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ChimeraViewFrame | 61 | 163 | 52 |
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 java.awt.event.ActionEvent; | |
24 | import java.awt.event.ActionListener; | |
25 | import java.awt.event.MouseAdapter; | |
26 | import java.awt.event.MouseEvent; | |
27 | import java.io.File; | |
28 | import java.util.ArrayList; | |
29 | import java.util.Collections; | |
30 | import java.util.List; | |
31 | import java.util.Map; | |
32 | ||
33 | import javax.swing.JInternalFrame; | |
34 | import javax.swing.JMenu; | |
35 | import javax.swing.JMenuItem; | |
36 | import javax.swing.event.InternalFrameAdapter; | |
37 | import javax.swing.event.InternalFrameEvent; | |
38 | ||
39 | import jalview.api.AlignmentViewPanel; | |
40 | import jalview.api.FeatureRenderer; | |
41 | import jalview.bin.Console; | |
42 | import jalview.datamodel.PDBEntry; | |
43 | import jalview.datamodel.SequenceI; | |
44 | import jalview.datamodel.StructureViewerModel; | |
45 | import jalview.datamodel.StructureViewerModel.StructureData; | |
46 | import jalview.ext.rbvi.chimera.JalviewChimeraBinding; | |
47 | import jalview.gui.StructureViewer.ViewerType; | |
48 | import jalview.io.DataSourceType; | |
49 | import jalview.io.StructureFile; | |
50 | import jalview.structures.models.AAStructureBindingModel; | |
51 | import jalview.util.ImageMaker.TYPE; | |
52 | import jalview.util.MessageManager; | |
53 | import jalview.util.Platform; | |
54 | ||
55 | /** | |
56 | * GUI elements for handling an external chimera display | |
57 | * | |
58 | * @author jprocter | |
59 | * | |
60 | */ | |
61 | public class ChimeraViewFrame extends StructureViewerBase | |
62 | { | |
63 | private JalviewChimeraBinding jmb; | |
64 | ||
65 | /* | |
66 | * Path to Chimera session file. This is set when an open Jalview/Chimera | |
67 | * session is saved, or on restore from a Jalview project (if it holds the | |
68 | * filename of any saved Chimera sessions). | |
69 | */ | |
70 | private String chimeraSessionFile = null; | |
71 | ||
72 | private int myWidth = 500; | |
73 | ||
74 | private int myHeight = 150; | |
75 | ||
76 | private JMenuItem writeFeatures = null; | |
77 | ||
78 | private JMenu fetchAttributes = null; | |
79 | ||
80 | /** | |
81 | * Initialise menu options. | |
82 | */ | |
83 | 0 | @Override |
84 | protected void initMenus() | |
85 | { | |
86 | 0 | super.initMenus(); |
87 | ||
88 | 0 | savemenu.setVisible(false); // not yet implemented |
89 | 0 | viewMenu.add(fitToWindow); |
90 | ||
91 | 0 | writeFeatures = new JMenuItem( |
92 | MessageManager.getString("label.create_viewer_attributes")); | |
93 | 0 | writeFeatures.setToolTipText( |
94 | MessageManager.getString("label.create_viewer_attributes_tip")); | |
95 | 0 | writeFeatures.addActionListener(new ActionListener() |
96 | { | |
97 | 0 | @Override |
98 | public void actionPerformed(ActionEvent e) | |
99 | { | |
100 | 0 | sendFeaturesToChimera(); |
101 | } | |
102 | }); | |
103 | 0 | viewerActionMenu.add(writeFeatures); |
104 | ||
105 | 0 | fetchAttributes = new JMenu(MessageManager.formatMessage( |
106 | "label.fetch_viewer_attributes", getViewerName())); | |
107 | 0 | fetchAttributes.setToolTipText(MessageManager.formatMessage( |
108 | "label.fetch_viewer_attributes_tip", getViewerName())); | |
109 | 0 | fetchAttributes.addMouseListener(new MouseAdapter() |
110 | { | |
111 | ||
112 | 0 | @Override |
113 | public void mouseEntered(MouseEvent e) | |
114 | { | |
115 | 0 | buildAttributesMenu(fetchAttributes); |
116 | } | |
117 | }); | |
118 | 0 | viewerActionMenu.add(fetchAttributes); |
