Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ConservationTest	38	182	6	1.0100%	Show methods

Class ConservationTest

Class ConservationTest	Line # 38	Total Statements 182	Complexity 6	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	1.0 1.0100%
testRecordConservation() : void   testRecordConservation() : void	4848	15.015	1.01	1.0 1.0100%
testCountConservationAndGaps() : void   testCountConservationAndGaps() : void	7272	18.018	1.01	1.0 1.0100%
testCalculate_noThreshold() : void   testCalculate_noThreshold() : void	9696	73.073	1.01	1.0 1.0100%
testCalculate_threshold() : void   testCalculate_threshold() : void	205205	54.054	1.01	1.0 1.0100%
testVerdict() : void   testVerdict() : void	297297	20.020	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.39361703	jalview.analysis.ConservationTest.testCalculate_noThresholdjalview.analysis.ConservationTest.testCalculate_noThreshold	1PASS
	0.2925532	jalview.analysis.ConservationTest.testCalculate_thresholdjalview.analysis.ConservationTest.testCalculate_threshold	1PASS
	0.11170213	jalview.analysis.ConservationTest.testVerdictjalview.analysis.ConservationTest.testVerdict	1PASS
	0.10106383	jalview.analysis.ConservationTest.testCountConservationAndGapsjalview.analysis.ConservationTest.testCountConservationAndGaps	1PASS
	0.08510638	jalview.analysis.ConservationTest.testRecordConservationjalview.analysis.ConservationTest.testRecordConservation	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.analysis;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertTrue;
25
26		import jalview.datamodel.Sequence;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.JvOptionPane;
29
30		import java.util.ArrayList;
31		import java.util.HashMap;
32		import java.util.List;
33		import java.util.Map;
34
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.Test;
37
		100% Uncovered Elements: 0 (188) Complexity: 6 Complexity Density: 0.03
38		public class ConservationTest
39		{
40
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
41	1	@BeforeClass(alwaysRun = true)...
42		public void setUpJvOptionPane()
43		{
44	1	JvOptionPane.setInteractiveMode(false);
45	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46		}
47
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
48	1	@Test(groups = "Functional")...
49		public void testRecordConservation()
50		{
51	1	Map<String, Integer> resultMap = new HashMap<String, Integer>();
52
53		// V is hydrophobic, aliphatic, small
54	1	Conservation.recordConservation(resultMap, "V");
55	1	assertEquals(resultMap.get("hydrophobic").intValue(), 1);
56	1	assertEquals(resultMap.get("aliphatic").intValue(), 1);
57	1	assertEquals(resultMap.get("small").intValue(), 1);
58	1	assertEquals(resultMap.get("tiny").intValue(), 0);
59	1	assertEquals(resultMap.get("polar").intValue(), 0);
60	1	assertEquals(resultMap.get("charged").intValue(), 0);
61
62		// now add S: not hydrophobic, small, tiny, polar, not aliphatic
63	1	Conservation.recordConservation(resultMap, "s");
64	1	assertEquals(resultMap.get("hydrophobic").intValue(), -1);
65	1	assertEquals(resultMap.get("aliphatic").intValue(), -1);
66	1	assertEquals(resultMap.get("small").intValue(), 1);
67	1	assertEquals(resultMap.get("tiny").intValue(), -1);
68	1	assertEquals(resultMap.get("polar").intValue(), -1);
69	1	assertEquals(resultMap.get("charged").intValue(), 0);
70		}
71
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
72	1	@Test(groups = "Functional")...
73		public void testCountConservationAndGaps()
74		{
75	1	List<SequenceI> seqs = new ArrayList<SequenceI>();
76	1	seqs.add(new Sequence("seq1", "VGnY")); // not case sensitive
77	1	seqs.add(new Sequence("seq2", "-G-y"));
78	1	seqs.add(new Sequence("seq3", "VG-Y"));
79	1	seqs.add(new Sequence("seq4", "VGNW"));
80
81	1	Conservation cons = new Conservation("", seqs, 0, 50);
82	1	int[] counts = cons.countConservationAndGaps(0);
83	1	assertEquals(counts[0], 1); // conserved
84	1	assertEquals(counts[1], 1); // gap count
85	1	counts = cons.countConservationAndGaps(1);
86	1	assertEquals(counts[0], 1);
87	1	assertEquals(counts[1], 0);
88	1	counts = cons.countConservationAndGaps(2);
89	1	assertEquals(counts[0], 1);
90	1	assertEquals(counts[1], 2);
91	1	counts = cons.countConservationAndGaps(3);
92	1	assertEquals(counts[0], 0); // not conserved
93	1	assertEquals(counts[1], 0);
94		}
95
		100% Uncovered Elements: 0 (73) Complexity: 1 Complexity Density: 0.01 1PASS
96	1	@Test(groups = "Functional")...
