Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceFeaturesTest	39	717	23	1.0100%	Show methods

Class SequenceFeaturesTest

Class SequenceFeaturesTest	Line # 39	Total Statements 717	Complexity 23	TOTAL Coverage 1.0100%
testConstructor() : void   testConstructor() : void	4141	20.020	1.01	1.0 1.0100%
testGetPositionalFeatures() : void   testGetPositionalFeatures() : void	7272	48.048	1.01	1.0 1.0100%
testGetContactFeatures() : void   testGetContactFeatures() : void	152152	27.027	1.01	1.0 1.0100%
testGetNonPositionalFeatures() : void   testGetNonPositionalFeatures() : void	204204	30.030	1.01	1.0 1.0100%
addFeature(SequenceFeaturesI,String,int,int) : SequenceFeature   addFeature(SequenceFeaturesI,String,int,int) : SequenceFeature	270270	3.03	1.01	1.0 1.0100%
testFindFeatures() : void   testFindFeatures() : void	279279	47.047	1.01	1.0 1.0100%
testDelete() : void   testDelete() : void	340340	8.08	1.01	1.0 1.0100%
testHasFeatures() : void   testHasFeatures() : void	354354	6.06	1.01	1.0 1.0100%
testGetFeatureGroups() : void   testGetFeatureGroups() : void	371371	60.060	1.01	1.0 1.0100%
testGetFeatureTypesForGroups() : void   testGetFeatureTypesForGroups() : void	467467	47.047	1.01	1.0 1.0100%
testGetFeatureTypes() : void   testGetFeatureTypes() : void	553553	36.036	1.01	1.0 1.0100%
testGetFeatureCount() : void   testGetFeatureCount() : void	622622	36.036	1.01	1.0 1.0100%
testGetAllFeatures() : void   testGetAllFeatures() : void	698698	44.044	1.01	1.0 1.0100%
testGetTotalFeatureLength() : void   testGetTotalFeatureLength() : void	779779	26.026	1.01	1.0 1.0100%
testGetMinimumScore_getMaximumScore() : void   testGetMinimumScore_getMaximumScore() : void	836836	44.044	1.01	1.0 1.0100%
testVarargsToTypes() : void   testVarargsToTypes() : void	898898	44.044	1.01	1.0 1.0100%
testGetFeatureTypes_byOntology() : void   testGetFeatureTypes_byOntology() : void	980980	20.020	1.01	1.0 1.0100%
testGetFeaturesByOntology() : void   testGetFeaturesByOntology() : void	10161016	24.024	1.01	1.0 1.0100%
testSortFeatures() : void   testSortFeatures() : void	10681068	23.023	1.01	1.0 1.0100%
testGetFeaturesForGroup() : void   testGetFeaturesForGroup() : void	11091109	50.050	1.01	1.0 1.0100%
testShiftFeatures() : void   testShiftFeatures() : void	11941194	57.057	1.01	1.0 1.0100%
testIsOntologyTerm() : void   testIsOntologyTerm() : void	12861286	8.08	1.01	1.0 1.0100%
testDeleteAll() : void   testDeleteAll() : void	12991299	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.testGetFeatureCountjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureCount	1PASS
	0.05	jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes	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.testGetFeatureTypes_byOntologyjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes_byOntology	1PASS
	0.028378379	jalview.datamodel.features.SequenceFeaturesTest.testConstructorjalview.datamodel.features.SequenceFeaturesTest.testConstructor	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		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.datamodel.features;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertSame;
26		import static org.testng.Assert.assertTrue;
27
28		import java.util.ArrayList;
29		import java.util.Iterator;
30		import java.util.List;
31		import java.util.Map;
32		import java.util.Set;
33
34		import org.testng.annotations.Test;
35
36		import jalview.datamodel.SequenceFeature;
37		import junit.extensions.PA;
38
		100% Uncovered Elements: 0 (740) Complexity: 23 Complexity Density: 0.03
39		public class SequenceFeaturesTest
40		{
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
41	1	@Test(groups = "Functional")...
42		public void testConstructor()
43		{
44	1	SequenceFeaturesI store = new SequenceFeatures();
45	1	assertFalse(store.hasFeatures());
46
47	1	store = new SequenceFeatures((List<SequenceFeature>) null);
48	1	assertFalse(store.hasFeatures());
49
50	1	List<SequenceFeature> features = new ArrayList<>();
51	1	store = new SequenceFeatures(features);
52	1	assertFalse(store.hasFeatures());
53
54	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
55		Float.NaN, null);
56	1	features.add(sf1);
57	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 15, 18,
58		Float.NaN, null);
59	1	features.add(sf2); // nested
60	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc2", 0, 0,
61		Float.NaN, null); // non-positional
62	1	features.add(sf3);
63	1	store = new SequenceFeatures(features);
64	1	assertTrue(store.hasFeatures());
65	1	assertEquals(2, store.getFeatureCount(true)); // positional
66	1	assertEquals(1, store.getFeatureCount(false)); // non-positional
67	1	assertFalse(store.add(sf1)); // already contained
68	1	assertFalse(store.add(sf2)); // already contained
69	1	assertFalse(store.add(sf3)); // already contained
70		}
71
		100% Uncovered Elements: 0 (48) Complexity: 1 Complexity Density: 0.02 1PASS
72	1	@Test(groups = "Functional")...
73		public void testGetPositionalFeatures()
74		{
75	1	SequenceFeaturesI store = new SequenceFeatures();
76	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
77		Float.NaN, null);
78	1	store.add(sf1);
79		// same range, different description
80	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20,
81		Float.NaN, null);
82	1	store.add(sf2);
83		// discontiguous range
84	1	SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 30, 40,
85		Float.NaN, null);
86	1	store.add(sf3);
87		// overlapping range
88	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 15, 35,
89		Float.NaN, null);
90	1	store.add(sf4);
91		// enclosing range
92	1	SequenceFeature sf5 = new SequenceFeature("Metal", "desc", 5, 50,
93		Float.NaN, null);
94	1	store.add(sf5);
95		// non-positional feature
96	1	SequenceFeature sf6 = new SequenceFeature("Metal", "desc", 0, 0,
97		Float.NaN, null);
98	1	store.add(sf6);
99		// contact feature
100	1	SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", 18,
101		45, Float.NaN, null);
102	1	store.add(sf7);
103		// different feature type
104	1	SequenceFeature sf8 = new SequenceFeature("Pfam", "desc", 30, 40,
105		Float.NaN, null);
106	1	store.add(sf8);
107	1	SequenceFeature sf9 = new SequenceFeature("Pfam", "desc", 15, 35,
108		Float.NaN, null);
109	1	store.add(sf9);
110
111		/*
112		* get all positional features
113		*/
114	1	List<SequenceFeature> features = store.getPositionalFeatures();
115	1	assertEquals(features.size(), 8);
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)); // non-positional
122	1	assertTrue(features.contains(sf7));
123	1	assertTrue(features.contains(sf8));
124	1	assertTrue(features.contains(sf9));
125
126		/*
127		* get features by type
128		*/
129	1	assertTrue(store.getPositionalFeatures((String) null).isEmpty());
130	1	assertTrue(store.getPositionalFeatures("Cath").isEmpty());
131	1	assertTrue(store.getPositionalFeatures("METAL").isEmpty());
132
133	1	features = store.getPositionalFeatures("Metal");
134	1	assertEquals(features.size(), 5);
135	1	assertTrue(features.contains(sf1));
136	1	assertTrue(features.contains(sf2));
137	1	assertTrue(features.contains(sf3));
138	1	assertTrue(features.contains(sf4));
139	1	assertTrue(features.contains(sf5));
140	1	assertFalse(features.contains(sf6));
141
142	1	features = store.getPositionalFeatures("Disulphide bond");
143	1	assertEquals(features.size(), 1);
144	1	assertTrue(features.contains(sf7));
145
146	1	features = store.getPositionalFeatures("Pfam");
147	1	assertEquals(features.size(), 2);
148	1	assertTrue(features.contains(sf8));
149	1	assertTrue(features.contains(sf9));
150		}
151
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
152	1	@Test(groups = "Functional")...
