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PymolViewer | 48 | 132 | 39 |
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.io.File; | |
26 | import java.util.ArrayList; | |
27 | import java.util.List; | |
28 | import java.util.Map; | |
29 | ||
30 | import javax.swing.JInternalFrame; | |
31 | import javax.swing.JMenuItem; | |
32 | import javax.swing.event.InternalFrameAdapter; | |
33 | import javax.swing.event.InternalFrameEvent; | |
34 | ||
35 | import jalview.api.AlignmentViewPanel; | |
36 | import jalview.api.FeatureRenderer; | |
37 | import jalview.bin.Console; | |
38 | import jalview.datamodel.PDBEntry; | |
39 | import jalview.datamodel.SequenceI; | |
40 | import jalview.datamodel.StructureViewerModel; | |
41 | import jalview.datamodel.StructureViewerModel.StructureData; | |
42 | import jalview.gui.StructureViewer.ViewerType; | |
43 | import jalview.io.DataSourceType; | |
44 | import jalview.io.StructureFile; | |
45 | import jalview.structures.models.AAStructureBindingModel; | |
46 | import jalview.util.MessageManager; | |
47 | ||
48 | public class PymolViewer extends StructureViewerBase | |
49 | { | |
50 | private static final int myWidth = 500; | |
51 | ||
52 | private static final int myHeight = 150; | |
53 | ||
54 | private PymolBindingModel binding; | |
55 | ||
56 | private String pymolSessionFile; | |
57 | ||
58 | 0 | public PymolViewer() |
59 | { | |
60 | 0 | super(); |
61 | ||
62 | /* | |
63 | * closeViewer will decide whether or not to close this frame | |
64 | * depending on whether user chooses to Cancel or not | |
65 | */ | |
66 | 0 | setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE); |
67 | } | |
68 | ||
69 | 0 | public PymolViewer(PDBEntry pdb, SequenceI[] seqs, Object object, |
70 | AlignmentPanel ap) | |
71 | { | |
72 | 0 | this(); |
73 | 0 | openNewPymol(ap, new PDBEntry[] { pdb }, new SequenceI[][] { seqs }); |
74 | } | |
75 | ||
76 | 0 | public PymolViewer(PDBEntry[] pe, boolean alignAdded, SequenceI[][] seqs, |
77 | AlignmentPanel ap) | |
78 | { | |
79 | 0 | this(); |
80 | 0 | setAlignAddedStructures(alignAdded); |
81 | 0 | openNewPymol(ap, pe, seqs); |
82 | } | |
83 | ||
84 | /** | |
85 | * Constructor given a session file to be restored | |
86 | * | |
87 | * @param sessionFile | |
88 | * @param alignPanel | |
89 | * @param pdbArray | |
90 | * @param seqsArray | |
91 | * @param colourByPymol | |
92 | * @param colourBySequence | |
93 | * @param newViewId | |
94 | */ | |
95 | 0 | public PymolViewer(StructureViewerModel viewerModel, |
96 | AlignmentPanel alignPanel, String sessionFile, String vid) | |
97 | { | |
98 | // TODO convert to base/factory class method | |
99 | 0 | this(); |
100 | 0 | setViewId(vid); |
101 | 0 | this.pymolSessionFile = sessionFile; |
102 | 0 | Map<File, StructureData> pdbData = viewerModel.getFileData(); |
103 | 0 | PDBEntry[] pdbArray = new PDBEntry[pdbData.size()]; |
104 | 0 | SequenceI[][] seqsArray = new SequenceI[pdbData.size()][]; |
105 | 0 | int i = 0; |
106 | 0 | for (StructureData data : pdbData.values()) |
107 | { | |
108 | 0 | PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null, |
109 | PDBEntry.Type.PDB, data.getFilePath()); | |
