Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBEntryTest	42	132	10	0.992907899.3%	Show methods

Class PDBEntryTest

Class PDBEntryTest	Line # 42	Total Statements 132	Complexity 10	TOTAL Coverage 0.992907899.3%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5252	0.00	1.01	-1.0 -1.0 -
tearDown() : void   tearDown() : void	5757	0.00	1.01	-1.0 -1.0 -
testEquals() : void   testEquals() : void	6262	32.032	1.01	1.0 1.0100%
testSetChainCode() : void   testSetChainCode() : void	126126	6.06	1.01	1.0 1.0100%
testGetType() : void   testGetType() : void	140140	4.04	1.01	1.0 1.0100%
testTypeMatches() : void   testTypeMatches() : void	149149	4.04	1.01	1.0 1.0100%
testUpdateFrom() : void   testUpdateFrom() : void	159159	70.070	1.01	1.0 1.0100%
testConstructor_fromDbref() : void   testConstructor_fromDbref() : void	289289	14.014	2.02	0.9285714 0.928571492.9%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5035461	jalview.datamodel.PDBEntryTest.testUpdateFromjalview.datamodel.PDBEntryTest.testUpdateFrom	1PASS
	0.23404256	jalview.datamodel.PDBEntryTest.testEqualsjalview.datamodel.PDBEntryTest.testEquals	1PASS
	0.09929078	jalview.datamodel.PDBEntryTest.testConstructor_fromDbrefjalview.datamodel.PDBEntryTest.testConstructor_fromDbref	1PASS
	0.04964539	jalview.datamodel.PDBEntryTest.testSetChainCodejalview.datamodel.PDBEntryTest.testSetChainCode	1PASS
	0.035460994	jalview.datamodel.PDBEntryTest.testGetTypejalview.datamodel.PDBEntryTest.testGetType	1PASS
	0.035460994	jalview.datamodel.PDBEntryTest.testTypeMatchesjalview.datamodel.PDBEntryTest.testTypeMatches	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
36		//import org.testng.Assert;
37		import org.testng.annotations.AfterMethod;
38		import org.testng.annotations.BeforeClass;
39		import org.testng.annotations.BeforeMethod;
40		import org.testng.annotations.Test;
41
		99.3% Uncovered Elements: 1 (141) Complexity: 10 Complexity Density: 0.08
42		public class PDBEntryTest
43		{
44
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
45	1	@BeforeClass(alwaysRun = true)...
46		public void setUpJvOptionPane()
47		{
48	1	JvOptionPane.setInteractiveMode(false);
49	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50		}
51
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
52	6	@BeforeMethod(alwaysRun = true)...
53		public void setUp() throws Exception
54		{
55		}
56
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
57	6	@AfterMethod(alwaysRun = true)...
58		public void tearDown() throws Exception
59		{
60		}
61
		100% Uncovered Elements: 0 (32) Complexity: 1 Complexity Density: 0.03 1PASS
62	1	@Test(groups = { "Functional" })...
63		public void testEquals()
64		{
65	1	PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
66		"x/y/z/File");
67
68		// id comparison is not case sensitive
69	1	PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
70		"x/y/z/File");
71		// chain code comparison is not case sensitive
72	1	PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
73		"x/y/z/File");
74		// different type
75	1	PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
76		"x/y/z/File");
77		// different everything
78	1	PDBEntry case4 = new PDBEntry(null, null, null, null);
79		// null id
80	1	PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
81		"x/y/z/File");
82		// null chain
83	1	PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
84		"x/y/z/File");
85		// null type
86	1	PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
87		// null file
88	1	PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
89		// identical to case7
90	1	PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
91		// different file only
92	1	PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
93
94		/*
95		* assertEquals will invoke PDBEntry.equals()
96		*/
97	1	assertFalse(pdbEntry.equals(null));
98	1	assertFalse(pdbEntry.equals("a"));
99	1	assertEquals(case1, pdbEntry);
100	1	assertEquals(case2, pdbEntry);
101	1	assertNotEquals(case3, pdbEntry);
102	1	assertNotEquals(case4, pdbEntry);
103	1	assertNotEquals(case5, pdbEntry);
104	1	assertNotEquals(case6, pdbEntry);
105	1	assertNotEquals(case7, pdbEntry);
106	1	assertNotEquals(case8, pdbEntry);
107	1	assertEquals(case7, case9);
108	1	assertNotEquals(case9, case10);
109
110		// add properties
111	1	case7.setProperty("hello", "world");
112	1	assertNotEquals(case7, case9);
113	1	case9.setProperty("hello", "world");
114	1	assertEquals(case7, case9);
115	1	case9.setProperty("hello", "WORLD");
116	1	assertNotEquals(case7, case9);
117
118		/*
119		* change string wrapper property to string...
