
778
779		/*
780		* add non-positional feature
781		*/
782	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
783		Float.NaN, null);
784	1	store.add(sf3);
785	1	assertEquals(store.getTotalFeatureLength(), 11);
786
787		/*
788		* add contact feature - counts 1 to feature length
789		*/
790	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
791		10, 20, Float.NaN, null);
792	1	store.add(sf4);
793	1	assertEquals(store.getTotalFeatureLength(), 12);
794
795		/*
796		* add another Pfam
797		*/
798	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
799		Float.NaN, null);
800	1	store.add(sf5);
801	1	assertEquals(store.getTotalFeatureLength(), 23);
802
803		/*
804		* delete features
805		*/
806	1	assertTrue(store.delete(sf3)); // non-positional
807	1	assertEquals(store.getTotalFeatureLength(), 23); // no change
808
809	1	assertTrue(store.delete(sf5));
810	1	assertEquals(store.getTotalFeatureLength(), 12);
811
812	1	assertTrue(store.delete(sf4)); // contact
813	1	assertEquals(store.getTotalFeatureLength(), 11);
814
815	1	assertTrue(store.delete(sf1));
816	1	assertEquals(store.getTotalFeatureLength(), 0);
817		}
818
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
819	1	@Test(groups = "Functional")...
820		public void testGetMinimumScore_getMaximumScore()
821		{
822	1	SequenceFeatures sf = new SequenceFeatures();
823	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 0, 0,
824		Float.NaN, "group"); // non-positional, no score
825	1	sf.add(sf1);
826	1	SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 10, 20,
827		Float.NaN, "group"); // positional, no score
828	1	sf.add(sf2);
829	1	SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 10, 20, 1f,
830		"group");
831	1	sf.add(sf3);
832	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 12, 16, 4f,
833		"group");
834	1	sf.add(sf4);
835	1	SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 0, 0, 11f,
836		"group");
837	1	sf.add(sf5);
838	1	SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, -7f,
839		"group");
840	1	sf.add(sf6);
841
842	1	assertEquals(sf.getMinimumScore("nosuchtype", true), Float.NaN);
843	1	assertEquals(sf.getMinimumScore("nosuchtype", false), Float.NaN);
844	1	assertEquals(sf.getMaximumScore("nosuchtype", true), Float.NaN);
845	1	assertEquals(sf.getMaximumScore("nosuchtype", false), Float.NaN);
846
847		// positional features min-max:
848	1	assertEquals(sf.getMinimumScore("Metal", true), 1f);
849	1	assertEquals(sf.getMaximumScore("Metal", true), 4f);
850	1	assertEquals(sf.getMinimumScore("Cath", true), Float.NaN);
851	1	assertEquals(sf.getMaximumScore("Cath", true), Float.NaN);
852
853		// non-positional features min-max:
854	1	assertEquals(sf.getMinimumScore("Cath", false), -7f);
855	1	assertEquals(sf.getMaximumScore("Cath", false), 11f);
856	1	assertEquals(sf.getMinimumScore("Metal", false), Float.NaN);
857	1	assertEquals(sf.getMaximumScore("Metal", false), Float.NaN);
858
859		// delete features; min-max should get recomputed
860	1	sf.delete(sf6);
861	1	assertEquals(sf.getMinimumScore("Cath", false), 11f);
862	1	assertEquals(sf.getMaximumScore("Cath", false), 11f);
863	1	sf.delete(sf4);
864	1	assertEquals(sf.getMinimumScore("Metal", true), 1f);
865	1	assertEquals(sf.getMaximumScore("Metal", true), 1f);
866	1	sf.delete(sf5);
867	1	assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
868	1	assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
869	1	sf.delete(sf3);
870	1	assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
871	1	assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
872	1	sf.delete(sf1);
873	1	sf.delete(sf2);
874	1	assertFalse(sf.hasFeatures());
875	1	assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
876	1	assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
877	1	assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
878	1	assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
879		}
880
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
881	1	@Test(groups = "Functional")...
