Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
SequenceGroupTest	23	165	9	3	0.9824561598.2%	Show methods

Class SequenceGroupTest

Class SequenceGroupTest	Line # 23	Total Statements 165	Complexity 9	Uncovered Elements 3	TOTAL Coverage 0.9824561598.2%
testAddSequence() : void   testAddSequence() : void	2525	20.020	1.01	0.00	1.0 1.0100%
testAddOrRemove() : void   testAddOrRemove() : void	5353	17.017	1.01	0.00	1.0 1.0100%
testGetColourScheme() : void   testGetColourScheme() : void	7777	8.08	1.01	0.00	1.0 1.0100%
testSetContext() : void   testSetContext() : void	9292	34.034	4.04	3.03	0.9117647 0.911764791.2%
testContains() : void   testContains() : void	158158	33.033	1.01	0.00	1.0 1.0100%
testCopyConstructor() : void   testCopyConstructor() : void	228228	53.053	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.31578946	jalview.datamodel.SequenceGroupTest.testCopyConstructorjalview.datamodel.SequenceGroupTest.testCopyConstructor	1PASS
	0.19883041	jalview.datamodel.SequenceGroupTest.testContainsjalview.datamodel.SequenceGroupTest.testContains	1PASS
	0.1871345	jalview.datamodel.SequenceGroupTest.testSetContextjalview.datamodel.SequenceGroupTest.testSetContext	1PASS
	0.12280702	jalview.datamodel.SequenceGroupTest.testAddSequencejalview.datamodel.SequenceGroupTest.testAddSequence	1PASS
	0.10526316	jalview.datamodel.SequenceGroupTest.testAddOrRemovejalview.datamodel.SequenceGroupTest.testAddOrRemove	1PASS
	0.05263158	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.Collections;
18
19		import junit.extensions.PA;
20
21		import org.testng.annotations.Test;
22
		98.2% Uncovered Elements: 3 (171) Complexity: 9 Complexity Density: 0.05
23		public class SequenceGroupTest
24		{
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
25	1	@Test(groups={"Functional"})...
26		public void testAddSequence()
27		{
28	1	SequenceGroup sg = new SequenceGroup();
29	1	assertTrue(sg.getSequences().isEmpty());
30
31	1	SequenceI seq1 = new Sequence("seq1", "abc");
32	1	SequenceI seq2 = new Sequence("seq2", "abc");
33	1	SequenceI seq3 = new Sequence(seq1);
34
35	1	sg.addSequence(null, false);
36	1	assertTrue(sg.getSequences().isEmpty());
37	1	sg.addSequence(seq1, false);
38	1	assertEquals(sg.getSequences().size(), 1);
39	1	assertTrue(sg.getSequences().contains(seq1));
40		// adding the same sequence again does nothing
41	1	sg.addSequence(seq1, false);
42	1	assertEquals(sg.getSequences().size(), 1);
43	1	assertTrue(sg.getSequences().contains(seq1));
44	1	sg.addSequence(seq2, false);
45	1	sg.addSequence(seq2, false);
46	1	sg.addSequence(seq3, false);
47	1	assertEquals(sg.getSequences().size(), 3);
48	1	assertTrue(sg.getSequences().contains(seq1));
49	1	assertTrue(sg.getSequences().contains(seq2));
50	1	assertTrue(sg.getSequences().contains(seq3));
51		}
52
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
53	1	@Test(groups={"Functional"})...
54		public void testAddOrRemove()
55		{
56	1	SequenceGroup sg = new SequenceGroup();
57	1	assertTrue(sg.getSequences().isEmpty());
58
59	1	SequenceI seq1 = new Sequence("seq1", "abc");
60	1	SequenceI seq2 = new Sequence("seq2", "abc");
61	1	SequenceI seq3 = new Sequence(seq1);
62
63	1	sg.addOrRemove(seq1, false);
64	1	assertEquals(sg.getSequences().size(), 1);
65	1	sg.addOrRemove(seq2, false);
66	1	assertEquals(sg.getSequences().size(), 2);
67	1	sg.addOrRemove(seq3, false);
68	1	assertEquals(sg.getSequences().size(), 3);
69	1	assertTrue(sg.getSequences().contains(seq1));
70	1	assertTrue(sg.getSequences().contains(seq2));
71	1	assertTrue(sg.getSequences().contains(seq3));
72	1	sg.addOrRemove(seq1, false);
73	1	assertEquals(sg.getSequences().size(), 2);
74	1	assertFalse(sg.getSequences().contains(seq1));
75		}
76
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
77	1	@Test(groups={"Functional"})...
