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  1. Project Clover database Mon Dec 1 2025 13:17:41 GMT
  2. Package jalview.ext.jmol

File JmolParserTest.java

 

Code metrics

8
87
10
1
303
211
15
0.17
8.7
10
1.5

Classes

Class Line # Actions
JmolParserTest 53 87 15
0.9333333493.3%
 

Contributing tests

This file is covered by 6 tests. .

Source view

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 jalview.ext.jmol;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertNotNull;
25    import static org.testng.AssertJUnit.assertTrue;
26   
27    import jalview.bin.Cache;
28    import jalview.datamodel.Alignment;
29    import jalview.datamodel.AlignmentAnnotation;
30    import jalview.datamodel.AlignmentI;
31    import jalview.datamodel.SequenceI;
32    import jalview.gui.AlignFrame;
33    import jalview.gui.JvOptionPane;
34    import jalview.io.DataSourceType;
35    import jalview.io.FileLoader;
36    import jalview.structure.StructureImportSettings;
37    import jalview.structure.StructureImportSettings.StructureParser;
38   
39    import java.util.Vector;
40   
41    import org.jmol.c.STR;
42    import org.testng.annotations.BeforeClass;
43    import org.testng.annotations.BeforeMethod;
44    import org.testng.annotations.Test;
45   
46    import jalview.util.Constants;
47    import mc_view.PDBfile;
48   
49    /**
50    * @author jimp
51    *
52    */
 
53    public class JmolParserTest
54    {
55   
 
56  1 toggle @BeforeClass(alwaysRun = true)
57    public void setUpJvOptionPane()
58    {
59  1 JvOptionPane.setInteractiveMode(false);
60  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
61    }
62   
63    /*
64    * 1GAQ has been reduced to alpha carbons only
65    * 1QCF is the full PDB file including headers, HETATM etc
66    */
67    String[] testFile = new String[] { "./examples/1gaq.txt",
68    "./test/jalview/ext/jmol/1xyz.pdb",
69    "./test/jalview/ext/jmol/1QCF.pdb" };
70   
71    //@formatter:off
72    // a modified and very cut-down extract of 4UJ4
73    String pastePDBDataWithChainBreak =
74    "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
75    // chain B has missing residues; these should all go in the same sequence:
76    "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
77    "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
78    "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
79    "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
80    // switch to chain C; should be a separate sequence
81    "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
82    "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
83    //@formatter:on
84   
85    //@formatter:off
86    // a very cut-down extract of 1ejg
87    String pdbWithAltLoc =
88    "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
89    "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
90    "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
91    // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
92    "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
93    // including the next altloc causes the unit test to fail but it works with the full file
94    // not sure why!
95    // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
96    "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
97    //@formatter:on
98   
 
99  6 toggle @BeforeMethod(alwaysRun = true)
100    public void setUp()
101    {
102  6 Cache.loadProperties("test/jalview/io/testProps.jvprops");
103  6 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
104    Boolean.TRUE.toString());
105  6 Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
106    Boolean.FALSE.toString());
107  6 Cache.applicationProperties.setProperty("ADD_SS_ANN",
108    Boolean.TRUE.toString());
109  6 StructureImportSettings.setDefaultStructureFileFormat("PDB");
110  6 StructureImportSettings
111    .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
112    }
113   
 
114  1 toggle @Test(groups = { "Functional" })
115    public void testAlignmentLoader() throws Exception
116    {
117  1 for (String f : testFile)
118    {
119  3 FileLoader fl = new jalview.io.FileLoader(false);
120  3 AlignFrame af = fl.LoadFileWaitTillLoaded(f, DataSourceType.FILE);
121  3 validateSecStrRows(af.getViewport().getAlignment());
122    }
123    }
124   
 
125  1 toggle @Test(groups = { "Functional" })
126    public void testFileParser() throws Exception
127    {
128  1 for (String pdbStr : testFile)
129    {
130  3 PDBfile mctest = new PDBfile(false, false, false, pdbStr,
131    DataSourceType.FILE);
132  3 JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE);
133  3 Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
134   
135  3 assertTrue("No sequences extracted from testfile\n"
136  3 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
137    : "(No warnings raised)"),
138    seqs != null && seqs.size() > 0);
139  3 for (SequenceI sq : seqs)
140    {
141  6 assertEquals(
142    "JMol didn't process " + pdbStr
143    + " to the same sequence as MCView",
144    sq.getSequenceAsString(),
145    mcseqs.remove(0).getSequenceAsString());
146  6 AlignmentI al = new Alignment(new SequenceI[] { sq });
147  6 validateSecStrRows(al);
148    }
149    }
150   
151    }
152   
 
153  9 toggle private void validateSecStrRows(AlignmentI al)
154    {
155  9 if (!al.isNucleotide())
156    {
157  9 for (SequenceI asq : al.getSequences())
158    {
159  12 SequenceI sq = asq;
160  12 boolean hasDs = false;
161  12 while (sq.getDatasetSequence() != null
162    && sq.getAnnotation() == null)
163    {
164  0 sq = sq.getDatasetSequence();
165  0 hasDs = true;
166    }
167  12 checkFirstAAIsAssoc(sq);
168  12 if (hasDs)
169    {
170    // also verify if alignment sequence has annotation on it
171    // that is correctly mapped
172  0 checkFirstAAIsAssoc(asq);
173    }
174    }
175    }
176    }
177   
 
