Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceGroupTest	25	180	10	0.9839572398.4%	Show methods

Class SequenceGroupTest

Class SequenceGroupTest	Line # 25	Total Statements 180	Complexity 10	TOTAL Coverage 0.9839572398.4%
testAddSequence() : void   testAddSequence() : void	2727	20.020	1.01	1.0 1.0100%
testAddOrRemove() : void   testAddOrRemove() : void	5555	17.017	1.01	1.0 1.0100%
testGetColourScheme() : void   testGetColourScheme() : void	7979	8.08	1.01	1.0 1.0100%
testSetContext() : void   testSetContext() : void	9494	34.034	4.04	0.9117647 0.911764791.2%
testContains() : void   testContains() : void	160160	33.033	1.01	1.0 1.0100%
testCopyConstructor() : void   testCopyConstructor() : void	230230	53.053	1.01	1.0 1.0100%
testConstructor_list() : void   testConstructor_list() : void	307307	15.015	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.28877005	jalview.datamodel.SequenceGroupTest.testCopyConstructorjalview.datamodel.SequenceGroupTest.testCopyConstructor	1PASS
	0.18181819	jalview.datamodel.SequenceGroupTest.testContainsjalview.datamodel.SequenceGroupTest.testContains	1PASS
	0.171123	jalview.datamodel.SequenceGroupTest.testSetContextjalview.datamodel.SequenceGroupTest.testSetContext	1PASS
	0.112299465	jalview.datamodel.SequenceGroupTest.testAddSequencejalview.datamodel.SequenceGroupTest.testAddSequence	1PASS
	0.09625668	jalview.datamodel.SequenceGroupTest.testAddOrRemovejalview.datamodel.SequenceGroupTest.testAddOrRemove	1PASS
	0.0855615	jalview.datamodel.SequenceGroupTest.testConstructor_listjalview.datamodel.SequenceGroupTest.testConstructor_list	1PASS
	0.04812834	jalview.datamodel.SequenceGroupTest.testGetColourSchemejalview.datamodel.SequenceGroupTest.testGetColourScheme	1PASS

 

Source view

1		package jalview.datamodel;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertFalse;
5		import static org.testng.Assert.assertNotNull;
6		import static org.testng.Assert.assertNotSame;
7		import static org.testng.Assert.assertNull;
8		import static org.testng.Assert.assertSame;
9		import static org.testng.Assert.assertTrue;
10		import static org.testng.Assert.fail;
11
12		import jalview.analysis.Conservation;
13		import jalview.schemes.NucleotideColourScheme;
14		import jalview.schemes.PIDColourScheme;
15
16		import java.awt.Color;
17		import java.util.ArrayList;
18		import java.util.Collections;
19		import java.util.List;
20
21		import org.testng.annotations.Test;
22
23		import junit.extensions.PA;
24
		98.4% Uncovered Elements: 3 (187) Complexity: 10 Complexity Density: 0.06
25		public class SequenceGroupTest
26		{
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
27	1	@Test(groups={"Functional"})...
28		public void testAddSequence()
29		{
30	1	SequenceGroup sg = new SequenceGroup();
31	1	assertTrue(sg.getSequences().isEmpty());
32
33	1	SequenceI seq1 = new Sequence("seq1", "abc");
34	1	SequenceI seq2 = new Sequence("seq2", "abc");
35	1	SequenceI seq3 = new Sequence(seq1);
36
37	1	sg.addSequence(null, false);
38	1	assertTrue(sg.getSequences().isEmpty());
39	1	sg.addSequence(seq1, false);
40	1	assertEquals(sg.getSequences().size(), 1);
41	1	assertTrue(sg.getSequences().contains(seq1));
42		// adding the same sequence again does nothing
43	1	sg.addSequence(seq1, false);
44	1	assertEquals(sg.getSequences().size(), 1);
45	1	assertTrue(sg.getSequences().contains(seq1));
46	1	sg.addSequence(seq2, false);
47	1	sg.addSequence(seq2, false);
48	1	sg.addSequence(seq3, false);
49	1	assertEquals(sg.getSequences().size(), 3);
50	1	assertTrue(sg.getSequences().contains(seq1));
51	1	assertTrue(sg.getSequences().contains(seq2));
52	1	assertTrue(sg.getSequences().contains(seq3));
53		}
54
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
55	1	@Test(groups={"Functional"})...
