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Coverage Report

  1. Project Clover database Wed Nov 12 2025 09:00:47 GMT
  2. Package jalview.gui

File StructureChooserTest.java

 

Code metrics

20
126
11
1
420
321
25
0.2
11.45
11
2.27

Classes

Class Line # Actions
StructureChooserTest 66 126 25
0.878980987.9%
 

Contributing tests

This file is covered by 10 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.gui;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.AssertJUnit.assertNotNull;
25    import static org.testng.AssertJUnit.assertTrue;
26   
27    import java.io.File;
28    import java.util.Collection;
29    import java.util.List;
30    import java.util.Vector;
31   
32    import org.junit.Assert;
33    import org.testng.annotations.AfterMethod;
34    import org.testng.annotations.BeforeClass;
35    import org.testng.annotations.BeforeMethod;
36    import org.testng.annotations.DataProvider;
37    import org.testng.annotations.Test;
38   
39    import jalview.api.AlignViewportI;
40    import jalview.bin.Cache;
41    import jalview.bin.Jalview;
42    import jalview.datamodel.AlignmentAnnotation;
43    import jalview.datamodel.AlignmentI;
44    import jalview.datamodel.DBRefEntry;
45    import jalview.datamodel.PDBEntry;
46    import jalview.datamodel.Sequence;
47    import jalview.datamodel.SequenceI;
48    import jalview.fts.api.FTSData;
49    import jalview.fts.core.FTSRestClient;
50    import jalview.fts.service.pdb.PDBFTSRestClient;
51    import jalview.fts.service.pdb.PDBFTSRestClientTest;
52    import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
53    import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
54    import jalview.gui.StructureViewer.ViewerType;
55    import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
56    import jalview.io.DataSourceType;
57    import jalview.io.FileFormatException;
58    import jalview.io.FileFormatI;
59    import jalview.io.FileLoader;
60    import jalview.io.IdentifyFile;
61    import jalview.jbgui.FilterOption;
62    import jalview.structure.StructureImportSettings.TFType;
63    import junit.extensions.PA;
64   
65    @Test(singleThreaded = true)
 
66    public class StructureChooserTest
67    {
68   
 
69  1 toggle @BeforeClass(alwaysRun = true)
70    public void setUpJvOptionPane()
71    {
72  1 JvOptionPane.setInteractiveMode(false);
73  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
74    }
75   
76    Sequence seq, upSeq, upSeq_nocanonical;
77   
 
78  10 toggle @BeforeMethod(alwaysRun = true)
79    public void setUp() throws Exception
80    {
81  10 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
82    26);
83  10 seq.createDatasetSequence();
84  50 for (int x = 1; x < 5; x++)
85    {
86  40 DBRefEntry dbRef = new DBRefEntry();
87  40 dbRef.setAccessionId("XYZ_" + x);
88  40 seq.addDBRef(dbRef);
89    }
90   
91  10 PDBEntry dbRef = new PDBEntry();
92  10 dbRef.setId("1tim");
93   
94  10 Vector<PDBEntry> pdbIds = new Vector<>();
95  10 pdbIds.add(dbRef);
96   
97  10 seq.setPDBId(pdbIds);
98   
99    // Uniprot sequence for 3D-Beacons mocks
100  10 upSeq = new Sequence("P38398",
101    "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
102    + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
103    + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
104    + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
105    + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
106    + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
107    + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
108    + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
109    + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
110    + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
111    + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
112    + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
113    + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
114    + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
115    + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
116    + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
117    + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
118    + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
119    + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
120    + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
121    + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
122    + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
123    + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
124    + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
125    + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
126    + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
127    + "",
128    1, 1863);
129  10 upSeq.setDescription("Breast cancer type 1 susceptibility protein");
130  10 upSeq_nocanonical = new Sequence(upSeq);
131  10 upSeq.createDatasetSequence();
132  10 upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
133   
134  10 upSeq_nocanonical.createDatasetSequence();
135    // not a canonical reference
136  10 upSeq_nocanonical.addDBRef(
137    new DBRefEntry("UNIPROT", "0", "P38398", null, false));
138   
139    }
140   
 
141  10 toggle @AfterMethod(alwaysRun = true)
142    public void tearDown() throws Exception
143    {
144  10 seq = null;
145  10 upSeq = null;
146  10 upSeq_nocanonical = null;
147    }
148   
 