120		*/
121	1	case1.setProperty("chain_code", "a");
122	1	assertFalse(pdbEntry.equals(case1));
123	1	assertFalse(case1.equals(pdbEntry));
124		}
125
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
126	1	@Test(groups = { "Functional" })...
127		public void testSetChainCode()
128		{
129	1	PDBEntry pdbEntry = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
130		"x/y/z/File");
131	1	assertNull(pdbEntry.getChainCode());
132
133	1	pdbEntry.setChainCode("a");
134	1	assertEquals("a", pdbEntry.getChainCode());
135
136	1	pdbEntry.setChainCode(null);
137	1	assertNull(pdbEntry.getChainCode());
138		}
139
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
140	1	@Test(groups = { "Functional" })...
141		public void testGetType()
142		{
143	1	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("FILE"));
144	1	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("File"));
145	1	assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file"));
146	1	assertNotSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file "));
147		}
148
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
149	1	@Test(groups = { "Functional" })...
150		public void testTypeMatches()
151		{
152		// TODO Type.matches() is not used - delete?
153	1	assertTrue(PDBEntry.Type.FILE.matches("FILE"));
154	1	assertTrue(PDBEntry.Type.FILE.matches("File"));
155	1	assertTrue(PDBEntry.Type.FILE.matches("file"));
156	1	assertFalse(PDBEntry.Type.FILE.matches("FILE "));
157		}
158
		100% Uncovered Elements: 0 (70) Complexity: 1 Complexity Density: 0.01 1PASS
159	1	@Test(groups = { "Functional" })...
160		public void testUpdateFrom()
161		{
162	1	PDBEntry pdb1 = new PDBEntry("3A6S", null, null, null);
163	1	PDBEntry pdb2 = new PDBEntry("3A6S", null, null, null);
164	1	assertTrue(pdb1.updateFrom(pdb2));
165
166		/*
167		* mismatch of pdb id not allowed
168		*/
169	1	pdb2 = new PDBEntry("1A70", "A", null, null);
170	1	assertFalse(pdb1.updateFrom(pdb2));
171	1	assertNull(pdb1.getChainCode());
172
173		/*
174		* match of pdb id is not case sensitive
175		*/
176	1	pdb2 = new PDBEntry("3a6s", "A", null, null);
177	1	assertTrue(pdb1.updateFrom(pdb2));
178	1	assertEquals(pdb1.getChainCode(), "A");
179	1	assertEquals(pdb1.getId(), "3A6S");
180
181		/*
182		* add chain - with differing case for id
183		*/
184	1	pdb1 = new PDBEntry("3A6S", null, null, null);
185	1	pdb2 = new PDBEntry("3a6s", "A", null, null);
186	1	assertTrue(pdb1.updateFrom(pdb2));
187	1	assertEquals(pdb1.getChainCode(), "A");
188
189		/*
190		* change of chain is not allowed
191		*/
192	1	pdb2 = new PDBEntry("3A6S", "B", null, null);
193	1	assertFalse(pdb1.updateFrom(pdb2));
194	1	assertEquals(pdb1.getChainCode(), "A");
195
196		/*
197		* change chain from null
198		*/
199	1	pdb1 = new PDBEntry("3A6S", null, null, null);
200	1	pdb2 = new PDBEntry("3A6S", "B", null, null);
201	1	assertTrue(pdb1.updateFrom(pdb2));
202	1	assertEquals(pdb1.getChainCode(), "B");
203
204		/*
205		* set file and type
206		*/
207	1	pdb2 = new PDBEntry("3A6S", "B", Type.FILE, "filePath");
208	1	assertTrue(pdb1.updateFrom(pdb2));
209	1	assertEquals(pdb1.getFile(), "filePath");
210	1	assertEquals(pdb1.getType(), Type.FILE.toString());
211	1	assertEquals(pdb1.getChainCode(), "B");
212		/*
213		* change of file is not allowed
214		*/
215	1	pdb1 = new PDBEntry("3A6S", null, null, "file1");
216	1	pdb2 = new PDBEntry("3A6S", "A", null, "file2");
217	1	assertFalse(pdb1.updateFrom(pdb2));
218	1	assertNull(pdb1.getChainCode());
219	1	assertEquals(pdb1.getFile(), "file1");
220
221		/*
