Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBEntryTest	43	134	11	0.993055699.3%	Show methods

Class PDBEntryTest

Class PDBEntryTest	Line # 43	Total Statements 134	Complexity 11	TOTAL Coverage 0.993055699.3%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	1.0 1.0100%
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	1.0 1.0100%
testSetChainCode() : void   testSetChainCode() : void	127127	6.06	1.01	1.0 1.0100%
testGetType() : void   testGetType() : void	141141	4.04	1.01	1.0 1.0100%
testTypeMatches() : void   testTypeMatches() : void	150150	4.04	1.01	1.0 1.0100%
testUpdateFrom() : void   testUpdateFrom() : void	160160	70.070	1.01	1.0 1.0100%
testConstructor_fromDbref() : void   testConstructor_fromDbref() : void	290290	14.014	2.02	0.9285714 0.928571492.9%
testMetadataProperties() : void   testMetadataProperties() : void	326326	2.02	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.49305555	jalview.datamodel.PDBEntryTest.testUpdateFromjalview.datamodel.PDBEntryTest.testUpdateFrom	1PASS
	0.22916667	jalview.datamodel.PDBEntryTest.testEqualsjalview.datamodel.PDBEntryTest.testEquals	1PASS
	0.097222224	jalview.datamodel.PDBEntryTest.testConstructor_fromDbrefjalview.datamodel.PDBEntryTest.testConstructor_fromDbref	1PASS
	0.048611112	jalview.datamodel.PDBEntryTest.testSetChainCodejalview.datamodel.PDBEntryTest.testSetChainCode	1PASS
	0.034722224	jalview.datamodel.PDBEntryTest.testGetTypejalview.datamodel.PDBEntryTest.testGetType	1PASS
	0.034722224	jalview.datamodel.PDBEntryTest.testTypeMatchesjalview.datamodel.PDBEntryTest.testTypeMatches	1PASS
	0.020833334	jalview.datamodel.PDBEntryTest.testMetadataPropertiesjalview.datamodel.PDBEntryTest.testMetadataProperties	1PASS

 

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
		99.3% Uncovered Elements: 1 (144) Complexity: 11 Complexity Density: 0.08
43		public class PDBEntryTest
44		{
45
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	1	JvOptionPane.setInteractiveMode(false);
50	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
53	7	@BeforeMethod(alwaysRun = true)...
54		public void setUp() throws Exception
55		{
56		}
57
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
58	7	@AfterMethod(alwaysRun = true)...
59		public void tearDown() throws Exception
60		{
61		}
62
		100% Uncovered Elements: 0 (32) Complexity: 1 Complexity Density: 0.03 1PASS
63	1	@Test(groups = { "Functional" })...
64		public void testEquals()
65		{
66	1	PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
67		"x/y/z/File");
68
69		// id comparison is not case sensitive
70	1	PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
71		"x/y/z/File");
72		// chain code comparison is not case sensitive
73	1	PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
74		"x/y/z/File");
75		// different type
76	1	PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
77		"x/y/z/File");
78		// different everything
79	1	PDBEntry case4 = new PDBEntry(null, null, null, null);
80		// null id
81	1	PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
82		"x/y/z/File");
83		// null chain
84	1	PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
85		"x/y/z/File");
86		// null type
87	1	PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
88		// null file
89	1	PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
90		// identical to case7
91	1	PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
92		// different file only
93	1	PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
94
95		/*
96		* assertEquals will invoke PDBEntry.equals()
97		*/
98	1	assertFalse(pdbEntry.equals(null));
99	1	assertFalse(pdbEntry.equals("a"));
100	1	assertEquals(case1, pdbEntry);
101	1	assertEquals(case2, pdbEntry);
102	1	assertNotEquals(case3, pdbEntry);
103	1	assertNotEquals(case4, pdbEntry);
104	1	assertNotEquals(case5, pdbEntry);
105	1	assertNotEquals(case6, pdbEntry);
106	1	assertNotEquals(case7, pdbEntry);
107	1	assertNotEquals(case8, pdbEntry);
108	1	assertEquals(case7, case9);
109	1	assertNotEquals(case9, case10);
110
111		// add properties
112	1	case7.setProperty("hello", "world");
113	1	assertNotEquals(case7, case9);
114	1	case9.setProperty("hello", "world");
115	1	assertEquals(case7, case9);
116	1	case9.setProperty("hello", "WORLD");
117	1	assertNotEquals(case7, case9);
118
119		/*
120		* change string wrapper property to string...
