1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.datamodel

File PDBEntryTest.java

 

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PDBEntryTest 42 132 10
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Contributing tests

This file is covered by 6 tests. .

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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   
 
42    public class PDBEntryTest
43    {
44   
 
45  1 toggle @BeforeClass(alwaysRun = true)
46    public void setUpJvOptionPane()
47    {
48  1 JvOptionPane.setInteractiveMode(false);
49  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50    }
51   
 
52  6 toggle @BeforeMethod(alwaysRun = true)
53    public void setUp() throws Exception
54    {
55    }
56   
 
57  6 toggle @AfterMethod(alwaysRun = true)
58    public void tearDown() throws Exception
59    {
60    }
61   
 
62  1 toggle @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   
 
126  1 toggle @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   
 
140  1 toggle @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   
 
149  1 toggle @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   
 
159  1 toggle @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   
 
289  1 toggle @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    }