Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
AppletJmol | 67 | 210 | 69 | ||
AppletJmol.RenderPanel | 646 | 9 | 3 |
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.appletgui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.CheckboxMenuItem; | |
25 | import java.awt.Color; | |
26 | import java.awt.Dimension; | |
27 | import java.awt.Font; | |
28 | import java.awt.Frame; | |
29 | import java.awt.Graphics; | |
30 | import java.awt.Menu; | |
31 | import java.awt.MenuBar; | |
32 | import java.awt.MenuItem; | |
33 | import java.awt.Panel; | |
34 | import java.awt.TextArea; | |
35 | import java.awt.TextField; | |
36 | import java.awt.event.ActionEvent; | |
37 | import java.awt.event.ActionListener; | |
38 | import java.awt.event.ItemEvent; | |
39 | import java.awt.event.ItemListener; | |
40 | import java.awt.event.KeyEvent; | |
41 | import java.awt.event.KeyListener; | |
42 | import java.awt.event.WindowAdapter; | |
43 | import java.awt.event.WindowEvent; | |
44 | import java.util.ArrayList; | |
45 | import java.util.List; | |
46 | import java.util.Vector; | |
47 | ||
48 | import jalview.bin.JalviewLite; | |
49 | import jalview.datamodel.AlignmentI; | |
50 | import jalview.datamodel.PDBEntry; | |
51 | import jalview.datamodel.SequenceI; | |
52 | import jalview.io.DataSourceType; | |
53 | import jalview.io.FileParse; | |
54 | import jalview.io.StructureFile; | |
55 | import jalview.schemes.BuriedColourScheme; | |
56 | import jalview.schemes.HelixColourScheme; | |
57 | import jalview.schemes.HydrophobicColourScheme; | |
58 | import jalview.schemes.PurinePyrimidineColourScheme; | |
59 | import jalview.schemes.StrandColourScheme; | |
60 | import jalview.schemes.TaylorColourScheme; | |
61 | import jalview.schemes.TurnColourScheme; | |
62 | import jalview.schemes.UserColourScheme; | |
63 | import jalview.schemes.ZappoColourScheme; | |
64 | import jalview.structure.StructureSelectionManager; | |
65 | import jalview.util.MessageManager; | |
66 | ||
67 | public class AppletJmol extends EmbmenuFrame implements | |
68 | // StructureListener, | |
69 | KeyListener, ActionListener, ItemListener | |
70 | ||
71 | { | |
72 | Menu fileMenu = new Menu(MessageManager.getString("action.file")); | |
73 | ||
74 | Menu viewMenu = new Menu(MessageManager.getString("action.view")); | |
75 | ||
76 | Menu coloursMenu = new Menu(MessageManager.getString("action.colour")); | |
77 | ||
78 | Menu chainMenu = new Menu(MessageManager.getString("action.show_chain")); | |
79 | ||
80 | Menu helpMenu = new Menu(MessageManager.getString("action.help")); | |
81 | ||
82 | MenuItem mappingMenuItem = new MenuItem( | |
83 | MessageManager.getString("label.view_mapping")); | |
84 | ||
85 | CheckboxMenuItem seqColour = new CheckboxMenuItem( | |
86 | MessageManager.getString("action.by_sequence"), true); | |
87 | ||
88 | CheckboxMenuItem jmolColour = new CheckboxMenuItem( | |
89 | MessageManager.getString("action.using_jmol"), false); | |
90 | ||
91 | MenuItem chain = new MenuItem( | |
92 | MessageManager.getString("action.by_chain")); | |
93 | ||
94 | MenuItem charge = new MenuItem( | |
95 | MessageManager.getString("label.charge_cysteine")); | |
96 | ||
97 | MenuItem zappo = new MenuItem( | |
98 | MessageManager.getString("label.colourScheme_zappo")); | |
99 | ||
100 | MenuItem taylor = new MenuItem( | |
