Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBEntryTest	43	134	11	0.00%	Show methods

Class PDBEntryTest

Class PDBEntryTest	Line # 43	Total Statements 134	Complexity 11	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	0.0 0.00%
setUp() : void   setUp() : void	5353	0.00	1.01	-1.0 -1.0 -
tearDown() : void   tearDown() : void	5858	0.00	1.01	-1.0 -1.0 -
testEquals() : void   testEquals() : void	6363	32.032	1.01	0.0 0.00%
testSetChainCode() : void   testSetChainCode() : void	127127	6.06	1.01	0.0 0.00%
testGetType() : void   testGetType() : void	141141	4.04	1.01	0.0 0.00%
testTypeMatches() : void   testTypeMatches() : void	150150	4.04	1.01	0.0 0.00%
testUpdateFrom() : void   testUpdateFrom() : void	160160	70.070	1.01	0.0 0.00%
testConstructor_fromDbref() : void   testConstructor_fromDbref() : void	290290	14.014	2.02	0.0 0.00%
testMetadataProperties() : void   testMetadataProperties() : void	326326	2.02	1.01	0.0 0.00%

 

Contributing tests

Source view

1		/*
2		assertEquals(case7, case9);
3		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4		* Copyright (C) $$Year-Rel$$ The Jalview Authors
5		*
6		* This file is part of Jalview.
7		*
8		* Jalview is free software: you can redistribute it and/or
9		* modify it under the terms of the GNU General Public License
10		* as published by the Free Software Foundation, either version 3
11		* of the License, or (at your option) any later version.
12		*
13		* Jalview is distributed in the hope that it will be useful, but
14		* WITHOUT ANY WARRANTY; without even the implied warranty
15		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16		* PURPOSE. See the GNU General Public License for more details.
17		*
18		* You should have received a copy of the GNU General Public License
19		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20		* The Jalview Authors are detailed in the 'AUTHORS' file.
21		*/
22		package jalview.datamodel;
23
24		import static org.testng.Assert.assertEquals;
25		import static org.testng.Assert.assertFalse;
26		import static org.testng.Assert.assertNotEquals;
27		import static org.testng.Assert.assertNotSame;
28		import static org.testng.Assert.assertNull;
29		import static org.testng.Assert.assertSame;
30		import static org.testng.Assert.assertTrue;
31		import static org.testng.Assert.fail;
32
33		import jalview.datamodel.PDBEntry.Type;
34		import jalview.gui.JvOptionPane;
35		import jalview.structure.StructureImportSettings.TFType;
36
37		//import org.testng.Assert;
38		import org.testng.annotations.AfterMethod;
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.BeforeMethod;
41		import org.testng.annotations.Test;
42
		0% Uncovered Elements: 144 (144) Complexity: 11 Complexity Density: 0.08
43		public class PDBEntryTest
44		{
45
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
46	0	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	0	JvOptionPane.setInteractiveMode(false);
50	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
53	0	@BeforeMethod(alwaysRun = true)...
54		public void setUp() throws Exception
55		{
56		}
57
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
58	0	@AfterMethod(alwaysRun = true)...
59		public void tearDown() throws Exception
60		{
61		}
62
		0% Uncovered Elements: 32 (32) Complexity: 1 Complexity Density: 0.03 4-
63	0	@Test(groups = { "Functional" })...
64		public void testEquals()
65		{
66	0	PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
67		"x/y/z/File");
68
69		// id comparison is not case sensitive
70	0	PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
71		"x/y/z/File");
72		// chain code comparison is not case sensitive
73	0	PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
74		"x/y/z/File");
75		// different type
76	0	PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
77		"x/y/z/File");
78		// different everything
79	0	PDBEntry case4 = new PDBEntry(null, null, null, null);
80		// null id
81	0	PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
82		"x/y/z/File");
83		// null chain
84	0	PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
85		"x/y/z/File");
86		// null type
87	0	PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
88		// null file