153		public void testGetContactFeatures()
154		{
155	1	SequenceFeaturesI store = new SequenceFeatures();
156		// non-contact
157	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
158		Float.NaN, null);
159	1	store.add(sf1);
160		// non-positional
161	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
162		Float.NaN, null);
163	1	store.add(sf2);
164		// contact feature
165	1	SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 18,
166		45, Float.NaN, null);
167	1	store.add(sf3);
168		// repeat for different feature type
169	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
170		Float.NaN, null);
171	1	store.add(sf4);
172	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
173		Float.NaN, null);
174	1	store.add(sf5);
175	1	SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
176		45, Float.NaN, null);
177	1	store.add(sf6);
178
179		/*
180		* get all contact features
181		*/
182	1	List<SequenceFeature> features = store.getContactFeatures();
183	1	assertEquals(features.size(), 2);
184	1	assertTrue(features.contains(sf3));
185	1	assertTrue(features.contains(sf6));
186
187		/*
188		* get contact features by type
189		*/
190	1	assertTrue(store.getContactFeatures((String) null).isEmpty());
191	1	assertTrue(store.getContactFeatures("Cath").isEmpty());
192	1	assertTrue(store.getContactFeatures("Pfam").isEmpty());
193	1	assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
194
195	1	features = store.getContactFeatures("Disulphide bond");
196	1	assertEquals(features.size(), 1);
197	1	assertTrue(features.contains(sf3));
198
199	1	features = store.getContactFeatures("Disulfide bond");
200	1	assertEquals(features.size(), 1);
201	1	assertTrue(features.contains(sf6));
202		}
203
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
204	1	@Test(groups = "Functional")...
205		public void testGetNonPositionalFeatures()
206		{
207	1	SequenceFeaturesI store = new SequenceFeatures();
208		// positional
209	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
210		Float.NaN, null);
211	1	store.add(sf1);
212		// non-positional
213	1	SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 0, 0,
214		Float.NaN, null);
215	1	store.add(sf2);
216		// contact feature
217	1	SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 18,
218		45, Float.NaN, null);
219	1	store.add(sf3);
220		// repeat for different feature type
221	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
222		Float.NaN, null);
223	1	store.add(sf4);
224	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 0, 0,
225		Float.NaN, null);
226	1	store.add(sf5);
227	1	SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
228		45, Float.NaN, null);
229	1	store.add(sf6);
230		// one more non-positional, different description
231	1	SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0,
232		Float.NaN, null);
233	1	store.add(sf7);
234
235		/*
236		* get all non-positional features
237		*/
238	1	List<SequenceFeature> features = store.getNonPositionalFeatures();
239	1	assertEquals(features.size(), 3);
240	1	assertTrue(features.contains(sf2));
241	1	assertTrue(features.contains(sf5));
242	1	assertTrue(features.contains(sf7));
243
244		/*
245		* get non-positional features by type
246		*/
247	1	assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
248	1	assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
249	1	assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
250
251	1	features = store.getNonPositionalFeatures("Metal");
252	1	assertEquals(features.size(), 1);
253	1	assertTrue(features.contains(sf2));
254
255	1	features = store.getNonPositionalFeatures("Pfam");
256	1	assertEquals(features.size(), 2);
257	1	assertTrue(features.contains(sf5));
258	1	assertTrue(features.contains(sf7));
259		}
260
261		/**
262		* Helper method to add a feature of no particular type
263		*
264		* @param sf
265		* @param type
266		* @param from
267		* @param to
268		* @return
269		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
270	14	SequenceFeature addFeature(SequenceFeaturesI sf, String type, int from,...
271		int to)
272		{
273	14	SequenceFeature sf1 = new SequenceFeature(type, "", from, to, Float.NaN,
274		null);
275	14	sf.add(sf1);
276	14	return sf1;
277		}
278
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
279	1	@Test(groups = "Functional")...
280		public void testFindFeatures()
281		{
282	1	SequenceFeaturesI sf = new SequenceFeatures();
283	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
284	1	SequenceFeature sf2 = addFeature(sf, "Pfam", 1, 15);
285	1	SequenceFeature sf3 = addFeature(sf, "Pfam", 20, 30);
286	1	SequenceFeature sf4 = addFeature(sf, "Pfam", 40, 100);
287	1	SequenceFeature sf5 = addFeature(sf, "Pfam", 60, 100);
288	1	SequenceFeature sf6 = addFeature(sf, "Pfam", 70, 70);
289	1	SequenceFeature sf7 = addFeature(sf, "Cath", 10, 50);
290	1	SequenceFeature sf8 = addFeature(sf, "Cath", 1, 15);
291	1	SequenceFeature sf9 = addFeature(sf, "Cath", 20, 30);
292	1	SequenceFeature sf10 = addFeature(sf, "Cath", 40, 100);
293	1	SequenceFeature sf11 = addFeature(sf, "Cath", 60, 100);
294	1	SequenceFeature sf12 = addFeature(sf, "Cath", 70, 70);
295
296	1	List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
297	1	assertTrue(overlaps.isEmpty());
298
299	1	overlaps = sf.findFeatures(1, 9, "Pfam");
300	1	assertEquals(overlaps.size(), 1);
301	1	assertTrue(overlaps.contains(sf2));
302
303	1	overlaps = sf.findFeatures(5, 18, "Pfam");
304	1	assertEquals(overlaps.size(), 2);
305	1	assertTrue(overlaps.contains(sf1));
306	1	assertTrue(overlaps.contains(sf2));
307
308	1	overlaps = sf.findFeatures(30, 40, "Pfam");
309	1	assertEquals(overlaps.size(), 3);
310	1	assertTrue(overlaps.contains(sf1));
311	1	assertTrue(overlaps.contains(sf3));
312	1	assertTrue(overlaps.contains(sf4));
313
314	1	overlaps = sf.findFeatures(80, 90, "Pfam");
315	1	assertEquals(overlaps.size(), 2);
316	1	assertTrue(overlaps.contains(sf4));
317	1	assertTrue(overlaps.contains(sf5));
318
319	1	overlaps = sf.findFeatures(68, 70, "Pfam");
320	1	assertEquals(overlaps.size(), 3);
321	1	assertTrue(overlaps.contains(sf4));
322	1	assertTrue(overlaps.contains(sf5));
323	1	assertTrue(overlaps.contains(sf6));
324
325	1	overlaps = sf.findFeatures(16, 69, "Cath");
326	1	assertEquals(overlaps.size(), 4);
327	1	assertTrue(overlaps.contains(sf7));
328	1	assertFalse(overlaps.contains(sf8));
329	1	assertTrue(overlaps.contains(sf9));
330	1	assertTrue(overlaps.contains(sf10));
331	1	assertTrue(overlaps.contains(sf11));
332	1	assertFalse(overlaps.contains(sf12));
333
334	1	assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());
335
336	1	overlaps = sf.findFeatures(7, 7, (String) null);
337	1	assertTrue(overlaps.isEmpty());
338		}
339
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
340	1	@Test(groups = "Functional")...
