Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
PDBfileTest | 47 | 121 | 10 |
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 mc_view; | |
22 | ||
23 | import static org.testng.AssertJUnit.assertEquals; | |
24 | import static org.testng.AssertJUnit.assertFalse; | |
25 | import static org.testng.AssertJUnit.assertNull; | |
26 | import static org.testng.AssertJUnit.assertSame; | |
27 | import static org.testng.AssertJUnit.assertTrue; | |
28 | ||
29 | import java.io.IOException; | |
30 | import java.util.List; | |
31 | ||
32 | import org.testng.annotations.BeforeClass; | |
33 | import org.testng.annotations.BeforeMethod; | |
34 | import org.testng.annotations.Test; | |
35 | ||
36 | import jalview.bin.Cache; | |
37 | import jalview.datamodel.Alignment; | |
38 | import jalview.datamodel.AlignmentAnnotation; | |
39 | import jalview.datamodel.AlignmentI; | |
40 | import jalview.datamodel.PDBEntry; | |
41 | import jalview.datamodel.Sequence; | |
42 | import jalview.datamodel.SequenceI; | |
43 | import jalview.gui.JvOptionPane; | |
44 | import jalview.io.DataSourceType; | |
45 | import jalview.structure.StructureImportSettings; | |
46 | ||
47 | public class PDBfileTest | |
48 | { | |
49 | ||
50 | 1 | @BeforeClass(alwaysRun = true) |
51 | public void setUpJvOptionPane() | |
52 | { | |
53 | 1 | JvOptionPane.setInteractiveMode(false); |
54 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
55 | } | |
56 | ||
57 | 1 | @Test(groups = { "Functional" }) |
58 | public void testIsRna() | |
59 | { | |
60 | 1 | SequenceI seq = new Sequence("Seq1", "CGAU"); |
61 | 1 | assertTrue(PDBfile.isRNA(seq)); |
62 | ||
63 | 1 | seq.setSequence("CGAu"); |
64 | 1 | assertFalse(PDBfile.isRNA(seq)); |
65 | ||
66 | 1 | seq.setSequence("CGAT"); |
67 | 1 | assertFalse(PDBfile.isRNA(seq)); |
68 | ||
69 | 1 | seq.setSequence("GRSWYFLAVM"); |
70 | 1 | assertFalse(PDBfile.isRNA(seq)); |
71 | } | |
72 | ||
73 | /** | |
74 | * Test the 'high level' outputs of parsing. More detailed tests in | |
75 | * PDBChainTest. | |
76 | * | |
77 | * @throws IOException | |
78 | */ | |
79 | 1 | @Test(groups = { "Functional" }) |
80 | public void testParse() throws IOException | |
81 | { | |
82 | /* | |
83 | * Constructor with file path performs parse() | |
84 | */ | |
85 | 1 | PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb", |
86 | DataSourceType.FILE); | |
87 | ||
88 | 1 | assertEquals("3W5V", pf.getId()); |
89 | // verify no alignment annotations created | |
90 | 1 | assertNull(getAlignmentAnnotations(pf)); |
91 | ||
92 | 1 | assertEquals(4, pf.getChains().size()); |
93 | 1 | assertEquals("A", pf.getChains().get(0).id); |
94 | 1 | assertEquals("B", pf.getChains().get(1).id); |
95 | 1 | assertEquals("C", pf.getChains().get(2).id); |
96 | 1 | assertEquals("D", pf.getChains().get(3).id); |
97 | ||
98 | 1 | PDBChain chainA = pf.getChains().get(0); |
99 | 1 | SequenceI seqA = pf.getSeqs().get(0); |
100 | ||
101 | 1 | assertEquals(0, chainA.seqstart); // not set |
102 | 1 | assertEquals(0, chainA.seqend); // not set |
103 | 1 | assertEquals(18, chainA.sequence.getStart()); |
104 | 1 | assertEquals(314, chainA.sequence.getEnd()); |
105 | 1 | assertTrue( |
106 | chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE")); | |
107 | 1 | assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY")); |
108 | 1 | assertEquals("3W5V|A", chainA.sequence.getName()); |
109 | 1 | assertNull(chainA.sequence.getAnnotation()); |
110 | 1 | assertEquals(1, seqA.getAllPDBEntries().size()); |
111 | 1 | PDBEntry pdb = seqA.getAllPDBEntries().get(0); |
112 | 1 | assertEquals("A", pdb.getChainCode()); |
113 | 1 | assertEquals("PDB", pdb.getType()); |
114 | 1 | assertEquals("3W5V", pdb.getId()); |
115 | ||
116 | 1 | PDBChain chainB = pf.getChains().get(1); |
117 | 1 | assertEquals(1, chainB.sequence.getStart()); |
118 | 1 | assertEquals(96, chainB.sequence.getEnd()); |
119 | 1 | assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK")); |
120 | 1 | assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT")); |
121 | 1 | assertEquals("3W5V|B", chainB.sequence.getName()); |
122 | ||
123 | 1 | PDBChain chainC = pf.getChains().get(2); |
124 | 1 | assertEquals(18, chainC.sequence.getStart()); |
125 | 1 | assertEquals(314, chainC.sequence.getEnd()); |
126 | 1 | assertTrue( |
127 | chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE")); | |