56		public void testAddOrRemove()
57		{
58	1	SequenceGroup sg = new SequenceGroup();
59	1	assertTrue(sg.getSequences().isEmpty());
60
61	1	SequenceI seq1 = new Sequence("seq1", "abc");
62	1	SequenceI seq2 = new Sequence("seq2", "abc");
63	1	SequenceI seq3 = new Sequence(seq1);
64
65	1	sg.addOrRemove(seq1, false);
66	1	assertEquals(sg.getSequences().size(), 1);
67	1	sg.addOrRemove(seq2, false);
68	1	assertEquals(sg.getSequences().size(), 2);
69	1	sg.addOrRemove(seq3, false);
70	1	assertEquals(sg.getSequences().size(), 3);
71	1	assertTrue(sg.getSequences().contains(seq1));
72	1	assertTrue(sg.getSequences().contains(seq2));
73	1	assertTrue(sg.getSequences().contains(seq3));
74	1	sg.addOrRemove(seq1, false);
75	1	assertEquals(sg.getSequences().size(), 2);
76	1	assertFalse(sg.getSequences().contains(seq1));
77		}
78
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
79	1	@Test(groups={"Functional"})...
80		public void testGetColourScheme()
81		{
82	1	SequenceGroup sg = new SequenceGroup();
83	1	assertNotNull(sg.getGroupColourScheme());
84	1	assertNull(sg.getColourScheme());
85
86	1	sg.setGroupColourScheme(null);
87	1	assertNull(sg.getColourScheme());
88
89	1	NucleotideColourScheme scheme = new NucleotideColourScheme();
90	1	sg.setColourScheme(scheme);
91	1	assertSame(scheme, sg.getColourScheme());
92		}
93
		91.2% Uncovered Elements: 3 (34) Complexity: 4 Complexity Density: 0.12 1PASS
94	1	@Test(groups={"Functional"})...
95		public void testSetContext()
96		{
97	1	SequenceGroup sg1 = new SequenceGroup();
98	1	SequenceGroup sg2 = new SequenceGroup();
99	1	SequenceGroup sg3 = new SequenceGroup();
100	1	assertNull(sg1.getContext());
101	1	sg1.setContext(null);
102	1	assertNull(sg1.getContext());
103	1	try
104		{
105	1	sg1.setContext(sg1); // self-reference :-O
106	0	fail("Expected exception");
107		} catch (IllegalArgumentException e)
108		{
109		// expected
110	1	assertNull(sg1.getContext());
111		}
112	1	sg1.setContext(sg2);
113	1	assertSame(sg2, sg1.getContext());
114	1	sg2.setContext(sg3);
115	1	try
116		{
117	1	sg3.setContext(sg1); // circular reference :-O
118	0	fail("Expected exception");
119		} catch (IllegalArgumentException e)
120		{
121		// expected
122	1	assertNull(sg3.getContext());
123		}
124
125		/*
126		* use PrivilegedAccessor to 'force' a SequenceGroup with
127		* a circular context reference
128		*/
129	1	PA.setValue(sg2, "context", sg2);
130	1	try
131		{
132	1	sg3.setContext(sg2, false); // circular reference in sg2
133	0	fail("Expected exception");
134		} catch (IllegalArgumentException e)
135		{
136		// expected
137	1	assertNull(sg3.getContext());
138		}
139
140		// test isDefined setting behaviour
141	1	sg2 = new SequenceGroup();
142	1	sg1.setContext(null, false);
143	1	assertFalse(sg1.isDefined());
144
145	1	sg1.setContext(sg2, false);
146	1	assertFalse(sg1.isDefined());
147
148	1	sg1.setContext(sg2, true);
149	1	assertTrue(sg1.isDefined());
150
151		// setContext without defined parameter does not change isDefined
152	1	sg1.setContext(null);
153	1	assertTrue(sg1.isDefined());
154
155	1	sg1.setContext(null, false);
156	1	sg1.setContext(sg2);
157	1	assertFalse(sg1.isDefined());
158		}
159
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
160	1	@Test(groups = { "Functional" })...