341		public void testDelete()
342		{
343	1	SequenceFeaturesI sf = new SequenceFeatures();
344	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
345	1	assertTrue(sf.getPositionalFeatures().contains(sf1));
346
347	1	assertFalse(sf.delete(null));
348	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 15, 0f, null);
349	1	assertFalse(sf.delete(sf2)); // not added, can't delete it
350	1	assertTrue(sf.delete(sf1));
351	1	assertTrue(sf.getPositionalFeatures().isEmpty());
352		}
353
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
354	1	@Test(groups = "Functional")...
355		public void testHasFeatures()
356		{
357	1	SequenceFeaturesI sf = new SequenceFeatures();
358	1	assertFalse(sf.hasFeatures());
359
360	1	SequenceFeature sf1 = addFeature(sf, "Pfam", 10, 50);
361	1	assertTrue(sf.hasFeatures());
362
363	1	sf.delete(sf1);
364	1	assertFalse(sf.hasFeatures());
365		}
366
367		/**
368		* Tests for the method that gets feature groups for positional or
369		* non-positional features
370		*/
		100% Uncovered Elements: 0 (60) Complexity: 1 Complexity Density: 0.02 1PASS
371	1	@Test(groups = "Functional")...
372		public void testGetFeatureGroups()
373		{
374	1	SequenceFeaturesI sf = new SequenceFeatures();
375	1	assertTrue(sf.getFeatureGroups(true).isEmpty());
376	1	assertTrue(sf.getFeatureGroups(false).isEmpty());
377
378		/*
379		* add a non-positional feature (begin/end = 0/0)
380		*/
381	1	SequenceFeature sfx = new SequenceFeature("AType", "Desc", 0, 0, 0f,
382		"AGroup");
383	1	sf.add(sfx);
384	1	Set<String> groups = sf.getFeatureGroups(true); // for positional
385	1	assertTrue(groups.isEmpty());
386	1	groups = sf.getFeatureGroups(false); // for non-positional
387	1	assertEquals(groups.size(), 1);
388	1	assertTrue(groups.contains("AGroup"));
389	1	groups = sf.getFeatureGroups(false, "AType");
390	1	assertEquals(groups.size(), 1);
391	1	assertTrue(groups.contains("AGroup"));
392	1	groups = sf.getFeatureGroups(true, "AnotherType");
393	1	assertTrue(groups.isEmpty());
394
395		/*
396		* add, then delete, more non-positional features of different types
397		*/
398	1	SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0,
399		0f, "AnotherGroup");
400	1	sf.add(sfy);
401	1	SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0,
402		0f, null);
403	1	sf.add(sfz);
404	1	groups = sf.getFeatureGroups(false);
405	1	assertEquals(groups.size(), 3);
406	1	assertTrue(groups.contains("AGroup"));
407	1	assertTrue(groups.contains("AnotherGroup"));
408	1	assertTrue(groups.contains(null)); // null is a possible group
409	1	sf.delete(sfz);
410	1	sf.delete(sfy);
411	1	groups = sf.getFeatureGroups(false);
412	1	assertEquals(groups.size(), 1);
413	1	assertTrue(groups.contains("AGroup"));
414
415		/*
416		* add positional features
417		*/
418	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "Desc", 10, 50, 0f,
419		"PfamGroup");
420	1	sf.add(sf1);
421	1	groups = sf.getFeatureGroups(true);
422	1	assertEquals(groups.size(), 1);
423	1	assertTrue(groups.contains("PfamGroup"));
424	1	groups = sf.getFeatureGroups(false); // non-positional unchanged
425	1	assertEquals(groups.size(), 1);
426	1	assertTrue(groups.contains("AGroup"));
427
428	1	SequenceFeature sf2 = new SequenceFeature("Cath", "Desc", 10, 50, 0f,
429		null);
430	1	sf.add(sf2);
431	1	groups = sf.getFeatureGroups(true);
432	1	assertEquals(groups.size(), 2);
433	1	assertTrue(groups.contains("PfamGroup"));
434	1	assertTrue(groups.contains(null));
435
436	1	sf.delete(sf1);
437	1	sf.delete(sf2);
438	1	assertTrue(sf.getFeatureGroups(true).isEmpty());
439
440	1	SequenceFeature sf3 = new SequenceFeature("CDS", "", 10, 50, 0f,
441		"Ensembl");
442	1	sf.add(sf3);
443	1	SequenceFeature sf4 = new SequenceFeature("exon", "", 10, 50, 0f,
444		"Ensembl");
445	1	sf.add(sf4);
446	1	groups = sf.getFeatureGroups(true);
447	1	assertEquals(groups.size(), 1);
448	1	assertTrue(groups.contains("Ensembl"));
449
450		/*
451		* delete last Ensembl group feature from CDS features
452		* but still have one in exon features
453		*/
454	1	sf.delete(sf3);
455	1	groups = sf.getFeatureGroups(true);
456	1	assertEquals(groups.size(), 1);
457	1	assertTrue(groups.contains("Ensembl"));
458
459		/*
460		* delete the last non-positional feature
461		*/
462	1	sf.delete(sfx);
463	1	groups = sf.getFeatureGroups(false);
464	1	assertTrue(groups.isEmpty());
465		}
466
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
467	1	@Test(groups = "Functional")...
