Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GeneticCodesTest	32	175	8	1.0100%	Show methods

Class GeneticCodesTest

Class GeneticCodesTest	Line # 32	Total Statements 175	Complexity 8	TOTAL Coverage 1.0100%
testGetCodeTable() : void   testGetCodeTable() : void	3434	7.07	1.01	1.0 1.0100%
testGetCodeTables() : void   testGetCodeTables() : void	4949	6.06	2.02	1.0 1.0100%
testTranslate() : void   testTranslate() : void	6464	13.013	1.01	1.0 1.0100%
testTranslate_standardTable() : void   testTranslate_standardTable() : void	9090	65.065	1.01	1.0 1.0100%
testTranslate_standardTableAmbiguityCodes() : void   testTranslate_standardTableAmbiguityCodes() : void	164164	56.056	1.01	1.0 1.0100%
testTranslate_nonStandardTableAmbiguityCodes() : void   testTranslate_nonStandardTableAmbiguityCodes() : void	256256	19.019	1.01	1.0 1.0100%
testTranslateCanonical() : void   testTranslateCanonical() : void	302302	9.09	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.35869566	jalview.analysis.GeneticCodesTest.testTranslate_standardTablejalview.analysis.GeneticCodesTest.testTranslate_standardTable	1PASS
	0.3097826	jalview.analysis.GeneticCodesTest.testTranslate_standardTableAmbiguityCodesjalview.analysis.GeneticCodesTest.testTranslate_standardTableAmbiguityCodes	1PASS
	0.10869565	jalview.analysis.GeneticCodesTest.testTranslate_nonStandardTableAmbiguityCodesjalview.analysis.GeneticCodesTest.testTranslate_nonStandardTableAmbiguityCodes	1PASS
	0.07608695	jalview.analysis.GeneticCodesTest.testTranslatejalview.analysis.GeneticCodesTest.testTranslate	1PASS
	0.054347824	jalview.analysis.GeneticCodesTest.testTranslateCanonicaljalview.analysis.GeneticCodesTest.testTranslateCanonical	1PASS
	0.048913043	jalview.analysis.GeneticCodesTest.testGetCodeTablesjalview.analysis.GeneticCodesTest.testGetCodeTables	1PASS
	0.04347826	jalview.analysis.GeneticCodesTest.testGetCodeTablejalview.analysis.GeneticCodesTest.testGetCodeTable	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.assertFalse;
25		import static org.testng.Assert.assertNull;
26		import static org.testng.Assert.assertSame;
27
28		import java.util.Iterator;
29
30		import org.testng.annotations.Test;
31
		100% Uncovered Elements: 0 (184) Complexity: 8 Complexity Density: 0.05
32		public class GeneticCodesTest
33		{
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
34	1	@Test(groups = "Functional")...
35		public void testGetCodeTable()
36		{
37	1	GeneticCodes codes = GeneticCodes.getInstance();
38	1	assertEquals(codes.getStandardCodeTable().getName(), "Standard");
39	1	assertEquals(codes.getStandardCodeTable().getId(), "1");
40	1	assertSame(codes.getStandardCodeTable(), codes.getCodeTable("1"));
41	1	assertEquals(codes.getCodeTable("2").getName(),
42		"Vertebrate Mitochondrial");
43	1	assertEquals(codes.getCodeTable("11").getName(),
44		"Bacterial, Archaeal and Plant Plastid");
45	1	assertEquals(codes.getCodeTable("31").getName(),
46		"Blastocrithidia Nuclear");
47		}
48
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33 1PASS
49	1	@Test(groups = "Functional")...
50		public void testGetCodeTables()
51		{
52	1	GeneticCodes codes = GeneticCodes.getInstance();
53	1	Iterator<GeneticCodeI> tableIterator = codes.getCodeTables().iterator();
54	1	String[] ids = new String[] { "1", "2", "3", "4", "5", "6", "9", "10",
55		"11", "12", "13", "14", "15", "16", "21", "22", "23", "24", "25",
56		"26", "27", "28", "29", "30", "31" };
57	26	for (int i = 0; i < ids.length; i++)
58		{
59	25	assertEquals(tableIterator.next().getId(), ids[i]);
60		}
61	1	assertFalse(tableIterator.hasNext());
62		}
63
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
64	1	@Test(groups = "Functional")...