161		public void testContains()
162		{
163		/*
164		* essentially the same tests as AlignmentI.findGroup
165		* but from a particular group's perspective
166		*/
167
168	1	SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
169	1	SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
170	1	AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
171		/*
172		* add a group consisting of just "DEF"
173		*/
174	1	SequenceGroup sg1 = new SequenceGroup();
175	1	sg1.addSequence(seq1, false);
176	1	sg1.setStartRes(3);
177	1	sg1.setEndRes(5);
178
179		/*
180		* test sequence membership
181		*/
182	1	assertTrue(sg1.contains(seq1));
183	1	assertFalse(sg1.contains(seq2));
184
185		/*
186		* test sequence+position
187		*/
188
189	1	assertFalse(sg1.contains(seq1, 2)); // position not in group
190	1	assertFalse(sg1.contains(seq1, 6)); // position not in group
191	1	assertFalse(sg1.contains(seq2, 5)); // sequence not in group
192	1	assertTrue(sg1.contains(seq1, 3)); // yes
193	1	assertTrue(sg1.contains(seq1, 4));
194	1	assertTrue(sg1.contains(seq1, 5));
195
196		/*
197		* add a group consisting of
198		* EF--
199		* KLMN
200		*/
201	1	SequenceGroup sg2 = new SequenceGroup();
202	1	sg2.addSequence(seq1, false);
203	1	sg2.addSequence(seq2, false);
204	1	sg2.setStartRes(4);
205	1	sg2.setEndRes(7);
206	1	a.addGroup(sg2);
207
208		/*
209		* if a residue is in more than one group, method returns
210		* the first found (in order groups were added)
211		*/
212	1	assertTrue(sg2.contains(seq1, 4));
213	1	assertTrue(sg2.contains(seq1, 5));
214
215		/*
216		* seq2 only belongs to the second group
217		*/
218	1	assertTrue(sg2.contains(seq2, 4));
219	1	assertTrue(sg2.contains(seq2, 5));
220	1	assertTrue(sg2.contains(seq2, 6));
221	1	assertTrue(sg2.contains(seq2, 7));
222	1	assertFalse(sg2.contains(seq2, 3));
223	1	assertFalse(sg2.contains(seq2, 8));
224	1	sg2.setEndRes(8);
225	1	assertTrue(sg2.contains(seq2, 8));
226	1	sg2.deleteSequence(seq2, false);
227	1	assertFalse(sg2.contains(seq2));
228		}
229
		100% Uncovered Elements: 0 (53) Complexity: 1 Complexity Density: 0.02 1PASS
230	1	@Test(groups = { "Functional" })...