121		*/
122	1	case1.setProperty("chain_code", "a");
123	1	assertFalse(pdbEntry.equals(case1));
124	1	assertFalse(case1.equals(pdbEntry));
125		}
126
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
127	1	@Test(groups = { "Functional" })...
128		public void testSetChainCode()
129		{
130	1	PDBEntry pdbEntry = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
131		"x/y/z/File");
132	1	assertNull(pdbEntry.getChainCode());
133
134	1	pdbEntry.setChainCode("a");
135	1	assertEquals("a", pdbEntry.getChainCode());
136
137	1	pdbEntry.setChainCode(null);
138	1	assertNull(pdbEntry.getChainCode());
139		}
140
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
141	1	@Test(groups = { "Functional" })...
142		public void testGetType()
143		{
144	1	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("FILE"));
145	1	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("File"));
146	1	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file"));
147	1	assertNotSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file "));
148		}
149
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
150	1	@Test(groups = { "Functional" })...
151		public void testTypeMatches()
152		{
153		// TODO Type.matches() is not used - delete?
154	1	assertTrue(PDBEntry.Type.FILE.matches("FILE"));
155	1	assertTrue(PDBEntry.Type.FILE.matches("File"));
156	1	assertTrue(PDBEntry.Type.FILE.matches("file"));
157	1	assertFalse(PDBEntry.Type.FILE.matches("FILE "));
158		}
159
		100% Uncovered Elements: 0 (70) Complexity: 1 Complexity Density: 0.01 1PASS
160	1	@Test(groups = { "Functional" })...
161		public void testUpdateFrom()
162		{
163	1	PDBEntry pdb1 = new PDBEntry("3A6S", null, null, null);
164	1	PDBEntry pdb2 = new PDBEntry("3A6S", null, null, null);
165	1	assertTrue(pdb1.updateFrom(pdb2));
166
167		/*
168		* mismatch of pdb id not allowed
169		*/
170	1	pdb2 = new PDBEntry("1A70", "A", null, null);
171	1	assertFalse(pdb1.updateFrom(pdb2));
172	1	assertNull(pdb1.getChainCode());
173
174		/*
175		* match of pdb id is not case sensitive
176		*/
177	1	pdb2 = new PDBEntry("3a6s", "A", null, null);
178	1	assertTrue(pdb1.updateFrom(pdb2));
179	1	assertEquals(pdb1.getChainCode(), "A");
180	1	assertEquals(pdb1.getId(), "3A6S");
181
182		/*
183		* add chain - with differing case for id
184		*/
185	1	pdb1 = new PDBEntry("3A6S", null, null, null);
186	1	pdb2 = new PDBEntry("3a6s", "A", null, null);
187	1	assertTrue(pdb1.updateFrom(pdb2));
188	1	assertEquals(pdb1.getChainCode(), "A");
189
190		/*
191		* change of chain is not allowed
192		*/
193	1	pdb2 = new PDBEntry("3A6S", "B", null, null);
194	1	assertFalse(pdb1.updateFrom(pdb2));
195	1	assertEquals(pdb1.getChainCode(), "A");
196
197		/*
198		* change chain from null
199		*/
200	1	pdb1 = new PDBEntry("3A6S", null, null, null);
201	1	pdb2 = new PDBEntry("3A6S", "B", null, null);
202	1	assertTrue(pdb1.updateFrom(pdb2));
203	1	assertEquals(pdb1.getChainCode(), "B");
204
205		/*
206		* set file and type
207		*/
208	1	pdb2 = new PDBEntry("3A6S", "B", Type.FILE, "filePath");
209	1	assertTrue(pdb1.updateFrom(pdb2));
210	1	assertEquals(pdb1.getFile(), "filePath");
211	1	assertEquals(pdb1.getType(), Type.FILE.toString());
212	1	assertEquals(pdb1.getChainCode(), "B");
213		/*
214		* change of file is not allowed
215		*/
216	1	pdb1 = new PDBEntry("3A6S", null, null, "file1");
217	1	pdb2 = new PDBEntry("3A6S", "A", null, "file2");
218	1	assertFalse(pdb1.updateFrom(pdb2));
219	1	assertNull(pdb1.getChainCode());
220	1	assertEquals(pdb1.getFile(), "file1");
221
222		/*
223		* set type without change of file
224		*/
225	1	pdb1 = new PDBEntry("3A6S", null, null, "file1");