89	0	PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
90		// identical to case7
91	0	PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
92		// different file only
93	0	PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
94
95		/*
96		* assertEquals will invoke PDBEntry.equals()
97		*/
98	0	assertFalse(pdbEntry.equals(null));
99	0	assertFalse(pdbEntry.equals("a"));
100	0	assertEquals(case1, pdbEntry);
101	0	assertEquals(case2, pdbEntry);
102	0	assertNotEquals(case3, pdbEntry);
103	0	assertNotEquals(case4, pdbEntry);
104	0	assertNotEquals(case5, pdbEntry);
105	0	assertNotEquals(case6, pdbEntry);
106	0	assertNotEquals(case7, pdbEntry);
107	0	assertNotEquals(case8, pdbEntry);
108	0	assertEquals(case7, case9);
109	0	assertNotEquals(case9, case10);
110
111		// add properties
112	0	case7.setProperty("hello", "world");
113	0	assertNotEquals(case7, case9);
114	0	case9.setProperty("hello", "world");
115	0	assertEquals(case7, case9);
116	0	case9.setProperty("hello", "WORLD");
117	0	assertNotEquals(case7, case9);
118
119		/*
120		* change string wrapper property to string...
121		*/
122	0	case1.setProperty("chain_code", "a");
123	0	assertFalse(pdbEntry.equals(case1));
124	0	assertFalse(case1.equals(pdbEntry));
125		}
126
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17 4-
127	0	@Test(groups = { "Functional" })...
128		public void testSetChainCode()
129		{
130	0	PDBEntry pdbEntry = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
131		"x/y/z/File");
132	0	assertNull(pdbEntry.getChainCode());
133
134	0	pdbEntry.setChainCode("a");
135	0	assertEquals("a", pdbEntry.getChainCode());
136
137	0	pdbEntry.setChainCode(null);
138	0	assertNull(pdbEntry.getChainCode());
139		}
140
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
141	0	@Test(groups = { "Functional" })...
142		public void testGetType()
143		{
144	0	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("FILE"));
145	0	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("File"));
146	0	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file"));
147	0	assertNotSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file "));
148		}
149
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
150	0	@Test(groups = { "Functional" })...
151		public void testTypeMatches()
152		{
153		// TODO Type.matches() is not used - delete?
154	0	assertTrue(PDBEntry.Type.FILE.matches("FILE"));
155	0	assertTrue(PDBEntry.Type.FILE.matches("File"));
156	0	assertTrue(PDBEntry.Type.FILE.matches("file"));
157	0	assertFalse(PDBEntry.Type.FILE.matches("FILE "));
158		}
159
		0% Uncovered Elements: 70 (70) Complexity: 1 Complexity Density: 0.01 4-
160	0	@Test(groups = { "Functional" })...
161		public void testUpdateFrom()
162		{
163	0	PDBEntry pdb1 = new PDBEntry("3A6S", null, null, null);
164	0	PDBEntry pdb2 = new PDBEntry("3A6S", null, null, null);
165	0	assertTrue(pdb1.updateFrom(pdb2));
166
167		/*
168		* mismatch of pdb id not allowed
169		*/
170	0	pdb2 = new PDBEntry("1A70", "A", null, null);
171	0	assertFalse(pdb1.updateFrom(pdb2));
172	0	assertNull(pdb1.getChainCode());
173
174		/*
175		* match of pdb id is not case sensitive
176		*/
177	0	pdb2 = new PDBEntry("3a6s", "A", null, null);
178	0	assertTrue(pdb1.updateFrom(pdb2));
179	0	assertEquals(pdb1.getChainCode(), "A");
180	0	assertEquals(pdb1.getId(), "3A6S");
181
182		/*
183		* add chain - with differing case for id
184		*/
185	0	pdb1 = new PDBEntry("3A6S", null, null, null);
186	0	pdb2 = new PDBEntry("3a6s", "A", null, null);
187	0	assertTrue(pdb1.updateFrom(pdb2));
188	0	assertEquals(pdb1.getChainCode(), "A");
189
190		/*
191		* change of chain is not allowed
192		*/
193	0	pdb2 = new PDBEntry("3A6S", "B", null, null);
194	0	assertFalse(pdb1.updateFrom(pdb2));
195	0	assertEquals(pdb1.getChainCode(), "A");
196
197		/*
198		* change chain from null
199		*/
200	0	pdb1 = new PDBEntry("3A6S", null, null, null);
201	0	pdb2 = new PDBEntry("3A6S", "B", null, null);
202	0	assertTrue(pdb1.updateFrom(pdb2));
203	0	assertEquals(pdb1.getChainCode(), "B");
204
205		/*
206		* set file and type
207		*/
208	0	pdb2 = new PDBEntry("3A6S", "B", Type.FILE, "filePath");
209	0	assertTrue(pdb1.updateFrom(pdb2));
210	0	assertEquals(pdb1.getFile(), "filePath");