101 | MessageManager.getString("label.colourScheme_taylor")); | |
102 | ||
103 | MenuItem hydro = new MenuItem( | |
104 | MessageManager.getString("label.colourScheme_hydrophobic")); | |
105 | ||
106 | MenuItem helix = new MenuItem( | |
107 | MessageManager.getString("label.colourScheme_helixpropensity")); | |
108 | ||
109 | MenuItem strand = new MenuItem( | |
110 | MessageManager.getString("label.colourScheme_strandpropensity")); | |
111 | ||
112 | MenuItem turn = new MenuItem( | |
113 | MessageManager.getString("label.colourScheme_turnpropensity")); | |
114 | ||
115 | MenuItem buried = new MenuItem( | |
116 | MessageManager.getString("label.colourScheme_buriedindex")); | |
117 | ||
118 | MenuItem purinepyrimidine = new MenuItem( | |
119 | MessageManager.getString("label.colourScheme_purine/pyrimidine")); | |
120 | ||
121 | MenuItem user = new MenuItem( | |
122 | MessageManager.getString("label.user_defined_colours")); | |
123 | ||
124 | MenuItem jmolHelp = new MenuItem( | |
125 | MessageManager.getString("label.jmol_help")); | |
126 | ||
127 | Panel scriptWindow; | |
128 | ||
129 | TextField inputLine; | |
130 | ||
131 | TextArea history; | |
132 | ||
133 | RenderPanel renderPanel; | |
134 | ||
135 | AlignmentPanel ap; | |
136 | ||
137 | List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never | |
138 | // added to | |
139 | ||
140 | String fileLoadingError; | |
141 | ||
142 | boolean loadedInline; | |
143 | ||
144 | // boolean colourBySequence = true; | |
145 | ||
146 | FeatureRenderer fr = null; | |
147 | ||
148 | AppletJmolBinding jmb; | |
149 | ||
150 | /** | |
151 | * datasource protocol for access to PDBEntry | |
152 | */ | |
153 | String protocol = null; | |
154 | ||
155 | /** | |
156 | * Load a bunch of pdb entries associated with sequences in the alignment and | |
157 | * display them - aligning them if necessary. | |
158 | * | |
159 | * @param pdbentries | |
160 | * each pdb file (at least one needed) | |
161 | * @param boundseqs | |
162 | * each set of sequences for each pdb file (must match number of pdb | |
163 | * files) | |
164 | * @param boundchains | |
165 | * the target pdb chain corresponding with each sequence associated | |
166 | * with each pdb file (may be null at any level) | |
167 | * @param align | |
168 | * true/false | |
169 | * @param ap | |
170 | * associated alignment | |
171 | * @param protocol | |
172 | * how to get pdb data | |
173 | */ | |
174 | 0 | public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, |
175 | String[][] boundchains, boolean align, AlignmentPanel ap, | |
176 | String protocol) | |
177 | { | |
178 | 0 | throw new Error(MessageManager.getString("error.not_yet_implemented")); |
179 | } | |
180 | ||
181 | 0 | public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, |
182 | AlignmentPanel ap, DataSourceType protocol) | |
183 | { | |
184 | 0 | this.ap = ap; |
185 | 0 | jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), |
186 | new PDBEntry[] | |
187 | { pdbentry }, new SequenceI[][] { seq }, protocol); | |
188 | 0 | jmb.setColourBySequence(true); |
189 | 0 | if (pdbentry.getId() == null || pdbentry.getId().length() < 1) |
190 | { | |
191 | 0 | if (protocol == DataSourceType.PASTE) |
192 | { | |
193 | 0 | pdbentry.setId( |
194 | 0 | "PASTED PDB" + (chains == null ? "_" : chains.toString())); |
195 | } | |