110 | 0 | pdbArray[i] = pdbentry; |
111 | 0 | List<SequenceI> sequencesForPdb = data.getSeqList(); |
112 | 0 | seqsArray[i] = sequencesForPdb |
113 | .toArray(new SequenceI[sequencesForPdb.size()]); | |
114 | 0 | i++; |
115 | } | |
116 | ||
117 | 0 | openNewPymol(alignPanel, pdbArray, seqsArray); |
118 | 0 | if (viewerModel.isColourByViewer()) |
119 | { | |
120 | 0 | binding.setColourBySequence(false); |
121 | 0 | seqColour.setSelected(false); |
122 | 0 | viewerColour.setSelected(true); |
123 | } | |
124 | 0 | else if (viewerModel.isColourWithAlignPanel()) |
125 | { | |
126 | 0 | binding.setColourBySequence(true); |
127 | 0 | seqColour.setSelected(true); |
128 | 0 | viewerColour.setSelected(false); |
129 | } | |
130 | } | |
131 | ||
132 | 0 | private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe, |
133 | SequenceI[][] seqs) | |
134 | { | |
135 | 0 | createProgressBar(); |
136 | 0 | binding = new PymolBindingModel(this, ap.getStructureSelectionManager(), |
137 | pe, seqs); | |
138 | 0 | addAlignmentPanel(ap); |
139 | 0 | useAlignmentPanelForColourbyseq(ap); |
140 | ||
141 | 0 | if (pe.length > 1) |
142 | { | |
143 | 0 | useAlignmentPanelForSuperposition(ap); |
144 | } | |
145 | 0 | binding.setColourBySequence(true); |
146 | 0 | setSize(myWidth, myHeight); |
147 | 0 | initMenus(); |
148 | 0 | viewerActionMenu.setText("PyMOL"); |
149 | 0 | updateTitleAndMenus(); |
150 | ||
151 | 0 | addingStructures = false; |
152 | 0 | worker = new Thread(this); |
153 | 0 | worker.start(); |
154 | ||
155 | 0 | this.addInternalFrameListener(new InternalFrameAdapter() |
156 | { | |
157 | 0 | @Override |
158 | public void internalFrameClosing( | |
159 | InternalFrameEvent internalFrameEvent) | |
160 | { | |
161 | 0 | closeViewer(false); |
162 | } | |
163 | }); | |
164 | ||
165 | } | |
166 | ||
167 | /** | |
168 | * Create a helper to manage progress bar display | |
169 | */ | |
170 | 0 | protected void createProgressBar() |
171 | { | |
172 | 0 | if (getProgressIndicator() == null) |
173 | { | |
174 | 0 | setProgressIndicator(new ProgressBar(statusPanel, statusBar)); |
175 | } | |
176 | } | |
177 | ||
178 | 0 | @Override |
179 | public void run() | |
180 | { | |
181 | // todo pull up much of this | |
182 | ||
183 | 0 | StringBuilder errormsgs = new StringBuilder(128); |
184 | 0 | List<PDBEntry> filePDB = new ArrayList<>(); |
185 | 0 | List<Integer> filePDBpos = new ArrayList<>(); |
186 | 0 | String[] curfiles = binding.getStructureFiles(); // files currently in |
187 | // viewer | |
188 | 0 | for (int pi = 0; pi < binding.getPdbCount(); pi++) |
189 | { | |
190 | 0 | String file = null; |
191 | 0 | PDBEntry thePdbEntry = binding.getPdbEntry(pi); |
192 | 0 | if (thePdbEntry.getFile() == null) |
193 | { | |
194 | /* | |
195 | * Retrieve PDB data, save to file, attach to PDBEntry | |
196 | */ | |
197 | 0 | file = fetchPdbFile(thePdbEntry); |
198 | 0 | if (file == null) |
199 | { | |
200 | 0 | errormsgs.append("'" + thePdbEntry.getId() + "' "); |
201 | } | |
202 | } | |
203 | else | |
204 | { | |
205 | /* | |
206 | * got file already | |
207 | */ | |
208 | 0 | file = new File(thePdbEntry.getFile()).getAbsoluteFile().getPath(); |