149  1 toggle @Test(groups = { "Functional" })
150    public void populateFilterComboBoxTest() throws InterruptedException
151    {
152  1 TDBeaconsFTSRestClientTest.setMock();
153  1 PDBFTSRestClientTest.setMock();
154   
155  1 SequenceI[] selectedSeqs = new SequenceI[] { seq };
156  1 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
157  1 ThreadwaitFor(200, sc);
158   
159    // if structures are not discovered then don't
160    // populate filter options
161  1 sc.populateFilterComboBox(false, false);
162  1 int optionsSize = sc.getCmbFilterOption().getItemCount();
163  1 System.out.println("Items (no data, no cache): ");
164  1 StringBuilder items = new StringBuilder();
165  3 for (int p = 0; p < optionsSize; p++)
166    {
167  2 items.append("- ")
168    .append(sc.getCmbFilterOption().getItemAt(p).getName())
169    .append("\n");
170   
171    }
172    // report items when this fails - seems to be a race condition
173  1 Assert.assertEquals(items.toString(), optionsSize, 2);
174   
175  1 sc.populateFilterComboBox(true, false);
176  1 optionsSize = sc.getCmbFilterOption().getItemCount();
177  1 assertTrue(optionsSize > 3); // if structures are found, filter options
178    // should be populated
179   
180  1 sc.populateFilterComboBox(true, true);
181  1 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
182  1 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
183    .getSelectedItem();
184  1 assertEquals("Cached Structures", filterOpt.getName());
185  1 FTSRestClient
186    .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
187  1 FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
188   
189    }
190   
 
191  1 toggle @Test(groups = { "Functional" })
192    public void displayTDBQueryTest() throws InterruptedException
193    {
194  1 TDBeaconsFTSRestClientTest.setMock();
195  1 PDBFTSRestClientTest.setMock();
196   
197  1 SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
198  1 StructureChooser sc = new StructureChooser(selectedSeqs,
199    upSeq_nocanonical, null);
200    // mock so should be quick. Exceptions from mocked PDBFTS are expected too
201  1 ThreadwaitFor(500, sc);
202   
203  1 assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
204    }
205   
 
206  0 toggle @Test(groups = { "Network" })
207    public void fetchStructuresInfoTest()
208    {
209  0 FTSRestClient
210    .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
211  0 PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
212  0 SequenceI[] selectedSeqs = new SequenceI[] { seq };
213  0 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
214    // not mocked, wait for 2s
215  0 ThreadwaitFor(2000, sc);
216   
217  0 sc.fetchStructuresMetaData();
218  0 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
219    "discoveredStructuresSet");
220  0 assertNotNull(ss);
221  0 assertTrue(ss.size() > 0);
222    }
223   
 
224  1 toggle @Test(groups = { "Functional" })
225    public void fetchStructuresInfoMockedTest()
226    {
227  1 TDBeaconsFTSRestClientTest.setMock();
228  1 PDBFTSRestClientTest.setMock();
229  1 SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
230  1 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
231  1 ThreadwaitFor(500, sc);
232   
233  1 sc.fetchStructuresMetaData();
234  1 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
235    "discoveredStructuresSet");
236  1 assertNotNull(ss);
237  1 assertTrue(ss.size() > 0);
238    }
239   
 
240  3 toggle private void ThreadwaitFor(int i, StructureChooser sc)
241    {
242  3 long timeout = i + System.currentTimeMillis();
243  12 while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
244    {
245  9 try
246    {
247  9 Thread.sleep(50);
248    } catch (InterruptedException x)
249    {
250   
251    }
252    }
253   
254    }
255   
 
256  1 toggle @Test(groups = { "Functional" })
257    public void sanitizeSeqNameTest()
258    {
259  1 String name = "ab_cdEF|fwxyz012349";
260  1 assertEquals(name,
261    PDBStructureChooserQuerySource.sanitizeSeqName(name));
262   
263    // remove a [nn] substring
264  1 name = "abcde12[345]fg";
265  1 assertEquals("abcde12fg",
266    PDBStructureChooserQuerySource.sanitizeSeqName(name));
267   
268    // remove characters other than a-zA-Z0-9 | or _
269  1 name = "ab[cd],.\t£$*!- \\\"@:e";
270  1 assertEquals("abcde",
271    PDBStructureChooserQuerySource.sanitizeSeqName(name));
272   
273  1 name = "abcde12[345a]fg";
274  1 assertEquals("abcde12345afg",
275    PDBStructureChooserQuerySource.sanitizeSeqName(name));
276    }
277   
 