882		public void testVarargsToTypes()
883		{
884	1	SequenceFeatures sf = new SequenceFeatures();
885	1	sf.add(new SequenceFeature("Metal", "desc", 0, 0, Float.NaN, "group"));
886	1	sf.add(new SequenceFeature("Cath", "desc", 10, 20, Float.NaN, "group"));
887
888		/*
889		* no type specified - get all types stored
890		* they are returned in keyset (alphabetical) order
891		*/
892	1	Map<String, FeatureStore> featureStores = (Map<String, FeatureStore>) PA
893		.getValue(sf, "featureStore");
894
895	1	Iterable<FeatureStore> types = sf.varargToTypes();
896	1	Iterator<FeatureStore> iterator = types.iterator();
897	1	assertTrue(iterator.hasNext());
898	1	assertSame(iterator.next(), featureStores.get("Cath"));
899	1	assertTrue(iterator.hasNext());
900	1	assertSame(iterator.next(), featureStores.get("Metal"));
901	1	assertFalse(iterator.hasNext());
902
903		/*
904		* empty array is the same as no vararg parameter supplied
905		* so treated as all stored types
906		*/
907	1	types = sf.varargToTypes(new String[] {});
908	1	iterator = types.iterator();
909	1	assertTrue(iterator.hasNext());
910	1	assertSame(iterator.next(), featureStores.get("Cath"));
911	1	assertTrue(iterator.hasNext());
912	1	assertSame(iterator.next(), featureStores.get("Metal"));
913	1	assertFalse(iterator.hasNext());
914
915		/*
916		* null type specified; this is passed as vararg
917		* String[1] {null}
918		*/
919	1	types = sf.varargToTypes((String) null);
920	1	assertFalse(types.iterator().hasNext());
921
922		/*
923		* null types array specified; this is passed as vararg null
924		*/
925	1	types = sf.varargToTypes((String[]) null);
926	1	iterator = types.iterator();
927	1	assertTrue(iterator.hasNext());
928	1	assertSame(iterator.next(), featureStores.get("Cath"));
929	1	assertTrue(iterator.hasNext());
930	1	assertSame(iterator.next(), featureStores.get("Metal"));
931	1	assertFalse(iterator.hasNext());
932
933		/*
934		* one type specified
935		*/
936	1	types = sf.varargToTypes("Metal");
937	1	iterator = types.iterator();
938	1	assertTrue(iterator.hasNext());
939	1	assertSame(iterator.next(), featureStores.get("Metal"));
940	1	assertFalse(iterator.hasNext());
941
942		/*
943		* two types specified - get sorted alphabetically
944		*/
945	1	types = sf.varargToTypes("Metal", "Cath");
946	1	iterator = types.iterator();
947	1	assertTrue(iterator.hasNext());
948	1	assertSame(iterator.next(), featureStores.get("Cath"));
949	1	assertTrue(iterator.hasNext());
950	1	assertSame(iterator.next(), featureStores.get("Metal"));
951	1	assertFalse(iterator.hasNext());
952
953		/*
954		* null type included - should be ignored
955		*/
956	1	types = sf.varargToTypes("Metal", null, "Helix");
957	1	iterator = types.iterator();
958	1	assertTrue(iterator.hasNext());
959	1	assertSame(iterator.next(), featureStores.get("Metal"));
960	1	assertFalse(iterator.hasNext());
961		}
962
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
963	1	@Test(groups = "Functional")...
964		public void testGetFeatureTypes_byOntology()
965		{
966	1	SequenceFeaturesI store = new SequenceFeatures();
967
968	1	SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
969		Float.NaN, null);
970	1	store.add(sf1);
971		// mRNA isA mature_transcript isA transcript
972	1	SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 10, 20,
973		Float.NaN, null);
974	1	store.add(sf2);
975		// just to prove non-positional feature types are included
976	1	SequenceFeature sf3 = new SequenceFeature("mRNA", "desc", 0, 0,
977		Float.NaN, null);
978	1	store.add(sf3);
979	1	SequenceFeature sf4 = new SequenceFeature("CDS", "desc", 0, 0,
980		Float.NaN, null);
981	1	store.add(sf4);
982
983	1	Set<String> types = store.getFeatureTypes("transcript");
984	1	assertEquals(types.size(), 2);
985	1	assertTrue(types.contains("transcript"));
986	1	assertTrue(types.contains("mRNA"));
987
988		// matches include arguments whether SO terms or not
989	1	types = store.getFeatureTypes("transcript", "CDS");
990	1	assertEquals(types.size(), 3);
991	1	assertTrue(types.contains("transcript"));
992	1	assertTrue(types.contains("mRNA"));
993	1	assertTrue(types.contains("CDS"));
994
995	1	types = store.getFeatureTypes("exon");
996	1	assertTrue(types.isEmpty());
997		}
998
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
999	1	@Test(groups = "Functional")...