196 | else | |
197 | { | |
198 | 0 | pdbentry.setId(pdbentry.getFile()); |
199 | } | |
200 | } | |
201 | ||
202 | 0 | if (JalviewLite.debug) |
203 | { | |
204 | 0 | System.err |
205 | .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'"); | |
206 | } | |
207 | ||
208 | 0 | String alreadyMapped = StructureSelectionManager |
209 | .getStructureSelectionManager(ap.av.applet) | |
210 | .alreadyMappedToFile(pdbentry.getId()); | |
211 | 0 | StructureFile reader = null; |
212 | 0 | if (alreadyMapped != null) |
213 | { | |
214 | 0 | reader = StructureSelectionManager |
215 | .getStructureSelectionManager(ap.av.applet) | |
216 | .setMapping(seq, chains, pdbentry.getFile(), protocol, null); | |
217 | // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW? | |
218 | // FOR NOW, LETS JUST OPEN A NEW WINDOW | |
219 | } | |
220 | 0 | MenuBar menuBar = new MenuBar(); |
221 | 0 | menuBar.add(fileMenu); |
222 | 0 | fileMenu.add(mappingMenuItem); |
223 | 0 | menuBar.add(viewMenu); |
224 | 0 | mappingMenuItem.addActionListener(this); |
225 | 0 | viewMenu.add(chainMenu); |
226 | 0 | menuBar.add(coloursMenu); |
227 | 0 | menuBar.add(helpMenu); |
228 | ||
229 | 0 | charge.addActionListener(this); |
230 | 0 | hydro.addActionListener(this); |
231 | 0 | chain.addActionListener(this); |
232 | 0 | seqColour.addItemListener(this); |
233 | 0 | jmolColour.addItemListener(this); |
234 | 0 | zappo.addActionListener(this); |
235 | 0 | taylor.addActionListener(this); |
236 | 0 | helix.addActionListener(this); |
237 | 0 | strand.addActionListener(this); |
238 | 0 | turn.addActionListener(this); |
239 | 0 | buried.addActionListener(this); |
240 | 0 | purinepyrimidine.addActionListener(this); |
241 | 0 | user.addActionListener(this); |
242 | ||
243 | 0 | jmolHelp.addActionListener(this); |
244 | ||
245 | 0 | coloursMenu.add(seqColour); |
246 | 0 | coloursMenu.add(chain); |
247 | 0 | coloursMenu.add(charge); |
248 | 0 | coloursMenu.add(zappo); |
249 | 0 | coloursMenu.add(taylor); |
250 | 0 | coloursMenu.add(hydro); |
251 | 0 | coloursMenu.add(helix); |
252 | 0 | coloursMenu.add(strand); |
253 | 0 | coloursMenu.add(turn); |
254 | 0 | coloursMenu.add(buried); |
255 | 0 | coloursMenu.add(purinepyrimidine); |
256 | 0 | coloursMenu.add(user); |
257 | 0 | coloursMenu.add(jmolColour); |
258 | 0 | helpMenu.add(jmolHelp); |
259 | 0 | this.setLayout(new BorderLayout()); |
260 | ||
261 | 0 | setMenuBar(menuBar); |
262 | ||
263 | 0 | renderPanel = new RenderPanel(); |
264 | 0 | embedMenuIfNeeded(renderPanel); |
265 | 0 | this.add(renderPanel, BorderLayout.CENTER); |
266 | 0 | scriptWindow = new Panel(); |
267 | 0 | scriptWindow.setVisible(false); |
268 | // this.add(scriptWindow, BorderLayout.SOUTH); | |
269 | ||
270 | 0 | try |
271 | { | |
272 | 0 | jmb.allocateViewer(renderPanel, true, |
273 | ap.av.applet.getName() + "_jmol_", | |
274 | ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(), | |
275 | "-applet", scriptWindow, null); | |
276 | } catch (Exception e) | |
277 | { | |
278 | 0 | jalview.bin.Console.errPrintln( |
279 | "Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase=" | |
280 | + ap.av.applet.getDocumentBase() + "\nCodebase=" | |
281 | + ap.av.applet.getCodeBase()); | |
282 | 0 | e.printStackTrace(); |
283 | 0 | dispose(); |
284 | 0 | return; |
285 | } | |
286 | // jmb.newJmolPopup(true, "Jmol", true); | |
