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

File JalviewChimeraView.java

 

Code metrics

20
170
8
1
524
336
24
0.14
21.25
8
3

Classes

Class Line # Actions
JalviewChimeraView 64 170 24
0.00%
 

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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 jalview.ext.rbvi.chimera;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertFalse;
25    import static org.testng.Assert.assertNotNull;
26    import static org.testng.Assert.assertTrue;
27   
28    import java.io.File;
29    import java.io.IOException;
30    import java.util.List;
31    import java.util.Vector;
32   
33    import org.testng.annotations.AfterClass;
34    import org.testng.annotations.AfterMethod;
35    import org.testng.annotations.BeforeClass;
36    import org.testng.annotations.Test;
37   
38    import jalview.api.FeatureRenderer;
39    import jalview.api.structures.JalviewStructureDisplayI;
40    import jalview.bin.Cache;
41    import jalview.bin.Jalview;
42    import jalview.datamodel.AlignmentI;
43    import jalview.datamodel.DBRefEntry;
44    import jalview.datamodel.PDBEntry;
45    import jalview.datamodel.Sequence;
46    import jalview.datamodel.SequenceFeature;
47    import jalview.datamodel.SequenceI;
48    import jalview.gui.AlignFrame;
49    import jalview.gui.Desktop;
50    import jalview.gui.JvOptionPane;
51    import jalview.gui.Preferences;
52    import jalview.gui.StructureViewer;
53    import jalview.gui.StructureViewer.ViewerType;
54    import jalview.io.DataSourceType;
55    import jalview.io.FileLoader;
56    import jalview.structure.StructureCommand;
57    import jalview.structure.StructureMapping;
58    import jalview.structure.StructureSelectionManager;
59    import jalview.ws.sifts.SiftsClient;
60    import jalview.ws.sifts.SiftsException;
61    import jalview.ws.sifts.SiftsSettings;
62   
63    @Test(singleThreaded = true)
 
64    public class JalviewChimeraView
65    {
66   
 
67  0 toggle @BeforeClass(alwaysRun = true)
68    public void setUpJvOptionPane()
69    {
70  0 JvOptionPane.setInteractiveMode(false);
71  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
72    }
73   
74    private JalviewStructureDisplayI chimeraViewer;
75   
76    /**
77    * @throws java.lang.Exception
78    */
 
79  0 toggle @BeforeClass(alwaysRun = true)
80    public static void setUpBeforeClass() throws Exception
81    {
82  0 Jalview.main(
83    new String[]
84    { "--noquestionnaire", "--nonews", "--props",
85    "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
86  0 Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
87    ViewerType.CHIMERA.name());
88  0 Cache.setProperty("SHOW_ANNOTATIONS", "false");
89  0 Cache.setProperty(Preferences.STRUCT_FROM_PDB, "false");
90  0 Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
91    ViewerType.CHIMERA.name());
92  0 Cache.setProperty("MAP_WITH_SIFTS", "true");
93    // TODO this should not be necessary!
94  0 SiftsSettings.setMapWithSifts(true);
95    }
96   
97    /**
98    * @throws java.lang.Exception
99    */
 
100  0 toggle @AfterClass(alwaysRun = true)
101    public static void tearDownAfterClass() throws Exception
102    {
103  0 if (Desktop.instance != null)
104  0 Desktop.instance.closeAll_actionPerformed(null);
105    }
106   
 
107  0 toggle @AfterMethod(alwaysRun = true)
108    public void tearDownAfterTest() throws Exception
109    {
110  0 SiftsClient.setMockSiftsFile(null);
111  0 if (chimeraViewer != null)
112    {
113  0 chimeraViewer.closeViewer(true);
114    }
115    }
116   
117    /**
118    * Load 1GAQ and view the first structure for which a PDB id is found. Note no
119    * network connection is needed - PDB file is read locally, SIFTS fetch fails
120    * so mapping falls back to Needleman-Wunsch - ok for this test.
121    */
122    // External as local install of Chimera required
 