1000		public void testGetFeaturesByOntology()
1001		{
1002	1	SequenceFeaturesI store = new SequenceFeatures();
1003	1	List<SequenceFeature> features = store.getFeaturesByOntology();
1004	1	assertTrue(features.isEmpty());
1005	1	assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty());
1006	1	assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty());
1007
1008	1	SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
1009		Float.NaN, null);
1010	1	store.add(sf1);
1011
1012		// mRNA isA transcript; added here 'as if' non-positional
1013		// just to show that non-positional features are included in results
1014	1	SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 0, 0,
1015		Float.NaN, null);
1016	1	store.add(sf2);
1017
1018	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 30, 40,
1019		Float.NaN, null);
1020	1	store.add(sf3);
1021
1022	1	features = store.getFeaturesByOntology("transcript");
1023	1	assertEquals(features.size(), 2);
1024	1	assertTrue(features.contains(sf1));
1025	1	assertTrue(features.contains(sf2));
1026
1027	1	features = store.getFeaturesByOntology("mRNA");
1028	1	assertEquals(features.size(), 1);
1029	1	assertTrue(features.contains(sf2));
1030
1031	1	features = store.getFeaturesByOntology("mRNA", "Pfam");
1032	1	assertEquals(features.size(), 2);
1033	1	assertTrue(features.contains(sf2));
1034	1	assertTrue(features.contains(sf3));
1035
1036	1	features = store.getFeaturesByOntology("sequence_variant");
1037	1	assertTrue(features.isEmpty());
1038		}
1039
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
1040	1	@Test(groups = "Functional")...
1041		public void testSortFeatures()
1042		{
1043	1	List<SequenceFeature> sfs = new ArrayList<SequenceFeature>();
1044	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80,
1045		Float.NaN, null);
1046	1	sfs.add(sf1);
1047	1	SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
1048		Float.NaN, null);
1049	1	sfs.add(sf2);
1050	1	SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
1051		Float.NaN, null);
1052	1	sfs.add(sf3);
1053
1054		// sort by end position descending
1055	1	SequenceFeatures.sortFeatures(sfs, false);
1056	1	assertSame(sfs.get(0), sf1);
1057	1	assertSame(sfs.get(1), sf3);
1058	1	assertSame(sfs.get(2), sf2);
1059
1060		// sort by start position ascending
1061	1	SequenceFeatures.sortFeatures(sfs, true);
1062	1	assertSame(sfs.get(0), sf1);
1063	1	assertSame(sfs.get(1), sf2);
1064	1	assertSame(sfs.get(2), sf3);
1065		}
1066
		100% Uncovered Elements: 0 (50) Complexity: 1 Complexity Density: 0.02 1PASS
1067	1	@Test(groups = "Functional")...
1068		public void testGetFeaturesForGroup()
1069		{
1070	1	SequenceFeaturesI store = new SequenceFeatures();
1071
1072	1	List<SequenceFeature> features = store.getFeaturesForGroup(true, null);
1073	1	assertTrue(features.isEmpty());
1074	1	assertTrue(store.getFeaturesForGroup(false, null).isEmpty());
1075	1	assertTrue(store.getFeaturesForGroup(true, "Uniprot").isEmpty());
1076	1	assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
1077
1078	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
1079		null);
1080	1	SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
1081		null);
1082	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
1083		"Uniprot");
1084	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 0, 0, 0f,
1085		"Rfam");
1086	1	SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 5, 15, 0f,
1087		null);
1088	1	store.add(sf1);
1089	1	store.add(sf2);
1090	1	store.add(sf3);
1091	1	store.add(sf4);
1092	1	store.add(sf5);
1093
1094		// positional features for null group, any type
1095	1	features = store.getFeaturesForGroup(true, null);
1096	1	assertEquals(features.size(), 2);
1097	1	assertTrue(features.contains(sf1));
1098	1	assertTrue(features.contains(sf5));
1099
1100		// positional features for null group, specified type
1101	1	features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
1102		"Xfam" });
1103	1	assertEquals(features.size(), 1);
1104	1	assertTrue(features.contains(sf1));
1105	1	features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
1106		"Xfam", "Cath" });
1107	1	assertEquals(features.size(), 2);
1108	1	assertTrue(features.contains(sf1));
1109	1	assertTrue(features.contains(sf5));
1110
1111		// positional features for non-null group, any type
1112	1	features = store.getFeaturesForGroup(true, "Uniprot");
1113	1	assertEquals(features.size(), 1);
1114	1	assertTrue(features.contains(sf3));
1115	1	assertTrue(store.getFeaturesForGroup(true, "Rfam").isEmpty());
1116
1117		// positional features for non-null group, specified type
1118	1	features = store.getFeaturesForGroup(true, "Uniprot", "Pfam", "Xfam",
1119		"Rfam");
1120	1	assertEquals(features.size(), 1);
1121	1	assertTrue(features.contains(sf3));
1122	1	assertTrue(store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty());
1123
1124		// non-positional features for null group, any type
1125	1	features = store.getFeaturesForGroup(false, null);
1126	1	assertEquals(features.size(), 1);
1127	1	assertTrue(features.contains(sf2));
1128
1129		// non-positional features for null group, specified type
1130	1	features = store.getFeaturesForGroup(false, null, "Pfam", "Xfam");
1131	1	assertEquals(features.size(), 1);
1132	1	assertTrue(features.contains(sf2));
1133	1	assertTrue(store.getFeaturesForGroup(false, null, "Cath").isEmpty());
1134
1135		// non-positional features for non-null group, any type
1136	1	features = store.getFeaturesForGroup(false, "Rfam");
1137	1	assertEquals(features.size(), 1);
1138	1	assertTrue(features.contains(sf4));
1139	1	assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
1140
1141		// non-positional features for non-null group, specified type
1142	1	features = store.getFeaturesForGroup(false, "Rfam", "Pfam", "Metal");
1143	1	assertEquals(features.size(), 1);
1144	1	assertTrue(features.contains(sf4));
1145	1	assertTrue(store.getFeaturesForGroup(false, "Rfam", "Cath", "Pfam")
1146		.isEmpty());
1147		}
1148
		100% Uncovered Elements: 0 (39) Complexity: 1 Complexity Density: 0.03 1PASS
1149	1	@Test(groups = "Functional")...