119 | } | |
120 | ||
121 | 0 | @Override |
122 | protected void buildActionMenu() | |
123 | { | |
124 | 0 | super.buildActionMenu(); |
125 | // add these back in after menu is refreshed | |
126 | 0 | viewerActionMenu.add(writeFeatures); |
127 | 0 | viewerActionMenu.add(fetchAttributes); |
128 | ||
129 | }; | |
130 | ||
131 | /** | |
132 | * Query the structure viewer for its residue attribute names and add them as | |
133 | * items off the attributes menu | |
134 | * | |
135 | * @param attributesMenu | |
136 | */ | |
137 | 0 | protected void buildAttributesMenu(JMenu attributesMenu) |
138 | { | |
139 | 0 | List<String> atts = jmb.getChimeraAttributes(); |
140 | 0 | attributesMenu.removeAll(); |
141 | 0 | Collections.sort(atts); |
142 | 0 | for (String attName : atts) |
143 | { | |
144 | 0 | JMenuItem menuItem = new JMenuItem(attName); |
145 | 0 | menuItem.addActionListener(new ActionListener() |
146 | { | |
147 | 0 | @Override |
148 | public void actionPerformed(ActionEvent e) | |
149 | { | |
150 | 0 | if (getBinding().copyStructureAttributesToFeatures(attName, |
151 | getAlignmentPanel()) > 0) | |
152 | { | |
153 | 0 | getAlignmentPanel().getFeatureRenderer().featuresAdded(); |
154 | } | |
155 | } | |
156 | }); | |
157 | 0 | attributesMenu.add(menuItem); |
158 | } | |
159 | } | |
160 | ||
161 | /** | |
162 | * Sends command(s) to the structure viewer to create residue attributes for | |
163 | * visible Jalview features | |
164 | */ | |
165 | 0 | protected void sendFeaturesToChimera() |
166 | { | |
167 | // todo pull up? | |
168 | 0 | int count = jmb.sendFeaturesToViewer(getAlignmentPanel()); |
169 | 0 | statusBar.setText(MessageManager.formatMessage("label.attributes_set", |
170 | count, getViewerName())); | |
171 | } | |
172 | ||
173 | /** | |
174 | * open a single PDB structure in a new Chimera view | |
175 | * | |
176 | * @param pdbentry | |
177 | * @param seq | |
178 | * @param chains | |
179 | * @param ap | |
180 | */ | |
181 | 0 | public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq, |
182 | String[] chains, final AlignmentPanel ap) | |
183 | { | |
184 | 0 | this(); |
185 | ||
186 | 0 | openNewChimera(ap, new PDBEntry[] { pdbentry }, |
187 | new SequenceI[][] | |
188 | { seq }); | |
189 | } | |
190 | ||
191 | /** | |
192 | * Create a helper to manage progress bar display | |
193 | */ | |
194 | 0 | protected void createProgressBar() |
195 | { | |
196 | 0 | if (getProgressIndicator() == null) |
197 | { | |
198 | 0 | setProgressIndicator(new ProgressBar(statusPanel, statusBar)); |
199 | } | |
200 | } | |
201 | ||
202 | 0 | private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys, |
203 | SequenceI[][] seqs) | |
204 | { | |
205 | 0 | createProgressBar(); |
206 | 0 | jmb = newBindingModel(ap, pdbentrys, seqs); |
207 | 0 | addAlignmentPanel(ap); |
208 | 0 | useAlignmentPanelForColourbyseq(ap); |
209 | ||
210 | 0 | if (pdbentrys.length > 1) |
211 | { | |
212 | 0 | useAlignmentPanelForSuperposition(ap); |
213 | } | |
214 | 0 | jmb.setColourBySequence(true); |
215 | 0 | setSize(myWidth, myHeight); |
216 | 0 | initMenus(); |
217 | ||
218 | 0 | addingStructures = false; |
219 | 0 | worker = new Thread(this); |
220 | 0 | worker.start(); |
221 | ||
222 | 0 | this.addInternalFrameListener(new InternalFrameAdapter() |
223 | { | |
224 | 0 | @Override |
225 | public void internalFrameClosing( | |
226 | InternalFrameEvent internalFrameEvent) | |
227 | { | |
228 | 0 | closeViewer(false); |
229 | } | |
230 | }); | |
231 | ||
232 | } | |
233 | ||
234 | 0 | protected JalviewChimeraBindingModel newBindingModel(AlignmentPanel ap, |
