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  1. Project Clover database Mon Nov 18 2024 09:56:54 GMT
  2. Package mc_view

File PDBfileTest.java

 

Code metrics

2
121
9
1
337
198
10
0.08
13.44
9
1.11

Classes

Class Line # Actions
PDBfileTest 47 121 10
0.984848598.5%
 

Contributing tests

This file is covered by 5 tests. .

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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 toggle @BeforeClass(alwaysRun = true)
51    public void setUpJvOptionPane()
52    {
53  1 JvOptionPane.setInteractiveMode(false);
54  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55    }
56   
 
57  1 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle 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 toggle @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    }