78		public void testGetColourScheme()
79		{
80	1	SequenceGroup sg = new SequenceGroup();
81	1	assertNotNull(sg.getGroupColourScheme());
82	1	assertNull(sg.getColourScheme());
83
84	1	sg.setGroupColourScheme(null);
85	1	assertNull(sg.getColourScheme());
86
87	1	NucleotideColourScheme scheme = new NucleotideColourScheme();
88	1	sg.setColourScheme(scheme);
89	1	assertSame(scheme, sg.getColourScheme());
90		}
91
		91.2% Uncovered Elements: 3 (34) Complexity: 4 Complexity Density: 0.12 1PASS
92	1	@Test(groups={"Functional"})...
93		public void testSetContext()
94		{
95	1	SequenceGroup sg1 = new SequenceGroup();
96	1	SequenceGroup sg2 = new SequenceGroup();
97	1	SequenceGroup sg3 = new SequenceGroup();
98	1	assertNull(sg1.getContext());
99	1	sg1.setContext(null);
100	1	assertNull(sg1.getContext());
101	1	try
102		{
103	1	sg1.setContext(sg1); // self-reference :-O
104	0	fail("Expected exception");
105		} catch (IllegalArgumentException e)
106		{
107		// expected
108	1	assertNull(sg1.getContext());
109		}
110	1	sg1.setContext(sg2);
111	1	assertSame(sg2, sg1.getContext());
112	1	sg2.setContext(sg3);
113	1	try
114		{
115	1	sg3.setContext(sg1); // circular reference :-O
116	0	fail("Expected exception");
117		} catch (IllegalArgumentException e)
118		{
119		// expected
120	1	assertNull(sg3.getContext());
121		}
122
123		/*
124		* use PrivilegedAccessor to 'force' a SequenceGroup with
125		* a circular context reference
126		*/
127	1	PA.setValue(sg2, "context", sg2);
128	1	try
129		{
130	1	sg3.setContext(sg2, false); // circular reference in sg2
131	0	fail("Expected exception");
132		} catch (IllegalArgumentException e)
133		{
134		// expected
135	1	assertNull(sg3.getContext());
136		}
137
138		// test isDefined setting behaviour
139	1	sg2 = new SequenceGroup();
140	1	sg1.setContext(null, false);
141	1	assertFalse(sg1.isDefined());
142
143	1	sg1.setContext(sg2, false);
144	1	assertFalse(sg1.isDefined());
145
146	1	sg1.setContext(sg2, true);
147	1	assertTrue(sg1.isDefined());
148
149		// setContext without defined parameter does not change isDefined
150	1	sg1.setContext(null);
151	1	assertTrue(sg1.isDefined());
152
153	1	sg1.setContext(null, false);
154	1	sg1.setContext(sg2);
155	1	assertFalse(sg1.isDefined());
156		}
157
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
158	1	@Test(groups = { "Functional" })...
159		public void testContains()
160		{
161		/*
162		* essentially the same tests as AlignmentI.findGroup
163		* but from a particular group's perspective
164		*/
165
166	1	SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
167	1	SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
168	1	AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
169		/*
170		* add a group consisting of just "DEF"
171		*/
172	1	SequenceGroup sg1 = new SequenceGroup();
173	1	sg1.addSequence(seq1, false);
174	1	sg1.setStartRes(3);
175	1	sg1.setEndRes(5);
176
177		/*
178		* test sequence membership
179		*/
180	1	assertTrue(sg1.contains(seq1));
181	1	assertFalse(sg1.contains(seq2));
182
183		/*
184		* test sequence+position
185		*/
186
187	1	assertFalse(sg1.contains(seq1, 2)); // position not in group
188	1	assertFalse(sg1.contains(seq1, 6)); // position not in group
189	1	assertFalse(sg1.contains(seq2, 5)); // sequence not in group
190	1	assertTrue(sg1.contains(seq1, 3)); // yes
191	1	assertTrue(sg1.contains(seq1, 4));
192	1	assertTrue(sg1.contains(seq1, 5));
193
194		/*
195		* add a group consisting of
196		* EF--
197		* KLMN
198		*/
199	1	SequenceGroup sg2 = new SequenceGroup();
200	1	sg2.addSequence(seq1, false);
201	1	sg2.addSequence(seq2, false);
202	1	sg2.setStartRes(4);
203	1	sg2.setEndRes(7);
204	1	a.addGroup(sg2);
205
206		/*
207		* if a residue is in more than one group, method returns
208		* the first found (in order groups were added)
209		*/
210	1	assertTrue(sg2.contains(seq1, 4));
211	1	assertTrue(sg2.contains(seq1, 5));
212
213		/*
214		* seq2 only belongs to the second group
215		*/
216	1	assertTrue(sg2.contains(seq2, 4));
217	1	assertTrue(sg2.contains(seq2, 5));
218	1	assertTrue(sg2.contains(seq2, 6));
219	1	assertTrue(sg2.contains(seq2, 7));
220	1	assertFalse(sg2.contains(seq2, 3));
221	1	assertFalse(sg2.contains(seq2, 8));
222	1	sg2.setEndRes(8);
223	1	assertTrue(sg2.contains(seq2, 8));
224	1	sg2.deleteSequence(seq2, false);
225	1	assertFalse(sg2.contains(seq2));
226		}
227
		100% Uncovered Elements: 0 (53) Complexity: 1 Complexity Density: 0.02 1PASS
228	1	@Test(groups = { "Functional" })...