65		public void testTranslate()
66		{
67	1	GeneticCodes codes = GeneticCodes.getInstance();
68
69	1	GeneticCodeI gc = codes.getCodeTable("1");
70	1	assertNull(gc.translate("XYZ"));
71	1	assertEquals(gc.translate("AGA"), "R");
72
73	1	gc = codes.getCodeTable("2");
74	1	assertEquals(gc.translate("AGA"), "*"); // variant
75	1	assertEquals(gc.translate("ttc"), "F"); // non-variant
76
77		// table 11 has no variant translations - should serve the standard values
78	1	gc = codes.getCodeTable("11");
79	1	assertEquals(gc.translate("ttc"), "F");
80
81	1	gc = codes.getCodeTable("31");
82	1	assertEquals(gc.translate("TGA"), "W"); // variant
83	1	assertEquals(gc.translate("tag"), "E"); // variant
84	1	assertEquals(gc.translate("AGC"), "S"); // non-variant
85		}
86
87		/**
88		* Test 'standard' codon translations (no ambiguity codes)
89		*/
		100% Uncovered Elements: 0 (65) Complexity: 1 Complexity Density: 0.02 1PASS
90	1	@Test(groups = { "Functional" })...
91		public void testTranslate_standardTable()
92		{
93	1	GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
94	1	assertEquals("F", st.translate("TTT"));
95	1	assertEquals("F", st.translate("TTC"));
96	1	assertEquals("L", st.translate("TTA"));
97	1	assertEquals("L", st.translate("TTG"));
98	1	assertEquals("L", st.translate("CTT"));
99	1	assertEquals("L", st.translate("CTC"));
100	1	assertEquals("L", st.translate("CTA"));
101	1	assertEquals("L", st.translate("CTG"));
102	1	assertEquals("I", st.translate("ATT"));
103	1	assertEquals("I", st.translate("ATC"));
104	1	assertEquals("I", st.translate("ATA"));
105	1	assertEquals("M", st.translate("ATG"));
106	1	assertEquals("V", st.translate("GTT"));
107	1	assertEquals("V", st.translate("GTC"));
108	1	assertEquals("V", st.translate("GTA"));
109	1	assertEquals("V", st.translate("GTG"));
110	1	assertEquals("S", st.translate("TCT"));
111	1	assertEquals("S", st.translate("TCC"));
112	1	assertEquals("S", st.translate("TCA"));
113	1	assertEquals("S", st.translate("TCG"));
114	1	assertEquals("P", st.translate("CCT"));
115	1	assertEquals("P", st.translate("CCC"));
116	1	assertEquals("P", st.translate("CCA"));
117	1	assertEquals("P", st.translate("CCG"));
118	1	assertEquals("T", st.translate("ACT"));
119	1	assertEquals("T", st.translate("ACC"));
120	1	assertEquals("T", st.translate("ACA"));
121	1	assertEquals("T", st.translate("ACG"));
122	1	assertEquals("A", st.translate("GCT"));
123	1	assertEquals("A", st.translate("GCC"));
124	1	assertEquals("A", st.translate("GCA"));
125	1	assertEquals("A", st.translate("GCG"));
126	1	assertEquals("Y", st.translate("TAT"));
127	1	assertEquals("Y", st.translate("TAC"));
128	1	assertEquals("*", st.translate("TAA"));
129	1	assertEquals("*", st.translate("TAG"));
130	1	assertEquals("H", st.translate("CAT"));
131	1	assertEquals("H", st.translate("CAC"));
132	1	assertEquals("Q", st.translate("CAA"));
133	1	assertEquals("Q", st.translate("CAG"));
134	1	assertEquals("N", st.translate("AAT"));
135	1	assertEquals("N", st.translate("AAC"));
136	1	assertEquals("K", st.translate("AAA"));
137	1	assertEquals("K", st.translate("AAG"));
138	1	assertEquals("D", st.translate("GAT"));
139	1	assertEquals("D", st.translate("GAC"));
140	1	assertEquals("E", st.translate("GAA"));
141	1	assertEquals("E", st.translate("GAG"));
142	1	assertEquals("C", st.translate("TGT"));
143	1	assertEquals("C", st.translate("TGC"));
144	1	assertEquals("*", st.translate("TGA"));
145	1	assertEquals("W", st.translate("TGG"));
146	1	assertEquals("R", st.translate("CGT"));
147	1	assertEquals("R", st.translate("CGC"));
148	1	assertEquals("R", st.translate("CGA"));
149	1	assertEquals("R", st.translate("CGG"));
150	1	assertEquals("S", st.translate("AGT"));
151	1	assertEquals("S", st.translate("AGC"));
152	1	assertEquals("R", st.translate("AGA"));
153	1	assertEquals("R", st.translate("AGG"));
154	1	assertEquals("G", st.translate("GGT"));
155	1	assertEquals("G", st.translate("GGC"));
156	1	assertEquals("G", st.translate("GGA"));
157	1	assertEquals("G", st.translate("GGG"));
158		}
159
160		/**
161		* Test a sample of codon translations involving ambiguity codes. Should
162		* return a protein value where the ambiguity does not affect the translation.