222		* set type without change of file
223		*/
224	1	pdb1 = new PDBEntry("3A6S", null, null, "file1");
225	1	pdb2 = new PDBEntry("3A6S", null, Type.PDB, "file1");
226	1	assertTrue(pdb1.updateFrom(pdb2));
227	1	assertEquals(pdb1.getType(), Type.PDB.toString());
228
229		/*
230		* set file with differing case of id and chain code
231		*/
232	1	pdb1 = new PDBEntry("3A6S", "A", null, null);
233	1	pdb2 = new PDBEntry("3a6s", "a", Type.PDB, "file1");
234	1	assertTrue(pdb1.updateFrom(pdb2));
235	1	assertEquals(pdb1.getType(), Type.PDB.toString());
236	1	assertEquals(pdb1.getId(), "3A6S"); // unchanged
237	1	assertEquals(pdb1.getFile(), "file1"); // updated
238	1	assertEquals(pdb1.getChainCode(), "A"); // unchanged
239
240		/*
241		* changing nothing returns true
242		*/
243	1	pdb1 = new PDBEntry("3A6S", "A", Type.PDB, "file1");
244	1	pdb2 = new PDBEntry("3A6S", null, null, null);
245	1	assertTrue(pdb1.updateFrom(pdb2));
246	1	assertEquals(pdb1.getChainCode(), "A");
247	1	assertEquals(pdb1.getType(), Type.PDB.toString());
248	1	assertEquals(pdb1.getFile(), "file1");
249
250		/*
251		* add and update properties only
252		*/
253	1	pdb1 = new PDBEntry("3A6S", null, null, null);
254	1	pdb2 = new PDBEntry("3A6S", null, null, null);
255	1	pdb1.setProperty("destination", "mars");
256	1	pdb1.setProperty("hello", "world");
257	1	pdb2.setProperty("hello", "moon");
258	1	pdb2.setProperty("goodbye", "world");
259	1	assertTrue(pdb1.updateFrom(pdb2));
260	1	assertEquals(pdb1.getProperty("destination"), "mars");
261	1	assertEquals(pdb1.getProperty("hello"), "moon");
262	1	assertEquals(pdb1.getProperty("goodbye"), "world");
263
264		/*
265		* add properties only
266		*/
267	1	pdb1 = new PDBEntry("3A6S", null, null, null);
268	1	pdb2 = new PDBEntry("3A6S", null, null, null);
269	1	pdb2.setProperty("hello", "moon");
270	1	assertTrue(pdb1.updateFrom(pdb2));
271	1	assertEquals(pdb1.getProperty("hello"), "moon");
272
273		/*
274		* different id but authoritative
275		*/
276	1	pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
277	1	pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
278	1	pdb1.setAuthoritative(true);
279
280	1	assertTrue(pdb1.isAuthoritative());
281	1	assertFalse(pdb2.isAuthoritative());
282		// can update pdb1 (authoritative) from pdb2 (non-authoritative)
283	1	assertTrue(pdb1.updateFrom(pdb2));
284		// but the ID must remain the same
285	1	assertEquals(pdb1.getId(), "af:1xyz");
286
287		}
288
		92.9% Uncovered Elements: 1 (14) Complexity: 2 Complexity Density: 0.14 1PASS
289	1	@Test(groups = { "Functional" })...
290		public void testConstructor_fromDbref()
291		{
292	1	PDBEntry pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70"));
293	1	assertEquals(pdb.getId(), "1A70");
294	1	assertNull(pdb.getChainCode());
295	1	assertNull(pdb.getType());
296	1	assertNull(pdb.getFile());
297
298		/*
299		* from dbref with chain code appended
300		*/
301	1	pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70B"));
302	1	assertEquals(pdb.getId(), "1A70");
303	1	assertEquals(pdb.getChainCode(), "B");
304
305		/*
306		* from dbref with overlong accession
307		*/
308	1	pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70BC"));
309	1	assertEquals(pdb.getId(), "1A70BC");
310	1	assertNull(pdb.getChainCode());
311
312		/*
313		* from dbref which is not for PDB
314		*/
315	1	try
316		{
317	1	pdb = new PDBEntry(new DBRefEntry("PDBe", "0", "1A70"));
318	0	fail("Expected exception");
319		} catch (IllegalArgumentException e)
320		{
321		// expected;
322		}
323		}
324
325		}