229		public void testCopyConstructor()
230		{
231	1	SequenceI seq = new Sequence("seq", "ABC");
232	1	SequenceGroup sg = new SequenceGroup();
233	1	sg.addSequence(seq, false);
234	1	sg.setName("g1");
235	1	sg.setDescription("desc");
236	1	sg.setColourScheme(new PIDColourScheme());
237	1	Conservation cons = new Conservation("Cons", 2,
238		Collections.<SequenceI> emptyList(), 3, 12);
239	1	PA.setValue(cons, "consSequence", new Sequence("s", "abc"));
240	1	sg.getGroupColourScheme().setConservation(cons);
241	1	sg.getGroupColourScheme().setConsensus(new Profiles(null));
242	1	sg.setDisplayBoxes(false);
243	1	sg.setDisplayText(false);
244	1	sg.setColourText(true);
245	1	sg.isDefined = true;
246	1	sg.setShowNonconserved(true);
247	1	sg.setOutlineColour(Color.red);
248	1	sg.setIdColour(Color.blue);
249	1	sg.thresholdTextColour = 1;
250	1	sg.textColour = Color.orange;
251	1	sg.textColour2 = Color.yellow;
252	1	sg.setIgnoreGapsConsensus(false);
253	1	sg.setshowSequenceLogo(true);
254	1	sg.setNormaliseSequenceLogo(true);
255	1	sg.setHidereps(true);
256	1	sg.setHideCols(true);
257	1	sg.setShowConsensusHistogram(true);
258	1	sg.setContext(new SequenceGroup());
259
260	1	SequenceGroup sg2 = new SequenceGroup(sg);
261	1	assertEquals(sg2.getName(), sg.getName());
262	1	assertEquals(sg2.getDescription(), sg.getDescription());
263	1	assertNotSame(sg2.getGroupColourScheme(), sg.getGroupColourScheme());
264	1	assertSame(sg2.getColourScheme(), sg.getColourScheme());
265	1	assertSame(PA.getValue(sg2.getGroupColourScheme(), "consensus"),
266		PA.getValue(sg.getGroupColourScheme(), "consensus"));
267	1	assertSame(PA.getValue(sg2.getGroupColourScheme(), "conservation"),
268		PA.getValue(sg.getGroupColourScheme(), "conservation"));
269	1	assertEquals(sg2.getDisplayBoxes(), sg.getDisplayBoxes());
270	1	assertEquals(sg2.getDisplayText(), sg.getDisplayText());
271	1	assertEquals(sg2.getColourText(), sg.getColourText());
272	1	assertEquals(sg2.getShowNonconserved(), sg.getShowNonconserved());
273	1	assertEquals(sg2.getOutlineColour(), sg.getOutlineColour());
274	1	assertEquals(sg2.getIdColour(), sg.getIdColour());
275	1	assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour);
276	1	assertEquals(sg2.textColour, sg.textColour);
277	1	assertEquals(sg2.textColour2, sg.textColour2);
278	1	assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus());
279	1	assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo());
280	1	assertEquals(sg2.isNormaliseSequenceLogo(),
281		sg.isNormaliseSequenceLogo());
282	1	assertEquals(sg2.isHidereps(), sg.isHidereps());
283	1	assertEquals(sg2.isHideCols(), sg.isHideCols());
284	1	assertEquals(sg2.isShowConsensusHistogram(),
285		sg.isShowConsensusHistogram());
286
287		/*
288		* copy of sequences
289		*/
290	1	assertNotSame(sg2.getSequences(), sg.getSequences());
291	1	assertEquals(sg2.getSequences(), sg.getSequences());
292
293		/*
294		* isDefined should only be set true when a new group is added to
295		* an alignment, not in the copy constructor
296		*/
297	1	assertFalse(sg2.isDefined());
298
299		/*
300		* context should be set explicitly, not by copy
301		*/
302	1	assertNull(sg2.getContext());
303		}
304		}