287 | ||
288 | 0 | this.addWindowListener(new WindowAdapter() |
289 | { | |
290 | 0 | @Override |
291 | public void windowClosing(WindowEvent evt) | |
292 | { | |
293 | 0 | closeViewer(); |
294 | } | |
295 | }); | |
296 | 0 | pdbentry.setProperty("protocol", protocol); |
297 | 0 | if (pdbentry.getFile() != null) |
298 | ||
299 | { | |
300 | // import structure data from pdbentry.getFile based on given protocol | |
301 | 0 | if (protocol == DataSourceType.PASTE) |
302 | { | |
303 | // TODO: JAL-623 : correctly record file contents for matching up later | |
304 | // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode()); | |
305 | 0 | loadInline(pdbentry.getFile()); |
306 | } | |
307 | 0 | else if (protocol == DataSourceType.FILE |
308 | || protocol == DataSourceType.URL) | |
309 | { | |
310 | 0 | jmb.jmolViewer.openFile(pdbentry.getFile()); |
311 | } | |
312 | else | |
313 | { | |
314 | // probably CLASSLOADER based datasource.. | |
315 | // Try and get a reader on the datasource, and pass that to Jmol | |
316 | 0 | try |
317 | { | |
318 | 0 | java.io.Reader freader = null; |
319 | 0 | if (reader != null) |
320 | { | |
321 | 0 | if (jalview.bin.JalviewLite.debug) |
322 | { | |
323 | 0 | jalview.bin.Console.errPrintln( |
324 | "AppletJmol:Trying to reuse existing PDBfile IO parser."); | |
325 | } | |
326 | // re-use the one we opened earlier | |
327 | 0 | freader = reader.getReader(); |
328 | } | |
329 | 0 | if (freader == null) |
330 | { | |
331 | 0 | if (jalview.bin.JalviewLite.debug) |
332 | { | |
333 | 0 | jalview.bin.Console.errPrintln( |
334 | "AppletJmol:Creating new PDBfile IO parser."); | |
335 | } | |
336 | 0 | FileParse fp = new FileParse(pdbentry.getFile(), protocol); |
337 | 0 | fp.mark(); |
338 | // reader = new mc_view.PDBfile(fp); | |
339 | // could set ID, etc. | |
340 | // if (!reader.isValid()) | |
341 | // { | |
342 | // throw new Exception("Invalid datasource. | |
343 | // "+reader.getWarningMessage()); | |
344 | // } | |
345 | // fp.reset(); | |
346 | 0 | freader = fp.getReader(); |
347 | } | |
348 | 0 | if (freader == null) |
349 | { | |
350 | 0 | throw new Exception(MessageManager.getString( |
351 | "exception.invalid_datasource_couldnt_obtain_reader")); | |
352 | } | |
353 | 0 | jmb.jmolViewer.openReader(pdbentry.getFile(), pdbentry.getId(), |
354 | freader); | |
355 | } catch (Exception e) | |
356 | { | |
357 | // give up! | |
358 | 0 | jalview.bin.Console.errPrintln("Couldn't access pdbentry id=" |
359 | + pdbentry.getId() + " and file=" + pdbentry.getFile() | |
360 | + " using protocol=" + protocol); | |
361 | 0 | e.printStackTrace(); |
362 | } | |
363 | } | |
364 | } | |
365 | ||
366 | 0 | jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400); |
367 | } | |
368 | ||
369 | 0 | public void loadInline(String string) |
370 | { | |
371 | 0 | loadedInline = true; |
372 | 0 | jmb.loadInline(string); |
373 | } | |
374 | ||
375 | 0 | void setChainMenuItems(List<String> chains) |
376 | { | |
377 | 0 | chainMenu.removeAll(); |
378 | ||
379 | 0 | MenuItem menuItem = new MenuItem(MessageManager.getString("label.all")); |
380 | 0 | menuItem.addActionListener(this); |
381 | ||
382 | 0 | chainMenu.add(menuItem); |
383 | ||
384 | 0 | CheckboxMenuItem menuItemCB; |
385 | 0 | for (String ch : chains) |
386 | { | |
387 | 0 | menuItemCB = new CheckboxMenuItem(ch, true); |