128 | 1 | assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY")); |
129 | 1 | assertEquals("3W5V|C", chainC.sequence.getName()); |
130 | ||
131 | 1 | PDBChain chainD = pf.getChains().get(3); |
132 | 1 | assertEquals(1, chainD.sequence.getStart()); |
133 | 1 | assertEquals(96, chainD.sequence.getEnd()); |
134 | 1 | assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK")); |
135 | 1 | assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT")); |
136 | 1 | assertEquals("3W5V|D", chainD.sequence.getName()); |
137 | ||
138 | /* | |
139 | * verify PDB-related data in parsed sequences | |
140 | */ | |
141 | 1 | List<SequenceI> seqs = pf.getSeqs(); |
142 | 1 | assertEquals(4, seqs.size()); |
143 | 1 | assertEquals("3W5V|A", seqs.get(0).getName()); |
144 | 1 | assertEquals("3W5V|B", seqs.get(1).getName()); |
145 | 1 | assertEquals("3W5V|C", seqs.get(2).getName()); |
146 | 1 | assertEquals("3W5V|D", seqs.get(3).getName()); |
147 | 1 | assertEquals(1, seqs.get(0).getAllPDBEntries().size()); |
148 | 1 | PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0); |
149 | 1 | assertEquals("A", pdbe.getChainCode()); |
150 | 1 | assertEquals("3W5V", pdbe.getId()); |
151 | 1 | assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType()); |
152 | } | |
153 | ||
154 | /** | |
155 | * Test parsing, with annotations added to the alignment but no secondary | |
156 | * structure prediction | |
157 | * | |
158 | * @throws IOException | |
159 | */ | |
160 | 1 | @Test(groups = { "Functional" }) |
161 | public void testParse_withAnnotations_noSS() throws IOException | |
162 | { | |
163 | 1 | PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb", |
164 | DataSourceType.FILE); | |
165 | ||
166 | 1 | AlignmentAnnotation[] anns = getAlignmentAnnotations(pf); |
167 | 1 | assertEquals(4, anns.length); |
168 | ||
169 | /* | |
170 | * Inspect temp factor annotation for chain A | |
171 | */ | |
172 | 1 | AlignmentAnnotation chainAnnotation = anns[0]; |
173 | 1 | assertEquals("Temperature Factor", chainAnnotation.label); |
174 | // PDBChain constructor changes PDB id to lower case (why?) | |
175 | 1 | assertEquals("Temperature Factor for 3w5vA", |
176 | chainAnnotation.description); | |
177 | 1 | assertSame(pf.getSeqs().get(0), chainAnnotation.sequenceRef); |
178 | 1 | assertEquals(AlignmentAnnotation.LINE_GRAPH, chainAnnotation.graph); |
179 | 1 | assertEquals(0f, chainAnnotation.graphMin, 0.001f); |
180 | 1 | assertEquals(40f, chainAnnotation.graphMax, 0.001f); |
181 | 1 | assertEquals(297, chainAnnotation.annotations.length); |
182 | 1 | assertEquals(40f, chainAnnotation.annotations[0].value, 0.001f); |
183 | ||
184 | /* | |
185 | * Chain B temp factor | |
186 | */ | |
187 | 1 | chainAnnotation = anns[1]; |
188 | 1 | assertEquals("Temperature Factor for 3w5vB", |
189 | chainAnnotation.description); | |
190 | 1 | assertSame(pf.getSeqs().get(1), chainAnnotation.sequenceRef); |
191 | 1 | assertEquals(96, chainAnnotation.annotations.length); |
192 | ||
193 | /* | |
194 | * Chain C temp factor | |
195 | */ | |
196 | 1 | chainAnnotation = anns[2]; |
197 | 1 | assertEquals("Temperature Factor for 3w5vC", |
198 | chainAnnotation.description); | |
199 | 1 | assertSame(pf.getSeqs().get(2), chainAnnotation.sequenceRef); |
200 | 1 | assertEquals(297, chainAnnotation.annotations.length); |
201 | ||
202 | /* | |
203 | * Chain D temp factor | |
204 | */ | |
205 | 1 | chainAnnotation = anns[3]; |
206 | 1 | assertEquals("Temperature Factor for 3w5vD", |
207 | chainAnnotation.description); | |
208 | 1 | assertSame(pf.getSeqs().get(3), chainAnnotation.sequenceRef); |
209 | 1 | assertEquals(96, chainAnnotation.annotations.length); |
210 | } | |
211 | ||
212 | /** | |
213 | * Test parsing including secondary structure annotation using JMol; this test | |
214 | * for the case where flag to add annotations to alignment is set false | |
215 | * | |
216 | * @throws IOException | |
217 | */ | |
218 | 1 | @Test(groups = { "Functional" }) |
219 | public void testParse_withJmol_noAnnotations() throws IOException | |
220 | { | |
221 | 1 | PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb", |
222 | DataSourceType.FILE); | |
223 | ||
224 | /* | |
225 | * alignment annotations _are_ created anyway (in | |
226 | * AlignSeq.replaceMatchingSeqsWith()) | |
227 | */ | |