1150		public void testShiftFeatures()
1151		{
1152	1	SequenceFeatures store = new SequenceFeatures();
1153	1	assertFalse(store.shiftFeatures(1));
1154
1155	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
1156	1	store.add(sf1);
1157		// nested feature:
1158	1	SequenceFeature sf2 = new SequenceFeature("Metal", "", 8, 14, 0f, null);
1159	1	store.add(sf2);
1160		// contact feature:
1161	1	SequenceFeature sf3 = new SequenceFeature("Disulfide bond", "", 23, 32,
1162		0f, null);
1163	1	store.add(sf3);
1164		// non-positional feature:
1165	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "", 0, 0, 0f, null);
1166	1	store.add(sf4);
1167
1168		/*
1169		* shift features right by 5
1170		*/
1171	1	assertTrue(store.shiftFeatures(5));
1172
1173		// non-positional features untouched:
1174	1	List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
1175	1	assertEquals(nonPos.size(), 1);
1176	1	assertTrue(nonPos.contains(sf4));
1177
1178		// positional features are replaced
1179	1	List<SequenceFeature> pos = store.getPositionalFeatures();
1180	1	assertEquals(pos.size(), 3);
1181	1	assertFalse(pos.contains(sf1));
1182	1	assertFalse(pos.contains(sf2));
1183	1	assertFalse(pos.contains(sf3));
1184	1	SequenceFeatures.sortFeatures(pos, true); // ascending start pos
1185	1	assertEquals(pos.get(0).getBegin(), 7);
1186	1	assertEquals(pos.get(0).getEnd(), 10);
1187	1	assertEquals(pos.get(0).getType(), "Cath");
1188	1	assertEquals(pos.get(1).getBegin(), 13);
1189	1	assertEquals(pos.get(1).getEnd(), 19);
1190	1	assertEquals(pos.get(1).getType(), "Metal");
1191	1	assertEquals(pos.get(2).getBegin(), 28);
1192	1	assertEquals(pos.get(2).getEnd(), 37);
1193	1	assertEquals(pos.get(2).getType(), "Disulfide bond");
1194
1195		/*
1196		* now shift left by 15
1197		* feature at [7-10] should be removed
1198		* feature at [13-19] should become [1-4]
1199		*/
1200	1	assertTrue(store.shiftFeatures(-15));
1201	1	pos = store.getPositionalFeatures();
1202	1	assertEquals(pos.size(), 2);
1203	1	SequenceFeatures.sortFeatures(pos, true);
1204	1	assertEquals(pos.get(0).getBegin(), 1);
1205	1	assertEquals(pos.get(0).getEnd(), 4);
1206	1	assertEquals(pos.get(0).getType(), "Metal");
1207	1	assertEquals(pos.get(1).getBegin(), 13);
1208	1	assertEquals(pos.get(1).getEnd(), 22);
1209	1	assertEquals(pos.get(1).getType(), "Disulfide bond");
1210		}
1211
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
1212	1	@Test(groups = "Functional")...
1213		public void testIsOntologyTerm()
1214		{
1215	1	SequenceFeatures store = new SequenceFeatures();
1216	1	assertTrue(store.isOntologyTerm("gobbledygook"));
1217	1	assertTrue(store.isOntologyTerm("transcript", "transcript"));
1218	1	assertTrue(store.isOntologyTerm("mRNA", "transcript"));
1219	1	assertFalse(store.isOntologyTerm("transcript", "mRNA"));
1220	1	assertTrue(store.isOntologyTerm("junk", "transcript", "junk"));
1221	1	assertTrue(store.isOntologyTerm("junk", new String[] {}));
1222	1	assertTrue(store.isOntologyTerm("junk", (String[]) null));
1223		}
1224		}