468		public void testGetFeatureTypesForGroups()
469		{
470	1	SequenceFeaturesI sf = new SequenceFeatures();
471	1	assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
472
473		/*
474		* add feature with group = "Uniprot", type = "helix"
475		*/
476	1	String groupUniprot = "Uniprot";
477	1	SequenceFeature sf1 = new SequenceFeature("helix", "Desc", 10, 50, 0f,
478		groupUniprot);
479	1	sf.add(sf1);
480	1	Set<String> groups = sf.getFeatureTypesForGroups(true, groupUniprot);
481	1	assertEquals(groups.size(), 1);
482	1	assertTrue(groups.contains("helix"));
483	1	assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
484
485		/*
486		* add feature with group = "Uniprot", type = "strand"
487		*/
488	1	SequenceFeature sf2 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
489		groupUniprot);
490	1	sf.add(sf2);
491	1	groups = sf.getFeatureTypesForGroups(true, groupUniprot);
492	1	assertEquals(groups.size(), 2);
493	1	assertTrue(groups.contains("helix"));
494	1	assertTrue(groups.contains("strand"));
495
496		/*
497		* delete the "strand" Uniprot feature - still have "helix"
498		*/
499	1	sf.delete(sf2);
500	1	groups = sf.getFeatureTypesForGroups(true, groupUniprot);
501	1	assertEquals(groups.size(), 1);
502	1	assertTrue(groups.contains("helix"));
503
504		/*
505		* delete the "helix" Uniprot feature - none left
506		*/
507	1	sf.delete(sf1);
508	1	assertTrue(sf.getFeatureTypesForGroups(true, groupUniprot).isEmpty());
509
510		/*
511		* add some null group features
512		*/
513	1	SequenceFeature sf3 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
514		null);
515	1	sf.add(sf3);
516	1	SequenceFeature sf4 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
517		null);
518	1	sf.add(sf4);
519	1	groups = sf.getFeatureTypesForGroups(true, (String) null);
520	1	assertEquals(groups.size(), 2);
521	1	assertTrue(groups.contains("strand"));
522	1	assertTrue(groups.contains("turn"));
523
524		/*
525		* add strand/Cath and turn/Scop and query for one or both groups
526		* (find feature types for groups selected in Feature Settings)
527		*/
528	1	SequenceFeature sf5 = new SequenceFeature("strand", "Desc", 10, 50, 0f,
529		"Cath");
530	1	sf.add(sf5);
531	1	SequenceFeature sf6 = new SequenceFeature("turn", "Desc", 10, 50, 0f,
532		"Scop");
533	1	sf.add(sf6);
534	1	groups = sf.getFeatureTypesForGroups(true, "Cath");
535	1	assertEquals(groups.size(), 1);
536	1	assertTrue(groups.contains("strand"));
537	1	groups = sf.getFeatureTypesForGroups(true, "Scop");
538	1	assertEquals(groups.size(), 1);
539	1	assertTrue(groups.contains("turn"));
540	1	groups = sf.getFeatureTypesForGroups(true, "Cath", "Scop");
541	1	assertEquals(groups.size(), 2);
542	1	assertTrue(groups.contains("turn"));
543	1	assertTrue(groups.contains("strand"));
544		// alternative vararg syntax
545	1	groups = sf.getFeatureTypesForGroups(true,
546		new String[]
547		{ "Cath", "Scop" });
548	1	assertEquals(groups.size(), 2);
549	1	assertTrue(groups.contains("turn"));
550	1	assertTrue(groups.contains("strand"));
551		}
552
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
553	1	@Test(groups = "Functional")...
554		public void testGetFeatureTypes()
555		{
556	1	SequenceFeaturesI store = new SequenceFeatures();
557	1	Set<String> types = store.getFeatureTypes();
558	1	assertTrue(types.isEmpty());
559
560	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
561		Float.NaN, null);
562	1	store.add(sf1);
563	1	types = store.getFeatureTypes();
564	1	assertEquals(types.size(), 1);
565	1	assertTrue(types.contains("Metal"));
566
567		// null type is rejected...
568	1	SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
569		Float.NaN, null);
570	1	assertFalse(store.add(sf2));
571	1	types = store.getFeatureTypes();
572	1	assertEquals(types.size(), 1);
573	1	assertFalse(types.contains(null));
574	1	assertTrue(types.contains("Metal"));
575
576		/*
577		* add non-positional feature
578		*/
579	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
580		Float.NaN, null);
581	1	store.add(sf3);
582	1	types = store.getFeatureTypes();
583	1	assertEquals(types.size(), 2);
584	1	assertTrue(types.contains("Pfam"));
585
586		/*
587		* add contact feature
588		*/
589	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
590		20, Float.NaN, null);
591	1	store.add(sf4);
592	1	types = store.getFeatureTypes();
593	1	assertEquals(types.size(), 3);
594	1	assertTrue(types.contains("Disulphide Bond"));
595
596		/*
597		* add another Pfam
598		*/
599	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
600		Float.NaN, null);
601	1	store.add(sf5);
602	1	types = store.getFeatureTypes();
603	1	assertEquals(types.size(), 3); // unchanged
604
605		/*
606		* delete first Pfam - still have one
607		*/
608	1	assertTrue(store.delete(sf3));
609	1	types = store.getFeatureTypes();
610	1	assertEquals(types.size(), 3);
611	1	assertTrue(types.contains("Pfam"));
612
613		/*
614		* delete second Pfam - no longer have one
615		*/
616	1	assertTrue(store.delete(sf5));
617	1	types = store.getFeatureTypes();
618	1	assertEquals(types.size(), 2);
619	1	assertFalse(types.contains("Pfam"));
620		}
621
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
622	1	@Test(groups = "Functional")...