388 | 0 | menuItemCB.addItemListener(this); |
389 | 0 | chainMenu.add(menuItemCB); |
390 | } | |
391 | } | |
392 | ||
393 | boolean allChainsSelected = false; | |
394 | ||
395 | 0 | void centerViewer() |
396 | { | |
397 | 0 | Vector<String> toshow = new Vector<>(); |
398 | 0 | for (int i = 0; i < chainMenu.getItemCount(); i++) |
399 | { | |
400 | 0 | if (chainMenu.getItem(i) instanceof CheckboxMenuItem) |
401 | { | |
402 | 0 | CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i); |
403 | 0 | if (item.getState()) |
404 | { | |
405 | 0 | toshow.addElement(item.getLabel()); |
406 | } | |
407 | } | |
408 | } | |
409 | 0 | jmb.showChains(toshow); |
410 | } | |
411 | ||
412 | 0 | void closeViewer() |
413 | { | |
414 | 0 | jmb.closeViewer(true); |
415 | 0 | jmb = null; |
416 | 0 | this.setVisible(false); |
417 | } | |
418 | ||
419 | 0 | @Override |
420 | public void actionPerformed(ActionEvent evt) | |
421 | { | |
422 | 0 | if (evt.getSource() == mappingMenuItem) |
423 | { | |
424 | 0 | jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer( |
425 | false, null); | |
426 | 0 | Frame frame = new Frame(); |
427 | 0 | frame.add(cap); |
428 | ||
429 | 0 | StringBuffer sb = new StringBuffer(); |
430 | 0 | try |
431 | { | |
432 | 0 | cap.setText(jmb.printMappings()); |
433 | } catch (OutOfMemoryError ex) | |
434 | { | |
435 | 0 | frame.dispose(); |
436 | 0 | jalview.bin.Console.errPrintln( |
437 | "Out of memory when trying to create dialog box with sequence-structure mapping."); | |
438 | 0 | return; |
439 | } | |
440 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
441 | MessageManager.getString("label.pdb_sequence_mapping"), 550, | |
442 | 600); | |
443 | } | |
444 | 0 | else if (evt.getSource() == charge) |
445 | { | |
446 | 0 | setEnabled(charge); |
447 | 0 | jmb.colourByCharge(); |
448 | } | |
449 | ||
450 | 0 | else if (evt.getSource() == chain) |
451 | { | |
452 | 0 | setEnabled(chain); |
453 | 0 | jmb.colourByChain(); |
454 | } | |
455 | 0 | else if (evt.getSource() == zappo) |
456 | { | |
457 | 0 | setEnabled(zappo); |
458 | 0 | jmb.colourByJalviewColourScheme(new ZappoColourScheme()); |
459 | } | |
460 | 0 | else if (evt.getSource() == taylor) |
461 | { | |
462 | 0 | setEnabled(taylor); |
463 | 0 | jmb.colourByJalviewColourScheme(new TaylorColourScheme()); |
464 | } | |
465 | 0 | else if (evt.getSource() == hydro) |
466 | { | |
467 | 0 | setEnabled(hydro); |
468 | 0 | jmb.colourByJalviewColourScheme(new HydrophobicColourScheme()); |
469 | } | |
470 | 0 | else if (evt.getSource() == helix) |
471 | { | |
472 | 0 | setEnabled(helix); |
473 | 0 | jmb.colourByJalviewColourScheme(new HelixColourScheme()); |
474 | } | |
475 | 0 | else if (evt.getSource() == strand) |
476 | { | |
477 | 0 | setEnabled(strand); |
478 | 0 | jmb.colourByJalviewColourScheme(new StrandColourScheme()); |
479 | } | |
480 | 0 | else if (evt.getSource() == turn) |
481 | { | |
482 | 0 | setEnabled(turn); |
483 | 0 | jmb.colourByJalviewColourScheme(new TurnColourScheme()); |
484 | } | |
485 | 0 | else if (evt.getSource() == buried) |
486 | { | |
487 | 0 | setEnabled(buried); |
488 | 0 | jmb.colourByJalviewColourScheme(new BuriedColourScheme()); |
489 | } | |
490 | 0 | else if (evt.getSource() == purinepyrimidine) |
491 | { | |
492 | 0 | jmb.colourByJalviewColourScheme(new PurinePyrimidineColourScheme()); |