235 | PDBEntry[] pdbentrys, SequenceI[][] seqs) | |
236 | { | |
237 | 0 | return new JalviewChimeraBindingModel(this, |
238 | ap.getStructureSelectionManager(), pdbentrys, seqs, null); | |
239 | } | |
240 | ||
241 | /** | |
242 | * Create a new viewer from saved session state data including Chimera session | |
243 | * file | |
244 | * | |
245 | * @param chimeraSessionFile | |
246 | * @param alignPanel | |
247 | * @param pdbArray | |
248 | * @param seqsArray | |
249 | * @param colourByChimera | |
250 | * @param colourBySequence | |
251 | * @param newViewId | |
252 | */ | |
253 | 0 | public ChimeraViewFrame(StructureViewerModel viewerData, |
254 | AlignmentPanel alignPanel, String sessionFile, String vid) | |
255 | { | |
256 | 0 | this(); |
257 | 0 | setViewId(vid); |
258 | 0 | this.chimeraSessionFile = sessionFile; |
259 | 0 | Map<File, StructureData> pdbData = viewerData.getFileData(); |
260 | 0 | PDBEntry[] pdbArray = new PDBEntry[pdbData.size()]; |
261 | 0 | SequenceI[][] seqsArray = new SequenceI[pdbData.size()][]; |
262 | 0 | int i = 0; |
263 | 0 | for (StructureData data : pdbData.values()) |
264 | { | |
265 | 0 | PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null, |
266 | PDBEntry.Type.PDB, data.getFilePath()); | |
267 | 0 | pdbArray[i] = pdbentry; |
268 | 0 | List<SequenceI> sequencesForPdb = data.getSeqList(); |
269 | 0 | seqsArray[i] = sequencesForPdb |
270 | .toArray(new SequenceI[sequencesForPdb.size()]); | |
271 | 0 | i++; |
272 | } | |
273 | 0 | openNewChimera(alignPanel, pdbArray, seqsArray); |
274 | 0 | if (viewerData.isColourByViewer()) |
275 | { | |
276 | 0 | jmb.setColourBySequence(false); |
277 | 0 | seqColour.setSelected(false); |
278 | 0 | viewerColour.setSelected(true); |
279 | } | |
280 | 0 | else if (viewerData.isColourWithAlignPanel()) |
281 | { | |
282 | 0 | jmb.setColourBySequence(true); |
283 | 0 | seqColour.setSelected(true); |
284 | 0 | viewerColour.setSelected(false); |
285 | } | |
286 | } | |
287 | ||
288 | /** | |
289 | * create a new viewer containing several structures, optionally superimposed | |
290 | * using the given alignPanel. | |
291 | * | |
292 | * @param pe | |
293 | * @param seqs | |
294 | * @param ap | |
295 | */ | |
296 | 0 | public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded, |
297 | SequenceI[][] seqs, AlignmentPanel ap) | |
298 | { | |
299 | 0 | this(); |
300 | 0 | setAlignAddedStructures(alignAdded); |
301 | 0 | openNewChimera(ap, pe, seqs); |
302 | } | |
303 | ||
304 | /** | |
305 | * Default constructor | |
306 | */ | |
307 | 0 | public ChimeraViewFrame() |
308 | { | |
309 | 0 | super(); |
310 | ||
311 | /* | |
312 | * closeViewer will decide whether or not to close this frame | |
313 | * depending on whether user chooses to Cancel or not | |
314 | */ | |
315 | 0 | setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE); |
316 | } | |
317 | ||
318 | /** | |
319 | * Launch Chimera. If we have a chimera session file name, send Chimera the | |
320 | * command to open its saved session file. | |
321 | */ | |
322 | 0 | void initChimera() |
323 | { | |
324 | 0 | jmb.setFinishedInit(false); |
325 | 0 | Desktop.addInternalFrame(this, |
326 | jmb.getViewerTitle(getViewerName(), true), getBounds().width, | |
327 | getBounds().height); | |
328 | ||
329 | 0 | if (!jmb.launchChimera()) |
330 | { | |
331 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
332 | MessageManager.formatMessage("label.open_viewer_failed", | |
333 | getViewerName()), | |
334 | MessageManager.getString("label.error_loading_file"), | |