163		*/
		100% Uncovered Elements: 0 (56) Complexity: 1 Complexity Density: 0.02 1PASS
164	1	@Test(groups = { "Functional" })...
165		public void testTranslate_standardTableAmbiguityCodes()
166		{
167	1	GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
168		// Y is C or T
169	1	assertEquals("C", st.translate("TGY"));
170		// Phenylalanine first base variation
171	1	assertEquals("L", st.translate("YTA"));
172
173		// W is A or T
174	1	assertEquals("L", st.translate("CTW"));
175	1	assertNull(st.translate("TTW"));
176
177		// S is G or C
178	1	assertEquals("G", st.translate("GGS"));
179	1	assertNull(st.translate("ATS"));
180
181		// K is T or G
182	1	assertEquals("S", st.translate("TCK"));
183	1	assertNull(st.translate("ATK"));
184
185		// M is C or A
186	1	assertEquals("T", st.translate("ACM"));
187		// Arginine first base variation
188	1	assertEquals("R", st.translate("MGA"));
189	1	assertEquals("R", st.translate("MGG"));
190	1	assertNull(st.translate("TAM"));
191
192		// D is A, G or T
193	1	assertEquals("P", st.translate("CCD"));
194	1	assertNull(st.translate("AAD"));
195
196		// V is A, C or G
197	1	assertEquals("V", st.translate("GTV"));
198	1	assertNull(st.translate("TTV"));
199
200		// H is A, C or T
201	1	assertEquals("A", st.translate("GCH"));
202	1	assertEquals("I", st.translate("ATH"));
203	1	assertNull(st.translate("AGH"));
204
205		// B is C, G or T
206	1	assertEquals("P", st.translate("CCB"));
207	1	assertNull(st.translate("TAB"));
208
209		// R is A or G
210		// additional tests for JAL-1685 (resolved)
211	1	assertEquals("L", st.translate("CTR"));
212	1	assertEquals("V", st.translate("GTR"));
213	1	assertEquals("S", st.translate("TCR"));
214	1	assertEquals("P", st.translate("CCR"));
215	1	assertEquals("T", st.translate("ACR"));
216	1	assertEquals("A", st.translate("GCR"));
217	1	assertEquals("R", st.translate("CGR"));
218	1	assertEquals("G", st.translate("GGR"));
219	1	assertEquals("R", st.translate("AGR"));
220	1	assertEquals("E", st.translate("GAR"));
221	1	assertEquals("K", st.translate("AAR"));
222	1	assertEquals("L", st.translate("TTR"));
223	1	assertEquals("Q", st.translate("CAR"));
224	1	assertEquals("*", st.translate("TAR"));
225	1	assertEquals("*", st.translate("TRA"));
226		// Arginine first and third base ambiguity
227	1	assertEquals("R", st.translate("MGR"));
228	1	assertNull(st.translate("ATR"));
229
230		// N is any base; 8 proteins accept any base in 3rd position
231	1	assertEquals("L", st.translate("CTN"));
232	1	assertEquals("V", st.translate("GTN"));
233	1	assertEquals("S", st.translate("TCN"));
234	1	assertEquals("P", st.translate("CCN"));
235	1	assertEquals("T", st.translate("ACN"));
236	1	assertEquals("A", st.translate("GCN"));
237	1	assertEquals("R", st.translate("CGN"));
238	1	assertEquals("G", st.translate("GGN"));
239	1	assertNull(st.translate("ATN"));
240	1	assertNull(st.translate("ANT"));
241	1	assertNull(st.translate("NAT"));
242	1	assertNull(st.translate("ANN"));
243	1	assertNull(st.translate("NNA"));
244	1	assertNull(st.translate("NNN"));
245
246		// some random stuff
247	1	assertNull(st.translate("YWB"));
248	1	assertNull(st.translate("VHD"));
249	1	assertNull(st.translate("WSK"));
250		}
251
252		/**
253		* Test a sample of codon translations involving ambiguity codes. Should
254		* return a protein value where the ambiguity does not affect the translation.