123  0 toggle @Test(groups = { "External" })
124    public void testSingleSeqViewChimera()
125    {
126   
127  0 String inFile = "examples/1gaq.txt";
128  0 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
129    DataSourceType.FILE);
130  0 assertNotNull(af, "Failed to create AlignFrame");
131  0 SequenceI sq = af.getViewport().getAlignment().getSequenceAt(0);
132  0 assertEquals(sq.getName(), "1GAQ|A");
133  0 SequenceI dsq = sq.getDatasetSequence();
134  0 Vector<PDBEntry> pdbIds = dsq.getAllPDBEntries();
135  0 assertEquals(pdbIds.size(), 1);
136  0 PDBEntry pdbEntry = pdbIds.get(0);
137  0 assertEquals(pdbEntry.getId(), "1GAQ");
138  0 StructureViewer structureViewer = new StructureViewer(
139    af.getViewport().getStructureSelectionManager());
140  0 chimeraViewer = structureViewer.viewStructures(pdbEntry,
141    new SequenceI[]
142    { sq }, af.getCurrentView().getAlignPanel());
143  0 JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
144    .getBinding();
145   
146    /*
147    * Wait for viewer load thread to complete
148    */
149  0 do
150    {
151  0 try
152    {
153  0 Thread.sleep(500);
154    } catch (InterruptedException e)
155    {
156    }
157  0 } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
158   
159  0 assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
160   
161  0 assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
162  0 assertTrue(chimeraViewer.hasViewerActionsMenu());
163   
164    // now add another sequence and bind to view
165    //
166  0 AlignmentI al = af.getViewport().getAlignment();
167  0 PDBEntry xpdb = al.getSequenceAt(0).getPDBEntry("1GAQ");
168  0 sq = new Sequence("1GAQ",
169    al.getSequenceAt(0).getSequence(25, 95).toString());
170  0 al.addSequence(sq);
171  0 structureViewer.viewStructures(new PDBEntry[] { xpdb },
172    new SequenceI[]
173    { sq }, af.getCurrentView().getAlignPanel());
174   
175    /*
176    * Wait for viewer load thread to complete
177    */
178  0 do
179    {
180  0 try
181    {
182  0 Thread.sleep(1500);
183    } catch (InterruptedException q)
184    {
185    }
186  0 ;
187  0 } while (!binding.isLoadingFinished());
188   
189    // still just one PDB structure shown
190  0 assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
191    // and the viewer action menu should still be visible
192  0 assertTrue(chimeraViewer.hasViewerActionsMenu());
193   
194  0 chimeraViewer.closeViewer(true);
195  0 chimeraViewer = null;
196  0 return;
197    }
198   
199    /**
200    * Test for writing Jalview features as attributes on mapped residues in
201    * Chimera. Note this uses local copies of PDB and SIFTS file, no network
202    * connection required.
203    *
204    * @throws IOException
205    * @throws SiftsException
206    */
207    // External as this requires a local install of Chimera
 