623		public void testGetFeatureCount()
624		{
625	1	SequenceFeaturesI store = new SequenceFeatures();
626	1	assertEquals(store.getFeatureCount(true), 0);
627	1	assertEquals(store.getFeatureCount(false), 0);
628
629		/*
630		* add positional
631		*/
632	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
633		Float.NaN, null);
634	1	store.add(sf1);
635	1	assertEquals(store.getFeatureCount(true), 1);
636	1	assertEquals(store.getFeatureCount(false), 0);
637
638		/*
639		* null feature type is rejected
640		*/
641	1	SequenceFeature sf2 = new SequenceFeature(null, "desc", 10, 20,
642		Float.NaN, null);
643	1	assertFalse(store.add(sf2));
644	1	assertEquals(store.getFeatureCount(true), 1);
645	1	assertEquals(store.getFeatureCount(false), 0);
646
647		/*
648		* add non-positional feature
649		*/
650	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
651		Float.NaN, null);
652	1	store.add(sf3);
653	1	assertEquals(store.getFeatureCount(true), 1);
654	1	assertEquals(store.getFeatureCount(false), 1);
655
656		/*
657		* add contact feature (counts as 1)
658		*/
659	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
660		20, Float.NaN, null);
661	1	store.add(sf4);
662	1	assertEquals(store.getFeatureCount(true), 2);
663	1	assertEquals(store.getFeatureCount(false), 1);
664
665		/*
666		* add another Pfam but this time as a positional feature
667		*/
668	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
669		Float.NaN, null);
670	1	store.add(sf5);
671	1	assertEquals(store.getFeatureCount(true), 3); // sf1, sf4, sf5
672	1	assertEquals(store.getFeatureCount(false), 1); // sf3
673	1	assertEquals(store.getFeatureCount(true, "Pfam"), 1); // positional
674	1	assertEquals(store.getFeatureCount(false, "Pfam"), 1); // non-positional
675		// search for type==null
676	1	assertEquals(store.getFeatureCount(true, (String) null), 0);
677		// search with no type specified
678	1	assertEquals(store.getFeatureCount(true, (String[]) null), 3);
679	1	assertEquals(store.getFeatureCount(true, "Metal", "Cath"), 1);
680	1	assertEquals(store.getFeatureCount(true, "Disulphide Bond"), 1);
681	1	assertEquals(store.getFeatureCount(true, "Metal", "Pfam", null), 2);
682
683		/*
684		* delete first Pfam (non-positional)
685		*/
686	1	assertTrue(store.delete(sf3));
687	1	assertEquals(store.getFeatureCount(true), 3);
688	1	assertEquals(store.getFeatureCount(false), 0);
689
690		/*
691		* delete second Pfam (positional)
692		*/
693	1	assertTrue(store.delete(sf5));
694	1	assertEquals(store.getFeatureCount(true), 2);
695	1	assertEquals(store.getFeatureCount(false), 0);
696		}
697
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
698	1	@Test(groups = "Functional")...
699		public void testGetAllFeatures()
700		{
701	1	SequenceFeaturesI store = new SequenceFeatures();
702	1	List<SequenceFeature> features = store.getAllFeatures();
703	1	assertTrue(features.isEmpty());
704
705	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
706		Float.NaN, null);
707	1	store.add(sf1);
708	1	features = store.getAllFeatures();
709	1	assertEquals(features.size(), 1);
710	1	assertTrue(features.contains(sf1));
711
712	1	SequenceFeature sf2 = new SequenceFeature("Metallic", "desc", 10, 20,
713		Float.NaN, null);
714	1	store.add(sf2);
715	1	features = store.getAllFeatures();
716	1	assertEquals(features.size(), 2);
717	1	assertTrue(features.contains(sf2));
718
719		/*
720		* add non-positional feature
721		*/
722	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
723		Float.NaN, null);
724	1	store.add(sf3);
725	1	features = store.getAllFeatures();
726	1	assertEquals(features.size(), 3);
727	1	assertTrue(features.contains(sf3));
728
729		/*
730		* add contact feature
731		*/
732	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
733		20, Float.NaN, null);
734	1	store.add(sf4);
735	1	features = store.getAllFeatures();
736	1	assertEquals(features.size(), 4);
737	1	assertTrue(features.contains(sf4));
738
739		/*
740		* add another Pfam
741		*/
742	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
743		Float.NaN, null);
744	1	store.add(sf5);
745	1	features = store.getAllFeatures();
746	1	assertEquals(features.size(), 5);
747	1	assertTrue(features.contains(sf5));
748
749		/*
750		* select by type does not apply to non-positional features
751		*/
752	1	features = store.getAllFeatures("Cath");
753	1	assertEquals(features.size(), 1);
754	1	assertTrue(features.contains(sf3));
755
756	1	features = store.getAllFeatures("Pfam", "Cath", "Metal");
757	1	assertEquals(features.size(), 3);
758	1	assertTrue(features.contains(sf1));
759	1	assertTrue(features.contains(sf3));
760	1	assertTrue(features.contains(sf5));
761
762		/*
763		* delete first Pfam
764		*/
765	1	assertTrue(store.delete(sf3));
766	1	features = store.getAllFeatures();
767	1	assertEquals(features.size(), 4);
768	1	assertFalse(features.contains(sf3));
769
770		/*
771		* delete second Pfam
772		*/
773	1	assertTrue(store.delete(sf5));
774	1	features = store.getAllFeatures();
775	1	assertEquals(features.size(), 3);
776	1	assertFalse(features.contains(sf3));
777		}
778
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
779	1	@Test(groups = "Functional")...
780		public void testGetTotalFeatureLength()
781		{
782	1	SequenceFeaturesI store = new SequenceFeatures();
783	1	assertEquals(store.getTotalFeatureLength(), 0);
784
785	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
786		Float.NaN, null);
787	1	assertTrue(store.add(sf1));
788	1	assertEquals(store.getTotalFeatureLength(), 11);
789	1	assertEquals(store.getTotalFeatureLength("Metal"), 11);
790	1	assertEquals(store.getTotalFeatureLength("Plastic"), 0);
791
792		// re-add does nothing!
793	1	assertFalse(store.add(sf1));
794	1	assertEquals(store.getTotalFeatureLength(), 11);
795
796		/*
797		* add non-positional feature
798		*/
799	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
800		Float.NaN, null);
801	1	store.add(sf3);
802	1	assertEquals(store.getTotalFeatureLength(), 11);
803
804		/*
805		* add contact feature - counts 1 to feature length
806		*/
807	1	SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
808		20, Float.NaN, null);
809	1	store.add(sf4);
810	1	assertEquals(store.getTotalFeatureLength(), 12);
811
812		/*
813		* add another Pfam
814		*/
815	1	SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
816		Float.NaN, null);
817	1	store.add(sf5);
818	1	assertEquals(store.getTotalFeatureLength(), 23);
819
820		/*
821		* delete features
822		*/
823	1	assertTrue(store.delete(sf3)); // non-positional
824	1	assertEquals(store.getTotalFeatureLength(), 23); // no change
825
826	1	assertTrue(store.delete(sf5));
827	1	assertEquals(store.getTotalFeatureLength(), 12);
828
829	1	assertTrue(store.delete(sf4)); // contact
830	1	assertEquals(store.getTotalFeatureLength(), 11);
831
832	1	assertTrue(store.delete(sf1));
833	1	assertEquals(store.getTotalFeatureLength(), 0);
834		}
835
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
836	1	@Test(groups = "Functional")...