178  12 toggle private void checkFirstAAIsAssoc(SequenceI sq)
179    {
180  12 assertTrue(
181    "No secondary structure assigned for protein sequence for "
182    + sq.getName(),
183    sq.getAnnotation() != null && sq.getAnnotation().length >= 1
184    && sq.getAnnotation()[0].hasIcons);
185  12 assertTrue(
186    "Secondary structure not associated for sequence "
187    + sq.getName(),
188    sq.getAnnotation()[0].sequenceRef == sq);
189    // validate metadata
190  12 AlignmentAnnotation aa = sq.getAnnotation()[0];
191  12 assertTrue("No chain ID for annotation",
192    aa.getProperty(Constants.CHAINID) != null
193    && !aa.getProperty(Constants.CHAINID).isBlank());
194  12 assertTrue("No PDB ID for annotation",
195    aa.getProperty(Constants.PDBID) != null
196    && !aa.getProperty(Constants.PDBID).isBlank());
197   
198    }
199   
200    /**
201    * Test parsing a chain with missing residues
202    *
203    * @throws Exception
204    */
 
205  1 toggle @Test(groups = { "Functional" })
206    public void testParse_missingResidues() throws Exception
207    {
208  1 PDBfile mctest = new PDBfile(false, false, false,
209    pastePDBDataWithChainBreak, DataSourceType.PASTE);
210  1 JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
211    DataSourceType.PASTE);
212  1 Vector<SequenceI> seqs = jtest.getSeqs();
213  1 Vector<SequenceI> mcseqs = mctest.getSeqs();
214   
215  1 assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
216  1 assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
217  1 assertEquals("VGKA", seqs.get(0).getSequenceAsString());
218  1 assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
219  1 assertEquals("SA", seqs.get(1).getSequenceAsString());
220  1 assertEquals("SA", mcseqs.get(1).getSequenceAsString());
221    }
222   
223    /**
224    * Test parsing a chain with 'altloc' residues
225    *
226    * @throws Exception
227    */
 
228  1 toggle @Test(groups = { "Functional" })
229    public void testParse_alternativeResidues() throws Exception
230    {
231  1 PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
232    DataSourceType.PASTE);
233  1 JmolParser jtest = new JmolParser(pdbWithAltLoc, DataSourceType.PASTE);
234  1 Vector<SequenceI> seqs = jtest.getSeqs();
235  1 Vector<SequenceI> mcseqs = mctest.getSeqs();
236   
237  1 assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
238  1 assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
239  1 assertEquals("ALC", seqs.get(0).getSequenceAsString());
240  1 assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
241    }
242   
 
243  1 toggle @Test(groups = "Functional")
244    public void testSetSecondaryStructure()
245    {
246  1 JmolParser testee = new JmolParser();
247  1 char[] struct = new char[10];
248  1 char[] structCode = new char[10];
249  1 struct[0] = '1';
250  1 structCode[0] = '1';
251   
252  1 testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
253  1 testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
254  1 testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
255  1 testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
256  1 testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
257  1 testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
258   
259  1 assertEquals(0, struct[0]);
260  1 assertEquals('H', struct[1]);
261  1 assertEquals('3', struct[2]);
262  1 assertEquals('H', struct[3]);
263  1 assertEquals('P', struct[4]);
264  1 assertEquals('E', struct[5]);
265   
266  1 assertEquals(0, structCode[0]);
267  1 assertEquals('H', structCode[1]);
268  1 assertEquals('H', structCode[2]);
269  1 assertEquals('H', structCode[3]);
270  1 assertEquals('H', structCode[4]);
271  1 assertEquals('E', structCode[5]);
272    }
273   
 
274  1 toggle @Test(groups = "Functional")
275    public void testLocalPDBId() throws Exception
276    {
277  1 JmolParser structureData;
278    /*
279    * reads a local structure
280    */
281  1 structureData = new JmolParser("examples/testdata/localstruct.pdb",
282    DataSourceType.FILE);
283  1 assertNotNull(structureData);
284    /*
285    * local structure files should yield a false ID based on the filename
286    */
287  1 assertNotNull(structureData.getId());
288  1 assertEquals(structureData.getId(), "localstruct");
289  1 assertNotNull(structureData.getSeqs());
290    /*
291    * local structures have a fake ID
292    */
293  1 assertTrue(structureData.getSeqs().get(0).getAllPDBEntries().get(0)
294    .fakedPDBId());
295    /*
296    * the ID is also the group for features derived from structure data
297    */
298  1 String featureGroup = structureData.getSeqs().get(0)
299    .getSequenceFeatures().get(0).featureGroup;
300  1 assertNotNull(featureGroup);
301  1 assertEquals(featureGroup, "localstruct");
302    }
303    }
  • Report generated by OpenClover v 4.4.1 on Mon Dec 1 2025 13:27:33 GMT using coverage data from Mon Dec 1 2025 13:27:18 GMT.
  • OpenClover is free and open-source software.