208  0 toggle @Test(groups = { "External" })
209    public void testTransferFeatures() throws IOException, SiftsException
210    {
211  0 String inFile = "examples/uniref50.fa";
212  0 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
213    DataSourceType.FILE);
214  0 assertNotNull(af, "Failed to create AlignFrame");
215  0 SequenceI sq = af.getViewport().getAlignment().findName("FER2_ARATH");
216  0 assertNotNull(sq, "Didn't find FER2_ARATH");
217   
218    /*
219    * need a Uniprot dbref for SIFTS mapping to work!!
220    */
221  0 sq.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
222   
223    /*
224    * use local test PDB and SIFTS files
225    */
226  0 String pdbFilePath = new File("test/jalview/ext/rbvi/chimera/4zho.pdb")
227    .getPath();
228  0 PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
229  0 String siftsFilePath = new File(
230    "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
231  0 SiftsClient.setMockSiftsFile(new File(siftsFilePath));
232   
233  0 StructureViewer structureViewer = new StructureViewer(
234    af.getViewport().getStructureSelectionManager());
235  0 chimeraViewer = structureViewer.viewStructures(pdbEntry,
236    new SequenceI[]
237    { sq }, af.getCurrentView().getAlignPanel());
238   
239  0 JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
240    .getBinding();
241  0 do
242    {
243  0 try
244    {
245  0 Thread.sleep(500);
246    } catch (InterruptedException e)
247    {
248    }
249  0 } while (!binding.isFinishedInit());
250   
251  0 assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
252   
253  0 assertEquals(binding.getPdbCount(), 1);
254   
255    /*
256    * check mapping is (sequence) 53-145 to (structure) 2-94 A/B
257    * (or possibly 52-145 to 1-94 - see JAL-2319)
258    */
259  0 StructureSelectionManager ssm = binding.getSsm();
260  0 String pdbFile = binding.getStructureFiles()[0];
261  0 StructureMapping[] mappings = ssm.getMapping(pdbFile);
262  0 assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"),
263    "Failed to perform SIFTS mapping");
264  0 assertEquals(mappings.length, 2);
265  0 assertEquals(mappings[0].getChain(), "A");
266  0 assertEquals(mappings[0].getPDBResNum(53), 2);
267  0 assertEquals(mappings[0].getPDBResNum(145), 94);
268  0 assertEquals(mappings[1].getChain(), "B");
269  0 assertEquals(mappings[1].getPDBResNum(53), 2);
270  0 assertEquals(mappings[1].getPDBResNum(145), 94);
271   
272    /*
273    * now add some features to FER2_ARATH
274    */
275    // feature on a sequence region not mapped to structure:
276  0 sq.addSequenceFeature(new SequenceFeature("transit peptide",
277    "chloroplast", 1, 51, Float.NaN, null));
278    // feature on a region mapped to structure:
279  0 sq.addSequenceFeature(new SequenceFeature("domain",
280    "2Fe-2S ferredoxin-type", 55, 145, Float.NaN, null));
281    // on sparse positions of the sequence
282  0 sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
283    "Iron-Sulfur (2Fe-2S)", 91, 91, Float.NaN, null));
284  0 sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
285    "Iron-Sulfur (2Fe-2S)", 96, 96, Float.NaN, null));
286    // on a sequence region that is partially mapped to structure:
287  0 sq.addSequenceFeature(
288    new SequenceFeature("helix", null, 50, 60, Float.NaN, null));
289    // and again:
290  0 sq.addSequenceFeature(
291    new SequenceFeature("chain", null, 50, 70, Float.NaN, null));
292    // add numeric valued features - score is set as attribute value
293  0 sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 62,
294    62, -2.1f, null));
295  0 sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 65,
296    65, 3.6f, null));
297  0 sq.addSequenceFeature(new SequenceFeature("RESNUM", "ALA: 2 4zhoA",
298    53, 53, Float.NaN, null));
299   
300    /*
301    * set all features visible except for chain
302    */
303  0 af.setShowSeqFeatures(true);
304  0 FeatureRenderer fr = af.getFeatureRenderer();
305  0 fr.setVisible("transit peptide");
306  0 fr.setVisible("domain");
307  0 fr.setVisible("metal ion-binding site");
308  0 fr.setVisible("helix");
309  0 fr.setVisible("kd");
310  0 fr.setVisible("RESNUM");
311   
312    /*
313    * 'perform' menu action to copy visible features to
314    * attributes in Chimera
315    */
316    // TODO rename and pull up method to binding interface
317    // once functionality is added for Jmol as well
318  0 binding.sendFeaturesToViewer(af.getViewport().getAlignPanel());
319   
320    /*
321    * give Chimera time to open the commands file and execute it
322    */
323  0 try
324    {
325  0 Thread.sleep(1000);
326    } catch (InterruptedException e)
327    {
328    }
329   
330    /*
331    * ask Chimera for its residue attribute names
332    */
333  0 List<String> reply = binding
334    .executeCommand(new StructureCommand("list resattr"), true);
335    // prefixed and sanitised attribute names for Jalview features:
336  0 assertTrue(reply.contains("resattr jv_domain"));
337  0 assertTrue(reply.contains("resattr jv_metal_ion_binding_site"));
338  0 assertTrue(reply.contains("resattr jv_helix"));
339  0 assertTrue(reply.contains("resattr jv_kd"));
340  0 assertTrue(reply.contains("resattr jv_RESNUM"));
341    // feature is not on a mapped region - no attribute created
342  0 assertFalse(reply.contains("resattr jv_transit_peptide"));
343    // feature is not visible - no attribute created
344  0 assertFalse(reply.contains("resattr jv_chain"));
345   
346    /*
347    * ask Chimera for residues with an attribute
348    * 91 and 96 on sequence --> residues 40 and 45 on chains A and B
349    */
350  0 reply = binding.executeCommand(
351    new StructureCommand("list resi att jv_metal_ion_binding_site"),
352    true);
353  0 assertEquals(reply.size(), 4);
354  0 assertTrue(reply.contains(
355    "residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
356  0 assertTrue(reply.contains(
357    "residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
358  0 assertTrue(reply.contains(
359    "residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
360  0 assertTrue(reply.contains(
361    "residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
362   
363    /*
364    * check attributes with score values
365    * sequence positions 62 and 65 --> residues 11 and 14 on chains A and B
366    */
367  0 reply = binding.executeCommand(
368    new StructureCommand("list resi att jv_kd"), true);
369  0 assertEquals(reply.size(), 4);
370  0 assertTrue(reply.contains("residue id #0:11.A jv_kd -2.1 index 11"));
371  0 assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
372  0 assertTrue(reply.contains("residue id #0:11.B jv_kd -2.1 index 11"));
373  0 assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14"));
374   
375    /*
376    * list residues with positive kd score
377    */
378  0 reply = binding.executeCommand(
379    new StructureCommand("list resi spec :*/jv_kd>0 attr jv_kd"),
380    true);
381  0 assertEquals(reply.size(), 2);
382  0 assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
383  0 assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14"));
384   
385  0 SiftsClient.setMockSiftsFile(null);
386  0 chimeraViewer.closeViewer(true);
387  0 chimeraViewer = null;
388    }
389   
390    /**
391    * Test for creating Jalview features from attributes on mapped residues in
392    * Chimera. Note this uses local copies of PDB and SIFTS file, no network
393    * connection required.
394    *
395    * @throws IOException
396    * @throws SiftsException
397    */
398    // External as this requires a local install of Chimera
 