228 | 1 | final AlignmentAnnotation[] anns = getAlignmentAnnotations(pf); |
229 | 1 | assertEquals(4, anns.length); |
230 | ||
231 | /* | |
232 | * no sequence annotations created - tempFactor annotation is not added | |
233 | * unless the flag to 'addAlignmentAnnotations' is set true | |
234 | */ | |
235 | 1 | for (PDBChain c : pf.getChains()) |
236 | { | |
237 | 4 | assertNull(c.sequence.getAnnotation()); |
238 | } | |
239 | } | |
240 | ||
241 | /** | |
242 | * Test parsing including secondary structure prediction and annotation using | |
243 | * JMol | |
244 | * | |
245 | * @throws IOException | |
246 | */ | |
247 | 1 | @Test(groups = { "Functional" }) |
248 | public void testParse_withJmolAddAlignmentAnnotations() throws IOException | |
249 | { | |
250 | 1 | PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb", |
251 | DataSourceType.FILE); | |
252 | ||
253 | /* | |
254 | * Alignment annotations for TempFactor, SecStruct, per sequence (chain) | |
255 | */ | |
256 | 1 | AlignmentAnnotation[] anns = getAlignmentAnnotations(pf); |
257 | 1 | assertEquals(8, anns.length); |
258 | ||
259 | /* | |
260 | * other tests have detailed assertions for Temp Factor annotations | |
261 | */ | |
262 | 1 | assertEquals("Temperature Factor for 3w5vA", anns[1].description); |
263 | 1 | assertEquals("Temperature Factor for 3w5vB", anns[3].description); |
264 | 1 | assertEquals("Temperature Factor for 3w5vC", anns[5].description); |
265 | 1 | assertEquals("Temperature Factor for 3w5vD", anns[7].description); |
266 | ||
267 | /* | |
268 | * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case | |
269 | */ | |
270 | 1 | assertEquals("Secondary Structure for 3w5vA", anns[0].description); |
271 | 1 | assertEquals("Secondary Structure for 3w5vB", anns[2].description); |
272 | 1 | assertEquals("Secondary Structure for 3w5vC", anns[4].description); |
273 | 1 | assertEquals("Secondary Structure for 3w5vD", anns[6].description); |
274 | ||
275 | /* | |
276 | * Verify SS annotations are linked to respective sequences (chains) | |
277 | */ | |
278 | 1 | assertSame(pf.getSeqs().get(0), anns[0].sequenceRef); |
279 | 1 | assertSame(pf.getSeqs().get(1), anns[2].sequenceRef); |
280 | 1 | assertSame(pf.getSeqs().get(2), anns[4].sequenceRef); |
281 | 1 | assertSame(pf.getSeqs().get(3), anns[6].sequenceRef); |
282 | ||
283 | /* | |
284 | * Verify a sample of SS predictions | |
285 | */ | |
286 | 21 | for (int i = 0; i < 20; i++) |
287 | { | |
288 | 20 | assertNull(anns[0].annotations[i]); |
289 | 20 | assertNull(anns[0].annotations[20].displayCharacter); |
290 | 20 | assertEquals('E', anns[0].annotations[20].secondaryStructure); |
291 | 20 | assertEquals('E', anns[2].annotations[18].secondaryStructure); |
292 | 20 | assertEquals('H', anns[2].annotations[23].secondaryStructure); |
293 | } | |
294 | } | |
295 | ||
296 | /** | |
297 | * Placeholder for a test of parsing RNA structure with secondary structure | |
298 | * prediction using the Annotate3D service | |
299 | * | |
300 | * @throws IOException | |
301 | */ | |
302 | ||
303 | 0 | @Test(groups = { "Functional" }, enabled = false) |
304 | public void testParse_withAnnotate3D() throws IOException | |
305 | { | |
306 | // TODO requires a mock for Annotate3D processing | |
307 | // and/or run as an integration test | |
308 | 0 | PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb", |
309 | DataSourceType.FILE); | |
310 | } | |
311 | ||
312 | /** | |
313 | * Helper method to extract parsed annotations from the PDBfile | |
314 | * | |
315 | * @param pf | |
316 | * @return | |
317 | */ | |
318 | 4 | private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf) |
319 | { | |
320 | 4 | AlignmentI al = new Alignment(pf.getSeqsAsArray()); |
321 | 4 | pf.addAnnotations(al); |
322 | 4 | return al.getAlignmentAnnotation(); |
323 | } | |
324 | ||
325 | 5 | @BeforeMethod(alwaysRun = true) |
326 | public void setUp() | |
327 | { | |
328 | 5 | Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
329 | 5 | Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", |
330 | Boolean.TRUE.toString()); | |
331 | 5 | Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN", |
332 | Boolean.TRUE.toString()); | |
333 | 5 | Cache.applicationProperties.setProperty("ADD_SS_ANN", |
334 | Boolean.TRUE.toString()); | |
335 | 5 | StructureImportSettings.setDefaultStructureFileFormat("PDB"); |
336 | } | |
337 | } |