209 | // todo - skip if already loaded in PyMOL | |
210 | } | |
211 | 0 | if (file != null) |
212 | { | |
213 | 0 | filePDB.add(thePdbEntry); |
214 | 0 | filePDBpos.add(Integer.valueOf(pi)); |
215 | } | |
216 | } | |
217 | ||
218 | 0 | if (!filePDB.isEmpty()) |
219 | { | |
220 | /* | |
221 | * at least one structure to add to viewer | |
222 | */ | |
223 | 0 | binding.setFinishedInit(false); |
224 | 0 | if (!addingStructures) |
225 | { | |
226 | 0 | try |
227 | { | |
228 | 0 | initPymol(); |
229 | } catch (Exception ex) | |
230 | { | |
231 | 0 | Console.error("Couldn't open PyMOL viewer!", ex); |
232 | // if we couldn't open Pymol, no point continuing | |
233 | 0 | return; |
234 | } | |
235 | } | |
236 | 0 | if (!binding.isViewerRunning()) |
237 | { | |
238 | // nothing to do | |
239 | // TODO: ensure we tidy up JAL-3619 | |
240 | ||
241 | 0 | return; |
242 | } | |
243 | ||
244 | 0 | int num = -1; |
245 | 0 | for (PDBEntry pe : filePDB) |
246 | { | |
247 | 0 | num++; |
248 | 0 | if (pe.getFile() != null) |
249 | { | |
250 | 0 | try |
251 | { | |
252 | 0 | int pos = filePDBpos.get(num).intValue(); |
253 | 0 | long startTime = startProgressBar(getViewerName() + " " |
254 | + MessageManager.getString("status.opening_file_for") | |
255 | + " " + pe.getId()); | |
256 | 0 | binding.openFile(pe); |
257 | 0 | binding.addSequence(pos, binding.getSequence()[pos]); |
258 | 0 | File fl = new File(pe.getFile()); |
259 | 0 | DataSourceType protocol = DataSourceType.URL; |
260 | 0 | try |
261 | { | |
262 | 0 | if (fl.exists()) |
263 | { | |
264 | 0 | protocol = DataSourceType.FILE; |
265 | } | |
266 | } catch (Throwable e) | |
267 | { | |
268 | } finally | |
269 | { | |
270 | 0 | stopProgressBar("", startTime); |
271 | } | |
272 | ||
273 | 0 | StructureFile pdb = null; |
274 | 0 | if (pe.hasStructureFile()) |
275 | { | |
276 | 0 | pdb = pe.getStructureFile(); |
277 | 0 | Console.debug("(Re)Using StructureFile " + pdb.getId()); |
278 | } | |
279 | else | |
280 | { | |
281 | 0 | pdb = binding.getSsm().setMapping(binding.getSequence()[pos], |
282 | binding.getChains()[pos], pe.getFile(), protocol, | |
283 | getProgressIndicator()); | |
284 | } | |
285 | 0 | binding.stashFoundChains(pdb, pe.getFile()); |
286 | } catch (Exception ex) | |
287 | { | |
288 | 0 | Console.error("Couldn't open " + pe.getFile() + " in " |
289 | + getViewerName() + "!", ex); | |
290 | } finally | |
291 | { | |
292 | // Cache.debug("File locations are " + files); | |
293 | } | |
294 | } | |
295 | } | |
296 | ||
297 | 0 | binding.refreshGUI(); |
298 | 0 | binding.setFinishedInit(true); |
299 | 0 | binding.setLoadingFromArchive(false); |
300 | ||
301 | /* | |
302 | * ensure that any newly discovered features (e.g. RESNUM) | |
303 | * are added to any open feature settings dialog | |
304 | */ | |
305 | 0 | FeatureRenderer fr = getBinding().getFeatureRenderer(null); |
306 | 0 | if (fr != null) |
307 | { | |
308 | 0 | fr.featuresAdded(); |
309 | } | |
310 | ||
311 | // refresh the sequence colours for the new structure(s) | |
312 | 0 | for (AlignmentViewPanel ap : _colourwith) |
313 | { | |
314 | 0 | binding.updateColours(ap); |
315 | } | |
316 | // do superposition if asked to | |