97		public void testCalculate_noThreshold()
98		{
99	1	List<SequenceI> seqs = new ArrayList<SequenceI>();
100	1	seqs.add(new Sequence("seq1", "VGIV-N"));
101	1	seqs.add(new Sequence("seq2", "V-iL-N")); // not case sensitive
102	1	seqs.add(new Sequence("seq3", "V-IW-N"));
103	1	seqs.add(new Sequence("seq4", "VGLH-L"));
104
105	1	Conservation cons = new Conservation("", 0, seqs, 0, 5);
106	1	cons.calculate();
107
108		/*
109		* column 0: all V (hydrophobic/aliphatic/small)
110		*/
111	1	Map<String, Integer> colCons = cons.total[0];
112	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
113	1	assertEquals(colCons.get("aliphatic").intValue(), 1);
114	1	assertEquals(colCons.get("small").intValue(), 1);
115	1	assertEquals(colCons.get("tiny").intValue(), 0);
116	1	assertEquals(colCons.get("proline").intValue(), 0);
117	1	assertEquals(colCons.get("charged").intValue(), 0);
118	1	assertEquals(colCons.get("negative").intValue(), 0);
119	1	assertEquals(colCons.get("polar").intValue(), 0);
120	1	assertEquals(colCons.get("positive").intValue(), 0);
121	1	assertEquals(colCons.get("aromatic").intValue(), 0);
122
123		/*
124		* column 1: all G (hydrophobic/small/tiny)
125		* gaps take default value of property present
126		*/
127	1	colCons = cons.total[1];
128	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
129	1	assertEquals(colCons.get("aliphatic").intValue(), -1);
130	1	assertEquals(colCons.get("small").intValue(), 1);
131	1	assertEquals(colCons.get("tiny").intValue(), 1);
132	1	assertEquals(colCons.get("proline").intValue(), -1);
133	1	assertEquals(colCons.get("charged").intValue(), -1);
134	1	assertEquals(colCons.get("negative").intValue(), -1);
135	1	assertEquals(colCons.get("polar").intValue(), -1);
136	1	assertEquals(colCons.get("positive").intValue(), -1);
137	1	assertEquals(colCons.get("aromatic").intValue(), -1);
138
139		/*
140		* column 2: I/L (aliphatic/hydrophobic), all others negatively conserved
141		*/
142	1	colCons = cons.total[2];
143	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
144	1	assertEquals(colCons.get("aliphatic").intValue(), 1);
145	1	assertEquals(colCons.get("small").intValue(), 0);
146	1	assertEquals(colCons.get("tiny").intValue(), 0);
147	1	assertEquals(colCons.get("proline").intValue(), 0);
148	1	assertEquals(colCons.get("charged").intValue(), 0);
149	1	assertEquals(colCons.get("negative").intValue(), 0);
150	1	assertEquals(colCons.get("polar").intValue(), 0);
151	1	assertEquals(colCons.get("positive").intValue(), 0);
152	1	assertEquals(colCons.get("aromatic").intValue(), 0);
153
154		/*
155		* column 3: VLWH all hydrophobic, none is tiny, negative or proline
156		*/
157	1	colCons = cons.total[3];
158	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
159	1	assertEquals(colCons.get("aliphatic").intValue(), -1);
160	1	assertEquals(colCons.get("small").intValue(), -1);
161	1	assertEquals(colCons.get("tiny").intValue(), 0);
162	1	assertEquals(colCons.get("proline").intValue(), 0);
163	1	assertEquals(colCons.get("charged").intValue(), -1);
164	1	assertEquals(colCons.get("negative").intValue(), 0);
165	1	assertEquals(colCons.get("polar").intValue(), -1);
166	1	assertEquals(colCons.get("positive").intValue(), -1);
167	1	assertEquals(colCons.get("aromatic").intValue(), -1);
168
169		/*
170		* column 4: all gaps - counted as having all properties
171		*/
172	1	colCons = cons.total[4];
173	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
174	1	assertEquals(colCons.get("aliphatic").intValue(), 1);
175	1	assertEquals(colCons.get("small").intValue(), 1);
176	1	assertEquals(colCons.get("tiny").intValue(), 1);
177	1	assertEquals(colCons.get("proline").intValue(), 1);
178	1	assertEquals(colCons.get("charged").intValue(), 1);
179	1	assertEquals(colCons.get("negative").intValue(), 1);
180	1	assertEquals(colCons.get("polar").intValue(), 1);
181	1	assertEquals(colCons.get("positive").intValue(), 1);
182	1	assertEquals(colCons.get("aromatic").intValue(), 1);
183
184		/*
185		* column 5: N (small polar) and L (aliphatic hydrophobic)
186		* have nothing in common!