399  0 toggle @Test(groups = { "External" })
400    public void testGetAttributes() throws IOException, SiftsException
401    {
402  0 String inFile = "examples/uniref50.fa";
403  0 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
404    DataSourceType.FILE);
405  0 assertNotNull(af, "Failed to create AlignFrame");
406  0 SequenceI fer2Arath = af.getViewport().getAlignment()
407    .findName("FER2_ARATH");
408  0 assertNotNull(fer2Arath, "Didn't find FER2_ARATH");
409   
410    /*
411    * need a Uniprot dbref for SIFTS mapping to work!!
412    */
413  0 fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
414   
415    /*
416    * use local test PDB and SIFTS files
417    */
418  0 String pdbFilePath = new File("test/jalview/ext/rbvi/chimera/4zho.pdb")
419    .getPath();
420  0 PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
421  0 String siftsFilePath = new File(
422    "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
423  0 SiftsClient.setMockSiftsFile(new File(siftsFilePath));
424   
425  0 StructureViewer structureViewer = new StructureViewer(
426    af.getViewport().getStructureSelectionManager());
427  0 chimeraViewer = structureViewer.viewStructures(pdbEntry,
428    new SequenceI[]
429    { fer2Arath }, af.getCurrentView().getAlignPanel());
430   
431  0 JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
432    .getBinding();
433  0 do
434    {
435  0 try
436    {
437  0 Thread.sleep(500);
438    } catch (InterruptedException e)
439    {
440    }
441  0 } while (!binding.isFinishedInit());
442   
443  0 assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
444   
445  0 assertEquals(binding.getPdbCount(), 1);
446   
447    /*
448    * 'perform' menu action to copy Chimera attributes
449    * to features in Jalview
450    */
451    // TODO rename and pull up method to binding interface
452    // once functionality is added for Jmol as well
453  0 binding.copyStructureAttributesToFeatures("isHelix",
454    af.getViewport().getAlignPanel());
455   
456    /*
457    * verify 22 residues have isHelix feature
458    * (may merge into ranges in future)
459    */
460  0 af.setShowSeqFeatures(true);
461  0 FeatureRenderer fr = af.getFeatureRenderer();
462  0 fr.setVisible("isHelix");
463  0 for (int res = 75; res <= 83; res++)
464    {
465  0 checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
466    }
467  0 for (int res = 117; res <= 123; res++)
468    {
469  0 checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
470    }
471  0 for (int res = 129; res <= 131; res++)
472    {
473  0 checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
474    }
475  0 for (int res = 143; res <= 145; res++)
476    {
477  0 checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
478    }
479   
480    /*
481    * fetch a numeric valued attribute
482    */
483  0 binding.copyStructureAttributesToFeatures("phi",
484    af.getViewport().getAlignPanel());
485  0 fr.setVisible("phi");
486  0 List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54,
487    "phi");
488  0 assertEquals(fs.size(), 2);
489  0 assertTrue(fs.contains(new SequenceFeature("phi", "A", 54, 54,
490    -131.0713f, "Chimera")));
491  0 assertTrue(fs.contains(new SequenceFeature("phi", "B", 54, 54,
492    -127.39512f, "Chimera")));
493   
494    /*
495    * tear down - also in AfterMethod
496    */
497  0 SiftsClient.setMockSiftsFile(null);
498  0 chimeraViewer.closeViewer(true);
499  0 chimeraViewer = null;
500    }
501   
502    /**
503    * Helper method to verify new feature at a sequence position
504    *
505    * @param seq
506    * @param fr
507    * @param res
508    * @param featureType
509    */
 
510  0 toggle protected void checkFeaturesAtRes(SequenceI seq, FeatureRenderer fr,
511    int res, String featureType)
512    {
513  0 String where = "at position " + res;
514  0 List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res,
515    featureType);
516   
517  0 assertEquals(fs.size(), 1, where);
518  0 SequenceFeature sf = fs.get(0);
519  0 assertEquals(sf.getType(), featureType, where);
520  0 assertEquals(sf.getFeatureGroup(), "Chimera", where);
521  0 assertEquals(sf.getDescription(), "True", where);
522  0 assertEquals(sf.getScore(), Float.NaN, where);
523    }
524    }
  • Report generated by OpenClover v 4.4.1 on Fri Dec 6 2024 13:54:25 GMT using coverage data from Fri Dec 6 2024 13:54:13 GMT.
  • OpenClover is free and open-source software.