255		*/
		100% Uncovered Elements: 0 (19) Complexity: 1 Complexity Density: 0.05 1PASS
256	1	@Test(groups = { "Functional" })...
257		public void testTranslate_nonStandardTableAmbiguityCodes()
258		{
259	1	GeneticCodeI standard = GeneticCodes.getInstance()
260		.getStandardCodeTable();
261
262		/*
263		* Vertebrate Mitochondrial (Table 2)
264		*/
265	1	GeneticCodeI gc = GeneticCodes.getInstance().getCodeTable("2");
266		// AGR is AGA or AGG - R in standard code, * in table 2
267	1	assertEquals(gc.translate("AGR"), "*");
268	1	assertEquals(standard.translate("AGR"), "R");
269		// TGR is TGA or TGG - ambiguous in standard code, W in table 2
270	1	assertEquals(gc.translate("TGR"), "W");
271	1	assertNull(standard.translate("TGR"));
272
273		/*
274		* Yeast Mitochondrial (Table 3)
275		*/
276	1	gc = GeneticCodes.getInstance().getCodeTable("3");
277		// CTN is L in standard code, T in table 3
278	1	assertEquals(gc.translate("ctn"), "T");
279	1	assertEquals(standard.translate("CTN"), "L");
280
281		/*
282		* Alternative Yeast Nuclear (Table 12)
283		*/
284	1	gc = GeneticCodes.getInstance().getCodeTable("12");
285		// CTG is S; in the standard code CTN is L
286	1	assertEquals(gc.translate("CTG"), "S");
287	1	assertNull(gc.translate("CTK")); // K is G or T -> S or L
288	1	assertEquals(standard.translate("CTK"), "L");
289	1	assertEquals(gc.translate("CTH"), "L"); // H is anything other than G
290	1	assertEquals(standard.translate("CTH"), "L");
291	1	assertEquals(standard.translate("CTN"), "L");
292
293		/*
294		* Trematode Mitochondrial (Table 21)
295		*/
296	1	gc = GeneticCodes.getInstance().getCodeTable("21");
297		// AAR is K in standard code, ambiguous in table 21 as AAA=N not K
298	1	assertNull(gc.translate("AAR"));
299	1	assertEquals(standard.translate("AAR"), "K");
300		}
301
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
302	1	@Test(groups = "Functional")...
303		public void testTranslateCanonical()
304		{
305	1	GeneticCodes codes = GeneticCodes.getInstance();
306
307	1	GeneticCodeI gc = codes.getCodeTable("1");
308	1	assertNull(gc.translateCanonical("XYZ"));
309	1	assertEquals(gc.translateCanonical("AGA"), "R");
310		// translateCanonical should not resolve ambiguity codes
311	1	assertNull(gc.translateCanonical("TGY"));
312
313	1	gc = codes.getCodeTable("2");
314	1	assertNull(gc.translateCanonical("AGR"));
315	1	assertEquals(gc.translateCanonical("AGA"), "*"); // variant
316	1	assertEquals(gc.translateCanonical("ttc"), "F"); // non-variant
317		}
318		}