187		*/
188	1	colCons = cons.total[5];
189	1	assertEquals(colCons.get("hydrophobic").intValue(), -1);
190	1	assertEquals(colCons.get("aliphatic").intValue(), -1);
191	1	assertEquals(colCons.get("small").intValue(), -1);
192	1	assertEquals(colCons.get("tiny").intValue(), 0);
193	1	assertEquals(colCons.get("proline").intValue(), 0);
194	1	assertEquals(colCons.get("charged").intValue(), 0);
195	1	assertEquals(colCons.get("negative").intValue(), 0);
196	1	assertEquals(colCons.get("polar").intValue(), -1);
197	1	assertEquals(colCons.get("positive").intValue(), 0);
198	1	assertEquals(colCons.get("aromatic").intValue(), 0);
199		}
200
201		/**
202		* Test for the case whether the number of non-gapped sequences in a column
203		* has to be above a threshold
204		*/
		100% Uncovered Elements: 0 (54) Complexity: 1 Complexity Density: 0.02 1PASS
205	1	@Test(groups = "Functional")...
206		public void testCalculate_threshold()
207		{
208	1	List<SequenceI> seqs = new ArrayList<SequenceI>();
209	1	seqs.add(new Sequence("seq1", "VGIV-"));
210	1	seqs.add(new Sequence("seq2", "V-iL-")); // not case sensitive
211	1	seqs.add(new Sequence("seq3", "V-IW-"));
212	1	seqs.add(new Sequence("seq4", "VGLH-"));
213	1	seqs.add(new Sequence("seq5", "VGLH-"));
214
215		/*
216		* threshold 50% means a residue has to occur 3 or more times
217		* in a column to be counted for conservation
218		*/
219		// TODO: ConservationThread uses a value of 3
220		// calculateConservation states it is the minimum number of sequences
221		// but it is treated as percentage threshold in calculate() ?
222	1	Conservation cons = new Conservation("", 50, seqs, 0, 4);
223	1	cons.calculate();
224
225		/*
226		* column 0: all V (hydrophobic/aliphatic/small)
227		*/
228	1	Map<String, Integer> colCons = cons.total[0];
229	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
230	1	assertEquals(colCons.get("aliphatic").intValue(), 1);
231	1	assertEquals(colCons.get("small").intValue(), 1);
232	1	assertEquals(colCons.get("tiny").intValue(), 0);
233	1	assertEquals(colCons.get("proline").intValue(), 0);
234	1	assertEquals(colCons.get("charged").intValue(), 0);
235	1	assertEquals(colCons.get("negative").intValue(), 0);
236	1	assertEquals(colCons.get("polar").intValue(), 0);
237	1	assertEquals(colCons.get("positive").intValue(), 0);
238	1	assertEquals(colCons.get("aromatic").intValue(), 0);
239
240		/*
241		* column 1: all G (hydrophobic/small/tiny)
242		* gaps are ignored as not above threshold
243		*/
244	1	colCons = cons.total[1];
245	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
246	1	assertEquals(colCons.get("aliphatic").intValue(), 0);
247	1	assertEquals(colCons.get("small").intValue(), 1);
248	1	assertEquals(colCons.get("tiny").intValue(), 1);
249	1	assertEquals(colCons.get("proline").intValue(), 0);
250	1	assertEquals(colCons.get("charged").intValue(), 0);
251	1	assertEquals(colCons.get("negative").intValue(), 0);
252	1	assertEquals(colCons.get("polar").intValue(), 0);
253	1	assertEquals(colCons.get("positive").intValue(), 0);
254	1	assertEquals(colCons.get("aromatic").intValue(), 0);
255
256		/*
257		* column 2: I/L (aliphatic/hydrophobic), all others negatively conserved
258		*/
259	1	colCons = cons.total[2];
260	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
261	1	assertEquals(colCons.get("aliphatic").intValue(), 1);
262	1	assertEquals(colCons.get("small").intValue(), 0);
263	1	assertEquals(colCons.get("tiny").intValue(), 0);