493 | } | |
494 | 0 | else if (evt.getSource() == user) |
495 | { | |
496 | 0 | setEnabled(user); |
497 | 0 | new UserDefinedColours(this); |
498 | } | |
499 | 0 | else if (evt.getSource() == jmolHelp) |
500 | { | |
501 | 0 | try |
502 | { | |
503 | 0 | ap.av.applet.getAppletContext() |
504 | .showDocument(new java.net.URL( | |
505 | "http://jmol.sourceforge.net/docs/JmolUserGuide/"), | |
506 | "jmolHelp"); | |
507 | } catch (java.net.MalformedURLException ex) | |
508 | { | |
509 | } | |
510 | } | |
511 | else | |
512 | { | |
513 | 0 | allChainsSelected = true; |
514 | 0 | for (int i = 0; i < chainMenu.getItemCount(); i++) |
515 | { | |
516 | 0 | if (chainMenu.getItem(i) instanceof CheckboxMenuItem) |
517 | { | |
518 | 0 | ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true); |
519 | } | |
520 | } | |
521 | ||
522 | 0 | centerViewer(); |
523 | 0 | allChainsSelected = false; |
524 | } | |
525 | } | |
526 | ||
527 | /** | |
528 | * tick or untick the seqColour menu entry or jmoColour entry depending upon | |
529 | * if it was selected or not. | |
530 | * | |
531 | * @param itm | |
532 | */ | |
533 | 0 | private void setEnabled(MenuItem itm) |
534 | { | |
535 | 0 | jmolColour.setState(itm == jmolColour); |
536 | 0 | seqColour.setState(itm == seqColour); |
537 | 0 | jmb.setColourBySequence(itm == seqColour); |
538 | } | |
539 | ||
540 | 0 | @Override |
541 | public void itemStateChanged(ItemEvent evt) | |
542 | { | |
543 | 0 | if (evt.getSource() == jmolColour) |
544 | { | |
545 | 0 | setEnabled(jmolColour); |
546 | 0 | jmb.setColourBySequence(false); |
547 | } | |
548 | 0 | else if (evt.getSource() == seqColour) |
549 | { | |
550 | 0 | setEnabled(seqColour); |
551 | 0 | jmb.colourBySequence(ap); |
552 | } | |
553 | 0 | else if (!allChainsSelected) |
554 | { | |
555 | 0 | centerViewer(); |
556 | } | |
557 | } | |
558 | ||
559 | 0 | @Override |
560 | public void keyPressed(KeyEvent evt) | |
561 | { | |
562 | 0 | if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible()) |
563 | { | |
564 | 0 | jmb.eval(inputLine.getText()); |
565 | 0 | addToHistory("$ " + inputLine.getText()); |
566 | 0 | inputLine.setText(""); |
567 | } | |
568 | ||
569 | } | |
570 | ||
571 | 0 | @Override |
572 | public void keyTyped(KeyEvent evt) | |
573 | { | |
574 | } | |
575 | ||
576 | 0 | @Override |
577 | public void keyReleased(KeyEvent evt) | |
578 | { | |
579 | } | |
580 | ||
581 | 0 | public void updateColours(Object source) |
582 | { | |
583 | 0 | AlignmentPanel panel = (AlignmentPanel) source; |
584 | 0 | jmb.colourBySequence(panel); |
585 | } | |
586 | ||
587 | 0 | public void updateTitleAndMenus() |
588 | { | |
589 | 0 | if (jmb.hasFileLoadingError()) |
590 | { | |
591 | 0 | repaint(); |
592 | 0 | return; |
593 | } | |
594 | 0 | setChainMenuItems(jmb.getChainNames()); |
595 | 0 | jmb.colourBySequence(ap); |
596 | ||
597 | 0 | setTitle(jmb.getViewerTitle()); |
598 | } | |
599 | ||
600 | 0 | public void showUrl(String url) |
601 | { | |
602 | 0 | try |
603 | { | |
604 | 0 | ap.av.applet.getAppletContext().showDocument(new java.net.URL(url), |
605 | "jmolOutput"); | |
606 | } catch (java.net.MalformedURLException ex) | |
607 | { | |
608 | } | |
609 | } | |
610 | ||
611 | Panel splitPane = null; | |
612 | ||
613 | 0 | public void showConsole(boolean showConsole) |
614 | { | |