317 | 0 | if (alignAddedStructures) |
318 | { | |
319 | 0 | new Thread(new Runnable() |
320 | { | |
321 | 0 | @Override |
322 | public void run() | |
323 | { | |
324 | 0 | alignStructsWithAllAlignPanels(); |
325 | } | |
326 | }).start(); | |
327 | } | |
328 | 0 | addingStructures = false; |
329 | } | |
330 | 0 | _started = false; |
331 | 0 | worker = null; |
332 | ||
333 | } | |
334 | ||
335 | /** | |
336 | * Launch PyMOL. If we have a session file name, send PyMOL the command to | |
337 | * open its saved session file. | |
338 | */ | |
339 | 0 | void initPymol() |
340 | { | |
341 | 0 | Desktop.addInternalFrame(this, |
342 | binding.getViewerTitle(getViewerName(), true), | |
343 | getBounds().width, getBounds().height); | |
344 | ||
345 | 0 | if (!binding.launchPymol()) |
346 | { | |
347 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
348 | MessageManager.formatMessage("label.open_viewer_failed", | |
349 | getViewerName()), | |
350 | MessageManager.getString("label.error_loading_file"), | |
351 | JvOptionPane.ERROR_MESSAGE); | |
352 | 0 | binding.closeViewer(true); |
353 | 0 | this.dispose(); |
354 | 0 | return; |
355 | } | |
356 | ||
357 | 0 | if (this.pymolSessionFile != null) |
358 | { | |
359 | 0 | boolean opened = binding.openSession(pymolSessionFile); |
360 | 0 | if (!opened) |
361 | { | |
362 | 0 | Console.error("An error occurred opening PyMOL session file " |
363 | + pymolSessionFile); | |
364 | } | |
365 | } | |
366 | // binding.startPymolListener(); | |
367 | } | |
368 | ||
369 | 0 | @Override |
370 | public AAStructureBindingModel getBinding() | |
371 | { | |
372 | 0 | return binding; |
373 | } | |
374 | ||
375 | 0 | @Override |
376 | public ViewerType getViewerType() | |
377 | { | |
378 | 0 | return ViewerType.PYMOL; |
379 | } | |
380 | ||
381 | 0 | @Override |
382 | protected String getViewerName() | |
383 | { | |
384 | 0 | return "PyMOL"; |
385 | } | |
386 | ||
387 | JMenuItem writeFeatures = null; | |
388 | ||
389 | 0 | @Override |
390 | protected void initMenus() | |
391 | { | |
392 | 0 | super.initMenus(); |
393 | ||
394 | 0 | savemenu.setVisible(false); // not yet implemented |
395 | 0 | viewMenu.add(fitToWindow); |
396 | ||
397 | 0 | writeFeatures = new JMenuItem( |
398 | MessageManager.getString("label.create_viewer_attributes")); | |
399 | 0 | writeFeatures.setToolTipText( |
400 | MessageManager.getString("label.create_viewer_attributes_tip")); | |
401 | 0 | writeFeatures.addActionListener(new ActionListener() |
402 | { | |
403 | 0 | @Override |
404 | public void actionPerformed(ActionEvent e) | |
405 | { | |
406 | 0 | sendFeaturesToPymol(); |
407 | } | |
408 | }); | |
409 | 0 | viewerActionMenu.add(writeFeatures); |
410 | } | |
411 | ||
412 | 0 | @Override |
413 | protected void buildActionMenu() | |
414 | { | |
415 | 0 | super.buildActionMenu(); |
416 | 0 | viewerActionMenu.add(writeFeatures); |
417 | } | |
418 | ||
419 | 0 | protected void sendFeaturesToPymol() |
420 | { | |
421 | 0 | int count = binding.sendFeaturesToViewer(getAlignmentPanel()); |
422 | 0 | statusBar.setText(MessageManager.formatMessage("label.attributes_set", |
423 | count, getViewerName())); | |
424 | } | |
425 | ||
426 | } |