264	1	assertEquals(colCons.get("proline").intValue(), 0);
265	1	assertEquals(colCons.get("charged").intValue(), 0);
266	1	assertEquals(colCons.get("negative").intValue(), 0);
267	1	assertEquals(colCons.get("polar").intValue(), 0);
268	1	assertEquals(colCons.get("positive").intValue(), 0);
269	1	assertEquals(colCons.get("aromatic").intValue(), 0);
270
271		/*
272		* column 3: nothing above threshold
273		*/
274	1	colCons = cons.total[3];
275	1	assertTrue(colCons.isEmpty());
276
277		/*
278		* column 4: all gaps - counted as having all properties
279		*/
280	1	colCons = cons.total[4];
281	1	assertEquals(colCons.get("hydrophobic").intValue(), 1);
282	1	assertEquals(colCons.get("aliphatic").intValue(), 1);
283	1	assertEquals(colCons.get("small").intValue(), 1);
284	1	assertEquals(colCons.get("tiny").intValue(), 1);
285	1	assertEquals(colCons.get("proline").intValue(), 1);
286	1	assertEquals(colCons.get("charged").intValue(), 1);
287	1	assertEquals(colCons.get("negative").intValue(), 1);
288	1	assertEquals(colCons.get("polar").intValue(), 1);
289	1	assertEquals(colCons.get("positive").intValue(), 1);
290	1	assertEquals(colCons.get("aromatic").intValue(), 1);
291		}
292
293		/**
294		* Test the method that derives the conservation 'sequence' and the mouseover
295		* tooltips from the computed conservation
296		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
297	1	@Test(groups = "Functional")...
298		public void testVerdict()
299		{
300	1	List<SequenceI> seqs = new ArrayList<SequenceI>();
301	1	seqs.add(new Sequence("seq1", "VGIVV-H"));
302	1	seqs.add(new Sequence("seq2", "VGILL-H"));
303	1	seqs.add(new Sequence("seq3", "VGIW--R"));
304	1	seqs.add(new Sequence("seq4", "VGLHH--"));
305	1	seqs.add(new Sequence("seq5", "VGLHH-R"));
306	1	seqs.add(new Sequence("seq6", "VGLHH--"));
307	1	seqs.add(new Sequence("seq7", "VGLHH-R"));
308	1	seqs.add(new Sequence("seq8", "VGLHH-R"));
309
310		// calculate with no threshold
311	1	Conservation cons = new Conservation("", 0, seqs, 0, 6);
312	1	cons.calculate();
313		// positive and negative conservation where <25% gaps in columns
314	1	cons.verdict(false, 25);
315
316		/*
317		* verify conservation 'sequence'
318		* cols 0 fully conserved and above threshold (*)
319		* col 2 properties fully conserved (+)
320		* col 3 VLWH 1 positively and 3 negatively conserved properties
321		* col 4 has 1 positively conserved property, but because gap contributes a
322		* 'positive' for all properties, no negative conservation is counted
323		* col 5 is all gaps
324		* col 6 has 25% gaps so fails threshold test
325		*/
326	1	assertEquals(cons.getConsSequence().getSequenceAsString(), "**+41--");
327
328		/*
329		* verify tooltips; conserved properties are sorted alphabetically within
330		* positive followed by negative
331		*/
332	1	assertEquals(cons.getTooltip(0),
333		"aliphatic hydrophobic small !aromatic !charged !negative !polar !positive !proline !tiny");
334	1	assertEquals(cons.getTooltip(1),
335		"hydrophobic small tiny !aliphatic !aromatic !charged !negative !polar !positive !proline");
336	1	assertEquals(cons.getTooltip(2),
337		"aliphatic hydrophobic !aromatic !charged !negative !polar !positive !proline !small !tiny");
338	1	assertEquals(cons.getTooltip(3),
339		"hydrophobic !negative !proline !tiny");
340	1	assertEquals(cons.getTooltip(4), "hydrophobic");
341	1	assertEquals(cons.getTooltip(5), "");
342	1	assertEquals(cons.getTooltip(6), "");
343		}
344		}