615 | 0 | if (showConsole) |
616 | { | |
617 | 0 | remove(renderPanel); |
618 | 0 | splitPane = new Panel(); |
619 | ||
620 | 0 | splitPane.setLayout(new java.awt.GridLayout(2, 1)); |
621 | 0 | splitPane.add(renderPanel); |
622 | 0 | splitPane.add(scriptWindow); |
623 | 0 | scriptWindow.setVisible(true); |
624 | 0 | this.add(splitPane, BorderLayout.CENTER); |
625 | 0 | splitPane.setVisible(true); |
626 | 0 | splitPane.validate(); |
627 | } | |
628 | else | |
629 | { | |
630 | 0 | scriptWindow.setVisible(false); |
631 | 0 | remove(splitPane); |
632 | 0 | add(renderPanel, BorderLayout.CENTER); |
633 | 0 | splitPane = null; |
634 | } | |
635 | 0 | validate(); |
636 | } | |
637 | ||
638 | 0 | public float[][] functionXY(String functionName, int x, int y) |
639 | { | |
640 | 0 | return null; |
641 | } | |
642 | ||
643 | // /End JmolStatusListener | |
644 | // ///////////////////////////// | |
645 | ||
646 | class RenderPanel extends Panel | |
647 | { | |
648 | Dimension currentSize = new Dimension(); | |
649 | ||
650 | 0 | @Override |
651 | public void update(Graphics g) | |
652 | { | |
653 | 0 | paint(g); |
654 | } | |
655 | ||
656 | 0 | @Override |
657 | public void paint(Graphics g) | |
658 | { | |
659 | 0 | currentSize = this.getSize(); |
660 | ||
661 | 0 | if (jmb.jmolViewer == null) |
662 | { | |
663 | 0 | g.setColor(Color.black); |
664 | 0 | g.fillRect(0, 0, currentSize.width, currentSize.height); |
665 | 0 | g.setColor(Color.white); |
666 | 0 | g.setFont(new Font("Verdana", Font.BOLD, 14)); |
667 | 0 | g.drawString(MessageManager.getString("label.retrieving_pdb_data"), |
668 | 20, currentSize.height / 2); | |
669 | } | |
670 | else | |
671 | { | |
672 | 0 | jmb.jmolViewer.renderScreenImage(g, currentSize.width, |
673 | currentSize.height); | |
674 | } | |
675 | } | |
676 | } | |
677 | ||
678 | /* | |
679 | * @Override public Color getColour(int atomIndex, int pdbResNum, String | |
680 | * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain, | |
681 | * pdbId); } | |
682 | * | |
683 | * @Override public String[] getPdbFile() { return jmb.getPdbFile(); } | |
684 | * | |
685 | * @Override public void highlightAtom(int atomIndex, int pdbResNum, String | |
686 | * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain, | |
687 | * pdbId); | |
688 | * | |
689 | * } | |
690 | * | |
691 | * @Override public void mouseOverStructure(int atomIndex, String strInfo) { | |
692 | * jmb.mouseOverStructure(atomIndex, strInfo); | |
693 | * | |
694 | * } | |
695 | */ | |
696 | 0 | public void colourByJalviewColourScheme(UserColourScheme ucs) |
697 | { | |
698 | 0 | jmb.colourByJalviewColourScheme(ucs); |
699 | } | |
700 | ||
701 | 0 | public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) |
702 | { | |
703 | 0 | for (int i = 0; i < _aps.size(); i++) |
704 | { | |
705 | 0 | if (_aps.get(i).av.getAlignment() == alignment) |
706 | { | |
707 | 0 | return (_aps.get(i)); |
708 | } | |
709 | } | |
710 | 0 | return ap; |
711 | } | |
712 | ||
713 | /** | |
714 | * Append the given text to the history object | |
715 | * | |
716 | * @param text | |
717 | */ | |
718 | 0 | public void addToHistory(String text) |
719 | { | |
720 | // actually currently never initialised | |
721 | 0 | if (history != null) |
722 | { | |
723 | 0 | history.append("\n" + text); |
724 | } | |
725 | } | |
726 | } |