335 | JvOptionPane.ERROR_MESSAGE); | |
336 | 0 | jmb.closeViewer(true); |
337 | 0 | this.dispose(); |
338 | 0 | return; |
339 | } | |
340 | ||
341 | 0 | if (this.chimeraSessionFile != null) |
342 | { | |
343 | 0 | boolean opened = jmb.openSession(chimeraSessionFile); |
344 | 0 | if (!opened) |
345 | { | |
346 | 0 | jalview.bin.Console.errPrintln( |
347 | "An error occurred opening Chimera session file " | |
348 | + chimeraSessionFile); | |
349 | } | |
350 | } | |
351 | ||
352 | 0 | jmb.startChimeraListener(); |
353 | } | |
354 | ||
355 | /** | |
356 | * Open any newly added PDB structures in Chimera, having first fetched data | |
357 | * from PDB (if not already saved). | |
358 | */ | |
359 | 0 | @Override |
360 | public void run() | |
361 | { | |
362 | 0 | _started = true; |
363 | // todo - record which pdbids were successfully imported. | |
364 | 0 | StringBuilder errormsgs = new StringBuilder(128); |
365 | 0 | StringBuilder files = new StringBuilder(128); |
366 | 0 | List<PDBEntry> filePDB = new ArrayList<>(); |
367 | 0 | List<Integer> filePDBpos = new ArrayList<>(); |
368 | 0 | PDBEntry thePdbEntry = null; |
369 | 0 | StructureFile pdb = null; |
370 | 0 | try |
371 | { | |
372 | 0 | String[] curfiles = jmb.getStructureFiles(); // files currently in viewer |
373 | // TODO: replace with reference fetching/transfer code (validate PDBentry | |
374 | // as a DBRef?) | |
375 | 0 | for (int pi = 0; pi < jmb.getPdbCount(); pi++) |
376 | { | |
377 | 0 | String file = null; |
378 | 0 | thePdbEntry = jmb.getPdbEntry(pi); |
379 | 0 | if (thePdbEntry.getFile() == null) |
380 | { | |
381 | /* | |
382 | * Retrieve PDB data, save to file, attach to PDBEntry | |
383 | */ | |
384 | 0 | file = fetchPdbFile(thePdbEntry); |
385 | 0 | if (file == null) |
386 | { | |
387 | 0 | errormsgs.append("'" + thePdbEntry.getId() + "' "); |
388 | } | |
389 | } | |
390 | else | |
391 | { | |
392 | /* | |
393 | * Got file already - ignore if already loaded in Chimera. | |
394 | */ | |
395 | 0 | file = new File(thePdbEntry.getFile()).getAbsoluteFile() |
396 | .getPath(); | |
397 | 0 | if (curfiles != null && curfiles.length > 0) |
398 | { | |
399 | 0 | addingStructures = true; // already files loaded. |
400 | 0 | for (int c = 0; c < curfiles.length; c++) |
401 | { | |
402 | 0 | if (curfiles[c].equals(file)) |
403 | { | |
404 | 0 | file = null; |
405 | 0 | break; |
406 | } | |
407 | } | |
408 | } | |
409 | } | |
410 | 0 | if (file != null) |
411 | { | |
412 | 0 | filePDB.add(thePdbEntry); |
413 | 0 | filePDBpos.add(Integer.valueOf(pi)); |
414 | 0 | files.append(" \"" + Platform.escapeBackslashes(file) + "\""); |
415 | } | |
416 | } | |
417 | } catch (OutOfMemoryError oomerror) | |
418 | { | |
419 | 0 | new OOMWarning("Retrieving PDB files: " + thePdbEntry.getId(), |
420 | oomerror); | |
421 | } catch (Exception ex) | |
422 | { | |
423 | 0 | ex.printStackTrace(); |
424 | 0 | errormsgs.append( |
425 | "When retrieving pdbfiles for '" + thePdbEntry.getId() + "'"); | |
426 | } | |
427 | 0 | if (errormsgs.length() > 0) |
428 | { | |
429 | ||
430 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
431 | MessageManager.formatMessage( | |
432 | "label.pdb_entries_couldnt_be_retrieved", new Object[] | |
433 | { errormsgs.toString() }), | |
434 | MessageManager.getString("label.couldnt_load_file"), | |
435 | JvOptionPane.ERROR_MESSAGE); | |
436 | } | |
437 | ||
438 | 0 | if (files.length() > 0) |
439 | { | |
440 | 0 | jmb.setFinishedInit(false); |
441 | 0 | if (!addingStructures) |
442 | { | |
443 | 0 | try |
444 | { | |
445 | 0 | initChimera(); |
446 | } catch (Exception ex) | |