837		public void testGetMinimumScore_getMaximumScore()
838		{
839	1	SequenceFeatures sf = new SequenceFeatures();
840	1	SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 0, 0,
841		Float.NaN, "group"); // non-positional, no score
842	1	sf.add(sf1);
843	1	SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 10, 20,
844		Float.NaN, "group"); // positional, no score
845	1	sf.add(sf2);
846	1	SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 10, 20, 1f,
847		"group");
848	1	sf.add(sf3);
849	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 12, 16, 4f,
850		"group");
851	1	sf.add(sf4);
852	1	SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 0, 0, 11f,
853		"group");
854	1	sf.add(sf5);
855	1	SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, -7f,
856		"group");
857	1	sf.add(sf6);
858
859	1	assertEquals(sf.getMinimumScore("nosuchtype", true), Float.NaN);
860	1	assertEquals(sf.getMinimumScore("nosuchtype", false), Float.NaN);
861	1	assertEquals(sf.getMaximumScore("nosuchtype", true), Float.NaN);
862	1	assertEquals(sf.getMaximumScore("nosuchtype", false), Float.NaN);
863
864		// positional features min-max:
865	1	assertEquals(sf.getMinimumScore("Metal", true), 1f);
866	1	assertEquals(sf.getMaximumScore("Metal", true), 4f);
867	1	assertEquals(sf.getMinimumScore("Cath", true), Float.NaN);
868	1	assertEquals(sf.getMaximumScore("Cath", true), Float.NaN);
869
870		// non-positional features min-max:
871	1	assertEquals(sf.getMinimumScore("Cath", false), -7f);
872	1	assertEquals(sf.getMaximumScore("Cath", false), 11f);
873	1	assertEquals(sf.getMinimumScore("Metal", false), Float.NaN);
874	1	assertEquals(sf.getMaximumScore("Metal", false), Float.NaN);
875
876		// delete features; min-max should get recomputed
877	1	sf.delete(sf6);
878	1	assertEquals(sf.getMinimumScore("Cath", false), 11f);
879	1	assertEquals(sf.getMaximumScore("Cath", false), 11f);
880	1	sf.delete(sf4);
881	1	assertEquals(sf.getMinimumScore("Metal", true), 1f);
882	1	assertEquals(sf.getMaximumScore("Metal", true), 1f);
883	1	sf.delete(sf5);
884	1	assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
885	1	assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
886	1	sf.delete(sf3);
887	1	assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
888	1	assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
889	1	sf.delete(sf1);
890	1	sf.delete(sf2);
891	1	assertFalse(sf.hasFeatures());
892	1	assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
893	1	assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
894	1	assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
895	1	assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
896		}
897
		100% Uncovered Elements: 0 (44) Complexity: 1 Complexity Density: 0.02 1PASS
898	1	@Test(groups = "Functional")...
899		public void testVarargsToTypes()
900		{
901	1	SequenceFeatures sf = new SequenceFeatures();
902	1	sf.add(new SequenceFeature("Metal", "desc", 0, 0, Float.NaN, "group"));
903	1	sf.add(new SequenceFeature("Cath", "desc", 10, 20, Float.NaN, "group"));
904
905		/*
906		* no type specified - get all types stored
907		* they are returned in keyset (alphabetical) order
908		*/
909	1	Map<String, FeatureStore> featureStores = (Map<String, FeatureStore>) PA
910		.getValue(sf, "featureStore");
911
912	1	Iterable<FeatureStore> types = sf.varargToTypes();
913	1	Iterator<FeatureStore> iterator = types.iterator();
914	1	assertTrue(iterator.hasNext());
915	1	assertSame(iterator.next(), featureStores.get("Cath"));
916	1	assertTrue(iterator.hasNext());
917	1	assertSame(iterator.next(), featureStores.get("Metal"));
918	1	assertFalse(iterator.hasNext());
919
920		/*
921		* empty array is the same as no vararg parameter supplied
922		* so treated as all stored types
923		*/
924	1	types = sf.varargToTypes(new String[] {});
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		* null type specified; this is passed as vararg
934		* String[1] {null}
935		*/
936	1	types = sf.varargToTypes((String) null);
937	1	assertFalse(types.iterator().hasNext());
938
939		/*
940		* null types array specified; this is passed as vararg null
941		*/
942	1	types = sf.varargToTypes((String[]) null);
943	1	iterator = types.iterator();
944	1	assertTrue(iterator.hasNext());
945	1	assertSame(iterator.next(), featureStores.get("Cath"));
946	1	assertTrue(iterator.hasNext());
947	1	assertSame(iterator.next(), featureStores.get("Metal"));
948	1	assertFalse(iterator.hasNext());
949
950		/*
951		* one type specified
952		*/
953	1	types = sf.varargToTypes("Metal");
954	1	iterator = types.iterator();
955	1	assertTrue(iterator.hasNext());
956	1	assertSame(iterator.next(), featureStores.get("Metal"));
957	1	assertFalse(iterator.hasNext());
958
959		/*
960		* two types specified - order is preserved
961		*/
962	1	types = sf.varargToTypes("Metal", "Cath");
963	1	iterator = types.iterator();
964	1	assertTrue(iterator.hasNext());
965	1	assertSame(iterator.next(), featureStores.get("Metal"));
966	1	assertTrue(iterator.hasNext());
967	1	assertSame(iterator.next(), featureStores.get("Cath"));
968	1	assertFalse(iterator.hasNext());
969
970		/*
971		* null type included - should be ignored
972		*/
973	1	types = sf.varargToTypes("Metal", null, "Helix");
974	1	iterator = types.iterator();
975	1	assertTrue(iterator.hasNext());
976	1	assertSame(iterator.next(), featureStores.get("Metal"));
977	1	assertFalse(iterator.hasNext());
978		}
979
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
980	1	@Test(groups = "Functional")...
981		public void testGetFeatureTypes_byOntology()
982		{
983	1	SequenceFeaturesI store = new SequenceFeatures();
984
985	1	SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
986		Float.NaN, null);
987	1	store.add(sf1);
988		// mRNA isA mature_transcript isA transcript
989	1	SequenceFeature sf2 = new SequenceFeature("mRNA", "desc", 10, 20,
990		Float.NaN, null);
991	1	store.add(sf2);
992		// just to prove non-positional feature types are included
993	1	SequenceFeature sf3 = new SequenceFeature("mRNA", "desc", 0, 0,
994		Float.NaN, null);
995	1	store.add(sf3);
996	1	SequenceFeature sf4 = new SequenceFeature("CDS", "desc", 0, 0,
997		Float.NaN, null);
998	1	store.add(sf4);
999
1000	1	Set<String> types = store.getFeatureTypes("transcript");
1001	1	assertEquals(types.size(), 2);
1002	1	assertTrue(types.contains("transcript"));
1003	1	assertTrue(types.contains("mRNA"));
1004
1005		// matches include arguments whether SO terms or not
1006	1	types = store.getFeatureTypes("transcript", "CDS");
1007	1	assertEquals(types.size(), 3);
1008	1	assertTrue(types.contains("transcript"));
1009	1	assertTrue(types.contains("mRNA"));
1010	1	assertTrue(types.contains("CDS"));
1011
1012	1	types = store.getFeatureTypes("exon");
1013	1	assertTrue(types.isEmpty());
1014		}
1015
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
1016	1	@Test(groups = "Functional")...