231		public void testCopyConstructor()
232		{
233	1	SequenceI seq = new Sequence("seq", "ABC");
234	1	SequenceGroup sg = new SequenceGroup();
235	1	sg.addSequence(seq, false);
236	1	sg.setName("g1");
237	1	sg.setDescription("desc");
238	1	sg.setColourScheme(new PIDColourScheme());
239	1	Conservation cons = new Conservation("Cons", 2,
240		Collections.<SequenceI> emptyList(), 3, 12);
241	1	PA.setValue(cons, "consSequence", new Sequence("s", "abc"));
242	1	sg.getGroupColourScheme().setConservation(cons);
243	1	sg.getGroupColourScheme().setConsensus(new Profiles(null));
244	1	sg.setDisplayBoxes(false);
245	1	sg.setDisplayText(false);
246	1	sg.setColourText(true);
247	1	sg.isDefined = true;
248	1	sg.setShowNonconserved(true);
249	1	sg.setOutlineColour(Color.red);
250	1	sg.setIdColour(Color.blue);
251	1	sg.thresholdTextColour = 1;
252	1	sg.textColour = Color.orange;
253	1	sg.textColour2 = Color.yellow;
254	1	sg.setIgnoreGapsConsensus(false);
255	1	sg.setshowSequenceLogo(true);
256	1	sg.setNormaliseSequenceLogo(true);
257	1	sg.setHidereps(true);
258	1	sg.setHideCols(true);
259	1	sg.setShowConsensusHistogram(true);
260	1	sg.setContext(new SequenceGroup());
261
262	1	SequenceGroup sg2 = new SequenceGroup(sg);
263	1	assertEquals(sg2.getName(), sg.getName());
264	1	assertEquals(sg2.getDescription(), sg.getDescription());
265	1	assertNotSame(sg2.getGroupColourScheme(), sg.getGroupColourScheme());
266	1	assertSame(sg2.getColourScheme(), sg.getColourScheme());
267	1	assertSame(PA.getValue(sg2.getGroupColourScheme(), "consensus"),
268		PA.getValue(sg.getGroupColourScheme(), "consensus"));
269	1	assertSame(PA.getValue(sg2.getGroupColourScheme(), "conservation"),
270		PA.getValue(sg.getGroupColourScheme(), "conservation"));
271	1	assertEquals(sg2.getDisplayBoxes(), sg.getDisplayBoxes());
272	1	assertEquals(sg2.getDisplayText(), sg.getDisplayText());
273	1	assertEquals(sg2.getColourText(), sg.getColourText());
274	1	assertEquals(sg2.getShowNonconserved(), sg.getShowNonconserved());
275	1	assertEquals(sg2.getOutlineColour(), sg.getOutlineColour());
276	1	assertEquals(sg2.getIdColour(), sg.getIdColour());
277	1	assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour);
278	1	assertEquals(sg2.textColour, sg.textColour);
279	1	assertEquals(sg2.textColour2, sg.textColour2);
280	1	assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus());
281	1	assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo());
282	1	assertEquals(sg2.isNormaliseSequenceLogo(),
283		sg.isNormaliseSequenceLogo());
284	1	assertEquals(sg2.isHidereps(), sg.isHidereps());
285	1	assertEquals(sg2.isHideCols(), sg.isHideCols());
286	1	assertEquals(sg2.isShowConsensusHistogram(),
287		sg.isShowConsensusHistogram());
288
289		/*
290		* copy of sequences
291		*/
292	1	assertNotSame(sg2.getSequences(), sg.getSequences());
293	1	assertEquals(sg2.getSequences(), sg.getSequences());
294
295		/*
296		* isDefined should only be set true when a new group is added to
297		* an alignment, not in the copy constructor
298		*/
299	1	assertFalse(sg2.isDefined());
300
301		/*
302		* context should be set explicitly, not by copy
303		*/
304	1	assertNull(sg2.getContext());
305		}
306
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
307	1	@Test(groups = { "Functional" })...
308		public void testConstructor_list()
309		{
310	1	SequenceI s1 = new Sequence("abcde", "fg");
311	1	SequenceI s2 = new Sequence("foo", "bar");
312	1	List<SequenceI> seqs = new ArrayList<SequenceI>();
313	1	seqs.add(s1);
314	1	seqs.add(s2);
315	1	SequenceGroup sg = new SequenceGroup(seqs);
316
317		/*
318		* verify sg has a copy of the original list
319		*/
320	1	List<SequenceI> sgList = sg.getSequences();
321	1	assertNotSame(sgList, seqs);
322	1	assertEquals(sgList, seqs);
323
324		/*
325		* add to sgList, original is unchanged
326		*/
327	1	sg.addSequence(new Sequence("bar", "foo"), false);
328	1	assertEquals(sgList.size(), 3);
329	1	assertEquals(seqs.size(), 2);
330
331		/*
332		* delete from original, sgList is unchanged
333		*/
334	1	seqs.remove(s1);
335	1	assertEquals(sgList.size(), 3);
336	1	assertEquals(seqs.size(), 1);
337		}
338		}