226	1	pdb2 = new PDBEntry("3A6S", null, Type.PDB, "file1");
227	1	assertTrue(pdb1.updateFrom(pdb2));
228	1	assertEquals(pdb1.getType(), Type.PDB.toString());
229
230		/*
231		* set file with differing case of id and chain code
232		*/
233	1	pdb1 = new PDBEntry("3A6S", "A", null, null);
234	1	pdb2 = new PDBEntry("3a6s", "a", Type.PDB, "file1");
235	1	assertTrue(pdb1.updateFrom(pdb2));
236	1	assertEquals(pdb1.getType(), Type.PDB.toString());
237	1	assertEquals(pdb1.getId(), "3A6S"); // unchanged
238	1	assertEquals(pdb1.getFile(), "file1"); // updated
239	1	assertEquals(pdb1.getChainCode(), "A"); // unchanged
240
241		/*
242		* changing nothing returns true
243		*/
244	1	pdb1 = new PDBEntry("3A6S", "A", Type.PDB, "file1");
245	1	pdb2 = new PDBEntry("3A6S", null, null, null);
246	1	assertTrue(pdb1.updateFrom(pdb2));
247	1	assertEquals(pdb1.getChainCode(), "A");
248	1	assertEquals(pdb1.getType(), Type.PDB.toString());
249	1	assertEquals(pdb1.getFile(), "file1");
250
251		/*
252		* add and update properties only
253		*/
254	1	pdb1 = new PDBEntry("3A6S", null, null, null);
255	1	pdb2 = new PDBEntry("3A6S", null, null, null);
256	1	pdb1.setProperty("destination", "mars");
257	1	pdb1.setProperty("hello", "world");
258	1	pdb2.setProperty("hello", "moon");
259	1	pdb2.setProperty("goodbye", "world");
260	1	assertTrue(pdb1.updateFrom(pdb2));
261	1	assertEquals(pdb1.getProperty("destination"), "mars");
262	1	assertEquals(pdb1.getProperty("hello"), "moon");
263	1	assertEquals(pdb1.getProperty("goodbye"), "world");
264
265		/*
266		* add properties only
267		*/
268	1	pdb1 = new PDBEntry("3A6S", null, null, null);
269	1	pdb2 = new PDBEntry("3A6S", null, null, null);
270	1	pdb2.setProperty("hello", "moon");
271	1	assertTrue(pdb1.updateFrom(pdb2));
272	1	assertEquals(pdb1.getProperty("hello"), "moon");
273
274		/*
275		* different id but authoritative
276		*/
277	1	pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
278	1	pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
279	1	pdb1.setAuthoritative(true);
280
281	1	assertTrue(pdb1.isAuthoritative());
282	1	assertFalse(pdb2.isAuthoritative());
283		// can update pdb1 (authoritative) from pdb2 (non-authoritative)
284	1	assertTrue(pdb1.updateFrom(pdb2));
285		// but the ID must remain the same
286	1	assertEquals(pdb1.getId(), "af:1xyz");
287
288		}
289
		92.9% Uncovered Elements: 1 (14) Complexity: 2 Complexity Density: 0.14 1PASS
290	1	@Test(groups = { "Functional" })...
291		public void testConstructor_fromDbref()
292		{
293	1	PDBEntry pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70"));
294	1	assertEquals(pdb.getId(), "1A70");
295	1	assertNull(pdb.getChainCode());
296	1	assertNull(pdb.getType());
297	1	assertNull(pdb.getFile());
298
299		/*
300		* from dbref with chain code appended
301		*/
302	1	pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70B"));
303	1	assertEquals(pdb.getId(), "1A70");
304	1	assertEquals(pdb.getChainCode(), "B");
305
306		/*
307		* from dbref with overlong accession
308		*/
309	1	pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70BC"));
310	1	assertEquals(pdb.getId(), "1A70BC");
311	1	assertNull(pdb.getChainCode());
312
313		/*
314		* from dbref which is not for PDB
315		*/
316	1	try
317		{
318	1	pdb = new PDBEntry(new DBRefEntry("PDBe", "0", "1A70"));
319	0	fail("Expected exception");
320		} catch (IllegalArgumentException e)
321		{
322		// expected;
323		}
324		}
325
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
326	1	@Test(groups= {"Functional"})...
327		public void testMetadataProperties()
328		{
329	1	PDBEntry pdb = new PDBEntry("af:1xyz","A",null,"a/b/c/File");
330	1	assertEquals(pdb.getTempFacTypeTFType(),null);
331		}
332		}