1017		public void testGetFeaturesByOntology()
1018		{
1019	1	SequenceFeaturesI store = new SequenceFeatures();
1020	1	List<SequenceFeature> features = store.getFeaturesByOntology();
1021	1	assertTrue(features.isEmpty());
1022	1	assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty());
1023	1	assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty());
1024
1025	1	SequenceFeature transcriptFeature = new SequenceFeature("transcript",
1026		"desc", 10, 20, Float.NaN, null);
1027	1	store.add(transcriptFeature);
1028
1029		/*
1030		* mRNA is a sub-type of transcript; added here 'as if' non-positional
1031		* just to show that non-positional features are included in results
1032		*/
1033	1	SequenceFeature mrnaFeature = new SequenceFeature("mRNA", "desc", 0, 0,
1034		Float.NaN, null);
1035	1	store.add(mrnaFeature);
1036
1037	1	SequenceFeature pfamFeature = new SequenceFeature("Pfam", "desc", 30,
1038		40, Float.NaN, null);
1039	1	store.add(pfamFeature);
1040
1041		/*
1042		* "transcript" matches both itself and the sub-term "mRNA"
1043		*/
1044	1	features = store.getFeaturesByOntology("transcript");
1045	1	assertEquals(features.size(), 2);
1046	1	assertTrue(features.contains(transcriptFeature));
1047	1	assertTrue(features.contains(mrnaFeature));
1048
1049		/*
1050		* "mRNA" matches itself but not parent term "transcript"
1051		*/
1052	1	features = store.getFeaturesByOntology("mRNA");
1053	1	assertEquals(features.size(), 1);
1054	1	assertTrue(features.contains(mrnaFeature));
1055
1056		/*
1057		* "pfam" is not an SO term but is included as an exact match
1058		*/
1059	1	features = store.getFeaturesByOntology("mRNA", "Pfam");
1060	1	assertEquals(features.size(), 2);
1061	1	assertTrue(features.contains(mrnaFeature));
1062	1	assertTrue(features.contains(pfamFeature));
1063
1064	1	features = store.getFeaturesByOntology("sequence_variant");
1065	1	assertTrue(features.isEmpty());
1066		}
1067
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
1068	1	@Test(groups = "Functional")...
1069		public void testSortFeatures()
1070		{
1071	1	List<SequenceFeature> sfs = new ArrayList<>();
1072	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 60,
1073		Float.NaN, null);
1074	1	sfs.add(sf1);
1075	1	SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
1076		Float.NaN, null);
1077	1	sfs.add(sf2);
1078	1	SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
1079		Float.NaN, null);
1080	1	sfs.add(sf3);
1081	1	SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30, 80,
1082		Float.NaN, null);
1083	1	sfs.add(sf4);
1084	1	SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30, 90,
1085		Float.NaN, null);
1086	1	sfs.add(sf5);
1087
1088		/*
1089		* sort by end position descending, order unchanged if matched
1090		*/
1091	1	SequenceFeatures.sortFeatures(sfs, false);
1092	1	assertSame(sfs.get(0), sf5); // end 90
1093	1	assertSame(sfs.get(1), sf4); // end 80
1094	1	assertSame(sfs.get(2), sf1); // end 60, start 50
1095	1	assertSame(sfs.get(3), sf3); // end 60, start 30
1096	1	assertSame(sfs.get(4), sf2); // end 50
1097
1098		/*
1099		* resort {5, 4, 1, 3, 2} by start position ascending, end descending
1100		*/
1101	1	SequenceFeatures.sortFeatures(sfs, true);
1102	1	assertSame(sfs.get(0), sf5); // start 30, end 90
1103	1	assertSame(sfs.get(1), sf4); // start 30, end 80
1104	1	assertSame(sfs.get(2), sf1); // start 30, end 60
1105	1	assertSame(sfs.get(3), sf2); // start 40
1106	1	assertSame(sfs.get(4), sf3); // start 50
1107		}
1108
		100% Uncovered Elements: 0 (50) Complexity: 1 Complexity Density: 0.02 1PASS
1109	1	@Test(groups = "Functional")...
1110		public void testGetFeaturesForGroup()
1111		{
1112	1	SequenceFeaturesI store = new SequenceFeatures();
1113
1114	1	List<SequenceFeature> features = store.getFeaturesForGroup(true, null);
1115	1	assertTrue(features.isEmpty());
1116	1	assertTrue(store.getFeaturesForGroup(false, null).isEmpty());
1117	1	assertTrue(store.getFeaturesForGroup(true, "Uniprot").isEmpty());
1118	1	assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
1119
1120	1	SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
1121		null);
1122	1	SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
1123		null);
1124	1	SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
1125		"Uniprot");
1126	1	SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 0, 0, 0f,
1127		"Rfam");
1128	1	SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 5, 15, 0f,
1129		null);
1130	1	store.add(sf1);
1131	1	store.add(sf2);
1132	1	store.add(sf3);
1133	1	store.add(sf4);
1134	1	store.add(sf5);
1135
1136		// positional features for null group, any type
1137	1	features = store.getFeaturesForGroup(true, null);
1138	1	assertEquals(features.size(), 2);
1139	1	assertTrue(features.contains(sf1));
1140	1	assertTrue(features.contains(sf5));
1141
1142		// positional features for null group, specified type
1143	1	features = store.getFeaturesForGroup(true, null,
1144		new String[]
1145		{ "Pfam", "Xfam" });
1146	1	assertEquals(features.size(), 1);
1147	1	assertTrue(features.contains(sf1));
1148	1	features = store.getFeaturesForGroup(true, null,
1149		new String[]
1150		{ "Pfam", "Xfam", "Cath" });
1151	1	assertEquals(features.size(), 2);
1152	1	assertTrue(features.contains(sf1));
1153	1	assertTrue(features.contains(sf5));
1154
1155		// positional features for non-null group, any type
1156	1	features = store.getFeaturesForGroup(true, "Uniprot");
1157	1	assertEquals(features.size(), 1);
1158	1	assertTrue(features.contains(sf3));
1159	1	assertTrue(store.getFeaturesForGroup(true, "Rfam").isEmpty());
1160
1161		// positional features for non-null group, specified type
1162	1	features = store.getFeaturesForGroup(true, "Uniprot", "Pfam", "Xfam",
1163		"Rfam");
1164	1	assertEquals(features.size(), 1);
1165	1	assertTrue(features.contains(sf3));
1166	1	assertTrue(
1167		store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty());
1168
1169		// non-positional features for null group, any type
1170	1	features = store.getFeaturesForGroup(false, null);
1171	1	assertEquals(features.size(), 1);
1172	1	assertTrue(features.contains(sf2));
1173
1174		// non-positional features for null group, specified type
1175	1	features = store.getFeaturesForGroup(false, null, "Pfam", "Xfam");
1176	1	assertEquals(features.size(), 1);
1177	1	assertTrue(features.contains(sf2));
1178	1	assertTrue(store.getFeaturesForGroup(false, null, "Cath").isEmpty());
1179
1180		// non-positional features for non-null group, any type
1181	1	features = store.getFeaturesForGroup(false, "Rfam");
1182	1	assertEquals(features.size(), 1);
1183	1	assertTrue(features.contains(sf4));
1184	1	assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
1185
1186		// non-positional features for non-null group, specified type
1187	1	features = store.getFeaturesForGroup(false, "Rfam", "Pfam", "Metal");
1188	1	assertEquals(features.size(), 1);
1189	1	assertTrue(features.contains(sf4));
1190	1	assertTrue(store.getFeaturesForGroup(false, "Rfam", "Cath", "Pfam")
1191		.isEmpty());
1192		}
1193
		100% Uncovered Elements: 0 (57) Complexity: 1 Complexity Density: 0.02 1PASS
1194	1	@Test(groups = "Functional")...