211	0	assertEquals(pdb1.getType(), Type.FILE.toString());
212	0	assertEquals(pdb1.getChainCode(), "B");
213		/*
214		* change of file is not allowed
215		*/
216	0	pdb1 = new PDBEntry("3A6S", null, null, "file1");
217	0	pdb2 = new PDBEntry("3A6S", "A", null, "file2");
218	0	assertFalse(pdb1.updateFrom(pdb2));
219	0	assertNull(pdb1.getChainCode());
220	0	assertEquals(pdb1.getFile(), "file1");
221
222		/*
223		* set type without change of file
224		*/
225	0	pdb1 = new PDBEntry("3A6S", null, null, "file1");
226	0	pdb2 = new PDBEntry("3A6S", null, Type.PDB, "file1");
227	0	assertTrue(pdb1.updateFrom(pdb2));
228	0	assertEquals(pdb1.getType(), Type.PDB.toString());
229
230		/*
231		* set file with differing case of id and chain code
232		*/
233	0	pdb1 = new PDBEntry("3A6S", "A", null, null);
234	0	pdb2 = new PDBEntry("3a6s", "a", Type.PDB, "file1");
235	0	assertTrue(pdb1.updateFrom(pdb2));
236	0	assertEquals(pdb1.getType(), Type.PDB.toString());
237	0	assertEquals(pdb1.getId(), "3A6S"); // unchanged
238	0	assertEquals(pdb1.getFile(), "file1"); // updated
239	0	assertEquals(pdb1.getChainCode(), "A"); // unchanged
240
241		/*
242		* changing nothing returns true
243		*/
244	0	pdb1 = new PDBEntry("3A6S", "A", Type.PDB, "file1");
245	0	pdb2 = new PDBEntry("3A6S", null, null, null);
246	0	assertTrue(pdb1.updateFrom(pdb2));
247	0	assertEquals(pdb1.getChainCode(), "A");
248	0	assertEquals(pdb1.getType(), Type.PDB.toString());
249	0	assertEquals(pdb1.getFile(), "file1");
250
251		/*
252		* add and update properties only
253		*/
254	0	pdb1 = new PDBEntry("3A6S", null, null, null);
255	0	pdb2 = new PDBEntry("3A6S", null, null, null);
256	0	pdb1.setProperty("destination", "mars");
257	0	pdb1.setProperty("hello", "world");
258	0	pdb2.setProperty("hello", "moon");
259	0	pdb2.setProperty("goodbye", "world");
260	0	assertTrue(pdb1.updateFrom(pdb2));
261	0	assertEquals(pdb1.getProperty("destination"), "mars");
262	0	assertEquals(pdb1.getProperty("hello"), "moon");
263	0	assertEquals(pdb1.getProperty("goodbye"), "world");
264
265		/*
266		* add properties only
267		*/
268	0	pdb1 = new PDBEntry("3A6S", null, null, null);
269	0	pdb2 = new PDBEntry("3A6S", null, null, null);
270	0	pdb2.setProperty("hello", "moon");
271	0	assertTrue(pdb1.updateFrom(pdb2));
272	0	assertEquals(pdb1.getProperty("hello"), "moon");
273
274		/*
275		* different id but authoritative
276		*/
277	0	pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
278	0	pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
279	0	pdb1.setAuthoritative(true);
280
281	0	assertTrue(pdb1.isAuthoritative());
282	0	assertFalse(pdb2.isAuthoritative());
283		// can update pdb1 (authoritative) from pdb2 (non-authoritative)
284	0	assertTrue(pdb1.updateFrom(pdb2));
285		// but the ID must remain the same
286	0	assertEquals(pdb1.getId(), "af:1xyz");
287
288		}
289
		0% Uncovered Elements: 14 (14) Complexity: 2 Complexity Density: 0.14 4-
290	0	@Test(groups = { "Functional" })...
291		public void testConstructor_fromDbref()
292		{
293	0	PDBEntry pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70"));
294	0	assertEquals(pdb.getId(), "1A70");
295	0	assertNull(pdb.getChainCode());
296	0	assertNull(pdb.getType());
297	0	assertNull(pdb.getFile());
298
299		/*
300		* from dbref with chain code appended
301		*/
302	0	pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70B"));
303	0	assertEquals(pdb.getId(), "1A70");
304	0	assertEquals(pdb.getChainCode(), "B");
305
306		/*
307		* from dbref with overlong accession
308		*/
309	0	pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70BC"));
310	0	assertEquals(pdb.getId(), "1A70BC");
311	0	assertNull(pdb.getChainCode());
312
313		/*
314		* from dbref which is not for PDB
315		*/
316	0	try
317		{
318	0	pdb = new PDBEntry(new DBRefEntry("PDBe", "0", "1A70"));
319	0	fail("Expected exception");
320		} catch (IllegalArgumentException e)
321		{
322		// expected;
323		}
324		}
325
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 4-
326	0	@Test(groups= {"Functional"})...
327		public void testMetadataProperties()
328		{
329	0	PDBEntry pdb = new PDBEntry("af:1xyz","A",null,"a/b/c/File");
330	0	assertEquals(pdb.getTempFacTypeTFType(),null);
331		}
332		}