447 | { | |
448 | 0 | Console.error("Couldn't open Chimera viewer!", ex); |
449 | } | |
450 | } | |
451 | 0 | if (!jmb.isViewerRunning()) |
452 | { | |
453 | // nothing to do | |
454 | // TODO: ensure we tidy up JAL-3619 | |
455 | 0 | return; |
456 | } | |
457 | 0 | int num = -1; |
458 | 0 | for (PDBEntry pe : filePDB) |
459 | { | |
460 | 0 | num++; |
461 | 0 | if (pe.getFile() != null) |
462 | { | |
463 | 0 | try |
464 | { | |
465 | 0 | int pos = filePDBpos.get(num).intValue(); |
466 | 0 | long startTime = startProgressBar(getViewerName() + " " |
467 | + MessageManager.getString("status.opening_file_for") | |
468 | + " " + pe.getId()); | |
469 | 0 | jmb.openFile(pe); |
470 | 0 | jmb.addSequence(pos, jmb.getSequence()[pos]); |
471 | 0 | File fl = new File(pe.getFile()); |
472 | 0 | DataSourceType protocol = DataSourceType.URL; |
473 | 0 | try |
474 | { | |
475 | 0 | if (fl.exists()) |
476 | { | |
477 | 0 | protocol = DataSourceType.FILE; |
478 | } | |
479 | } catch (Throwable e) | |
480 | { | |
481 | } finally | |
482 | { | |
483 | 0 | stopProgressBar("", startTime); |
484 | } | |
485 | // Explicitly map to the filename used by Chimera ; | |
486 | ||
487 | 0 | pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], |
488 | jmb.getChains()[pos], pe.getFile(), protocol, | |
489 | getProgressIndicator()); | |
490 | 0 | jmb.stashFoundChains(pdb, pe.getFile()); |
491 | ||
492 | } catch (OutOfMemoryError oomerror) | |
493 | { | |
494 | 0 | new OOMWarning( |
495 | "When trying to open and map structures from Chimera!", | |
496 | oomerror); | |
497 | } catch (Exception ex) | |
498 | { | |
499 | 0 | Console.error( |
500 | "Couldn't open " + pe.getFile() + " in Chimera viewer!", | |
501 | ex); | |
502 | } finally | |
503 | { | |
504 | 0 | Console.debug("File locations are " + files); |
505 | } | |
506 | } | |
507 | } | |
508 | ||
509 | 0 | jmb.refreshGUI(); |
510 | 0 | jmb.setFinishedInit(true); |
511 | 0 | jmb.setLoadingFromArchive(false); |
512 | ||
513 | /* | |
514 | * ensure that any newly discovered features (e.g. RESNUM) | |
515 | * are notified to the FeatureRenderer (and added to any | |
516 | * open feature settings dialog) | |
517 | */ | |
518 | 0 | FeatureRenderer fr = getBinding().getFeatureRenderer(null); |
519 | 0 | if (fr != null) |
520 | { | |
521 | 0 | fr.featuresAdded(); |
522 | } | |
523 | ||
524 | // refresh the sequence colours for the new structure(s) | |
525 | 0 | for (AlignmentViewPanel ap : _colourwith) |
526 | { | |
527 | 0 | jmb.updateColours(ap); |
528 | } | |
529 | // do superposition if asked to | |
530 | 0 | if (alignAddedStructures) |
531 | { | |
532 | 0 | new Thread(new Runnable() |
533 | { | |
534 | 0 | @Override |
535 | public void run() | |
536 | { | |
537 | 0 | alignStructsWithAllAlignPanels(); |
538 | } | |
539 | }).start(); | |
540 | } | |
541 | 0 | addingStructures = false; |
542 | } | |
543 | 0 | _started = false; |
544 | 0 | worker = null; |
545 | } | |
546 | ||
547 | 0 | @Override |
548 | public void makePDBImage(TYPE imageType) | |
549 | { | |
550 | 0 | throw new UnsupportedOperationException( |
551 | "Image export for Chimera is not implemented"); | |
552 | } | |
553 | ||
554 | 0 | @Override |
555 | public AAStructureBindingModel getBinding() | |
556 | { | |
557 | 0 | return jmb; |
558 | } | |
559 | ||
560 | 0 | @Override |
561 | public ViewerType getViewerType() | |
562 | { | |
563 | 0 | return ViewerType.CHIMERA; |
564 | } | |
565 | ||
566 | 0 | @Override |
567 | protected String getViewerName() | |
568 | { | |
569 | 0 | return "Chimera"; |
570 | } | |
571 | } |