1195		public void testShiftFeatures()
1196		{
1197	1	SequenceFeatures store = new SequenceFeatures();
1198	1	assertFalse(store.shiftFeatures(0, 1));
1199
1200	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
1201	1	store.add(sf1);
1202		// nested feature:
1203	1	SequenceFeature sf2 = new SequenceFeature("Metal", "", 8, 14, 0f, null);
1204	1	store.add(sf2);
1205		// contact feature:
1206	1	SequenceFeature sf3 = new SequenceFeature("Disulfide bond", "", 23, 32,
1207		0f, null);
1208	1	store.add(sf3);
1209		// non-positional feature:
1210	1	SequenceFeature sf4 = new SequenceFeature("Pfam", "", 0, 0, 0f, null);
1211	1	store.add(sf4);
1212
1213		/*
1214		* shift features right by 5
1215		*/
1216	1	assertTrue(store.shiftFeatures(0, 5));
1217
1218		// non-positional features untouched:
1219	1	List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
1220	1	assertEquals(nonPos.size(), 1);
1221	1	assertTrue(nonPos.contains(sf4));
1222
1223		// positional features are replaced
1224	1	List<SequenceFeature> pos = store.getPositionalFeatures();
1225	1	assertEquals(pos.size(), 3);
1226	1	assertFalse(pos.contains(sf1));
1227	1	assertFalse(pos.contains(sf2));
1228	1	assertFalse(pos.contains(sf3));
1229	1	SequenceFeatures.sortFeatures(pos, true); // ascending start pos
1230	1	assertEquals(pos.get(0).getBegin(), 7);
1231	1	assertEquals(pos.get(0).getEnd(), 10);
1232	1	assertEquals(pos.get(0).getType(), "Cath");
1233	1	assertEquals(pos.get(1).getBegin(), 13);
1234	1	assertEquals(pos.get(1).getEnd(), 19);
1235	1	assertEquals(pos.get(1).getType(), "Metal");
1236	1	assertEquals(pos.get(2).getBegin(), 28);
1237	1	assertEquals(pos.get(2).getEnd(), 37);
1238	1	assertEquals(pos.get(2).getType(), "Disulfide bond");
1239
1240		/*
1241		* now shift left by 15
1242		* feature at [7-10] should be removed
1243		* feature at [13-19] should become [1-4]
1244		*/
1245	1	assertTrue(store.shiftFeatures(0, -15));
1246	1	pos = store.getPositionalFeatures();
1247	1	assertEquals(pos.size(), 2);
1248	1	SequenceFeatures.sortFeatures(pos, true);
1249	1	assertEquals(pos.get(0).getBegin(), 1);
1250	1	assertEquals(pos.get(0).getEnd(), 4);
1251	1	assertEquals(pos.get(0).getType(), "Metal");
1252	1	assertEquals(pos.get(1).getBegin(), 13);
1253	1	assertEquals(pos.get(1).getEnd(), 22);
1254	1	assertEquals(pos.get(1).getType(), "Disulfide bond");
1255
1256		/*
1257		* shift right by 4 from column 2
1258		* feature at [1-4] should be unchanged
1259		* feature at [13-22] should become [17-26]
1260		*/
1261	1	assertTrue(store.shiftFeatures(2, 4));
1262	1	pos = store.getPositionalFeatures();
1263	1	assertEquals(pos.size(), 2);
1264	1	SequenceFeatures.sortFeatures(pos, true);
1265	1	assertEquals(pos.get(0).getBegin(), 1);
1266	1	assertEquals(pos.get(0).getEnd(), 4);
1267	1	assertEquals(pos.get(0).getType(), "Metal");
1268	1	assertEquals(pos.get(1).getBegin(), 17);
1269	1	assertEquals(pos.get(1).getEnd(), 26);
1270	1	assertEquals(pos.get(1).getType(), "Disulfide bond");
1271
1272		/*
1273		* shift right from column 18
1274		* should be no updates
1275		*/
1276	1	SequenceFeature f1 = pos.get(0);
1277	1	SequenceFeature f2 = pos.get(1);
1278	1	assertFalse(store.shiftFeatures(18, 6));
1279	1	pos = store.getPositionalFeatures();
1280	1	assertEquals(pos.size(), 2);
1281	1	SequenceFeatures.sortFeatures(pos, true);
1282	1	assertSame(pos.get(0), f1);
1283	1	assertSame(pos.get(1), f2);
1284		}
1285
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
1286	1	@Test(groups = "Functional")...
1287		public void testIsOntologyTerm()
1288		{
1289	1	SequenceFeatures store = new SequenceFeatures();
1290	1	assertTrue(store.isOntologyTerm("gobbledygook"));
1291	1	assertTrue(store.isOntologyTerm("transcript", "transcript"));
1292	1	assertTrue(store.isOntologyTerm("mRNA", "transcript"));
1293	1	assertFalse(store.isOntologyTerm("transcript", "mRNA"));
1294	1	assertTrue(store.isOntologyTerm("junk", "transcript", "junk"));
1295	1	assertTrue(store.isOntologyTerm("junk", new String[] {}));
1296	1	assertTrue(store.isOntologyTerm("junk", (String[]) null));
1297		}
1298
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
1299	1	@Test(groups = "Functional")...
1300		public void testDeleteAll()
1301		{
1302	1	SequenceFeaturesI store = new SequenceFeatures();
1303	1	assertFalse(store.hasFeatures());
1304	1	store.deleteAll();
1305	1	assertFalse(store.hasFeatures());
1306	1	store.add(new SequenceFeature("Cath", "Desc", 12, 20, 0f, "Group"));
1307	1	store.add(new SequenceFeature("Pfam", "Desc", 6, 12, 2f, "Group2"));
1308	1	assertTrue(store.hasFeatures());
1309	1	store.deleteAll();
1310	1	assertFalse(store.hasFeatures());
1311		}
1312		}