278  6 toggle @Test(groups = { "Functional" }, dataProvider = "openStructureFileParams")
279    public void openStructureFileForSequenceTest(String alfile, String seqid,
280    String sFilename, TFType tft, String paeFilename,
281    boolean showRefAnnotations, boolean doXferSettings,
282    ViewerType viewerType, int seqNum, int annNum, int viewerNum,
283    String propsFile)
284    {
285  6 Cache.loadProperties(
286  6 propsFile == null ? "test/jalview/io/testProps.jvprops"
287    : propsFile);
288   
289  6 Jalview.main(
290  6 propsFile == null ? null : new String[]
291    { "--props", propsFile });
292  6 if (Desktop.instance != null)
293  6 Desktop.instance.closeAll_actionPerformed(null);
294  6 JvOptionPane.setInteractiveMode(false);
295  6 JvOptionPane.setMockResponse(JvOptionPane.OK_OPTION);
296   
297  6 FileLoader fileLoader = new FileLoader(true);
298  6 FileFormatI format = null;
299  6 File alFile = new File(alfile);
300  6 try
301    {
302  6 format = new IdentifyFile().identify(alFile, DataSourceType.FILE);
303    } catch (FileFormatException e1)
304    {
305  0 Assert.fail(
306    "Unknown file format for '" + alFile.getAbsolutePath() + "'");
307    }
308   
309  6 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(alFile,
310    DataSourceType.FILE, format);
311  6 AlignmentPanel ap = af.alignPanel;
312  6 Assert.assertNotNull("No alignPanel", ap);
313   
314  6 AlignmentI al = ap.getAlignment();
315  6 Assert.assertNotNull(al);
316   
317  6 SequenceI seq = al.findName(seqid);
318  6 Assert.assertNotNull("Sequence '" + seqid + "' not found in alignment",
319    seq);
320   
321  6 StructureChooser.openStructureFileForSequence(null, null, ap, seq,
322    false, sFilename, tft, paeFilename, false, showRefAnnotations,
323    doXferSettings, viewerType);
324   
325  6 List<SequenceI> seqs = al.getSequences();
326  6 Assert.assertNotNull(seqs);
327   
328  6 Assert.assertEquals("Wrong number of sequences", seqNum, seqs.size());
329   
330  6 AlignViewportI av = ap.getAlignViewport();
331  6 Assert.assertNotNull(av);
332   
333  6 AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
334  6 int visibleAnn = 0;
335  6 for (AlignmentAnnotation aa : aas)
336    {
337  36 if (aa.visible)
338  36 visibleAnn++;
339    }
340  6 Assert.assertEquals("Wrong number of viewed annotations", annNum,
341    visibleAnn);
342   
343  6 if (viewerNum > -1)
344    {
345  6 try
346    {
347  6 Thread.sleep(100);
348    } catch (InterruptedException e)
349    {
350    // TODO Auto-generated catch block
351  0 e.printStackTrace();
352    }
353  6 List<StructureViewerBase> openViewers = Desktop.instance
354    .getStructureViewers(ap, null);
355  6 Assert.assertNotNull(openViewers);
356  6 int count = 0;
357  6 for (StructureViewerBase svb : openViewers)
358    {
359  3 if (svb.isVisible())
360  3 count++;
361    }
362  6 Assert.assertEquals("Wrong number of structure viewers opened",
363    viewerNum, count);
364   
365    }
366   
367  6 if (af != null)
368    {
369  6 af.setVisible(false);
370  6 af.dispose();
371    }
372    }
373   
 
374  1 toggle @DataProvider(name = "openStructureFileParams")
375    public Object[][] openStructureFileParams()
376    {
377    /*
378    String alFile,
379    String seqid,
380    String structureFilename,
381    TFType tft,
382    String paeFilename,
383    boolean showRefAnnotations,
384    boolean doXferSettings, // false for Commands
385    ViewerType viewerType,
386    int seqNum,
387    int annNum,
388    int viewerNum,
389    String propsFile
390    */
391  1 return new Object[][] {
392    /*
393    */
394    { "examples/uniref50.fa", "FER1_SPIOL",
395    "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
396    "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
397    true, false, null, 15, 7, 0, null },
398    { "examples/uniref50.fa", "FER1_SPIOL",
399    "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
400    "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
401    true, false, null, 15, 7, 0, null },
402    { "examples/uniref50.fa", "FER1_SPIOL",
403    "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
404    "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
405    false, false, null, 15, 4, 0, null },
406    { "examples/uniref50.fa", "FER1_SPIOL",
407    "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
408    "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
409    true, false, ViewerType.JMOL, 15, 7, 1, null },
410    { "examples/uniref50.fa", "FER1_SPIOL",
411    "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
412    "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
413    true, false, ViewerType.JMOL, 15, 7, 1, null },
414    { "examples/uniref50.fa", "FER1_SPIOL",
415    "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
416    "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
417    false, false, ViewerType.JMOL, 15, 4, 1, null }, };
418    }
419   
420    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 09:10:40 GMT using coverage data from Wed Nov 12 2025 09:10:27 GMT.
  • OpenClover is free and open-source software.