Class |
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Actions |
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---|---|---|---|---|---|
Desktop | 168 | 1,126 | 470 | ||
Desktop.MyDesktopManager | 300 | 25 | 19 | ||
Desktop.MyDesktopPane | 2670 | 27 | 13 |
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.BorderLayout; | |
24 | import java.awt.Color; | |
25 | import java.awt.Component; | |
26 | import java.awt.Container; | |
27 | import java.awt.Dimension; | |
28 | import java.awt.FontMetrics; | |
29 | import java.awt.Graphics; | |
30 | import java.awt.Graphics2D; | |
31 | import java.awt.GridLayout; | |
32 | import java.awt.Point; | |
33 | import java.awt.Rectangle; | |
34 | import java.awt.Toolkit; | |
35 | import java.awt.Window; | |
36 | import java.awt.datatransfer.Clipboard; | |
37 | import java.awt.datatransfer.ClipboardOwner; | |
38 | import java.awt.datatransfer.DataFlavor; | |
39 | import java.awt.datatransfer.Transferable; | |
40 | import java.awt.dnd.DnDConstants; | |
41 | import java.awt.dnd.DropTargetDragEvent; | |
42 | import java.awt.dnd.DropTargetDropEvent; | |
43 | import java.awt.dnd.DropTargetEvent; | |
44 | import java.awt.dnd.DropTargetListener; | |
45 | import java.awt.event.ActionEvent; | |
46 | import java.awt.event.ActionListener; | |
47 | import java.awt.event.InputEvent; | |
48 | import java.awt.event.KeyEvent; | |
49 | import java.awt.event.MouseAdapter; | |
50 | import java.awt.event.MouseEvent; | |
51 | import java.awt.event.WindowAdapter; | |
52 | import java.awt.event.WindowEvent; | |
53 | import java.awt.geom.AffineTransform; | |
54 | import java.beans.PropertyChangeEvent; | |
55 | import java.beans.PropertyChangeListener; | |
56 | import java.beans.PropertyVetoException; | |
57 | import java.io.File; | |
58 | import java.io.FileNotFoundException; | |
59 | import java.io.FileWriter; | |
60 | import java.io.IOException; | |
61 | import java.lang.reflect.Field; | |
62 | import java.net.URL; | |
63 | import java.util.ArrayList; | |
64 | import java.util.Arrays; | |
65 | import java.util.HashMap; | |
66 | import java.util.Hashtable; | |
67 | import java.util.List; | |
68 | import java.util.ListIterator; | |
69 | import java.util.Locale; | |
70 | import java.util.Map; | |
71 | import java.util.Vector; | |
72 | import java.util.concurrent.ExecutorService; | |
73 | import java.util.concurrent.Executors; | |
74 | import java.util.concurrent.Semaphore; | |
75 | ||
76 | import javax.swing.AbstractAction; | |
77 | import javax.swing.Action; | |
78 | import javax.swing.ActionMap; | |
79 | import javax.swing.Box; | |
80 | import javax.swing.BoxLayout; | |
81 | import javax.swing.DefaultDesktopManager; | |
82 | import javax.swing.DesktopManager; | |
83 | import javax.swing.InputMap; | |
84 | import javax.swing.JButton; | |
85 | import javax.swing.JCheckBox; | |
86 | import javax.swing.JComboBox; | |
87 | import javax.swing.JComponent; | |
88 | import javax.swing.JDesktopPane; | |
89 | import javax.swing.JFrame; | |
90 | import javax.swing.JInternalFrame; | |
91 | import javax.swing.JLabel; | |
92 | import javax.swing.JMenuItem; | |
93 | import javax.swing.JOptionPane; | |
94 | import javax.swing.JPanel; | |
95 | import javax.swing.JPopupMenu; | |
96 | import javax.swing.JProgressBar; | |
97 | import javax.swing.JScrollPane; | |
98 | import javax.swing.JTextArea; | |
99 | import javax.swing.JTextField; | |
100 | import javax.swing.JTextPane; | |
101 | import javax.swing.KeyStroke; | |
102 | import javax.swing.SwingUtilities; | |
103 | import javax.swing.WindowConstants; | |
104 | import javax.swing.event.HyperlinkEvent; | |
105 | import javax.swing.event.HyperlinkEvent.EventType; | |
106 | import javax.swing.event.InternalFrameAdapter; | |
107 | import javax.swing.event.InternalFrameEvent; | |
108 | import javax.swing.text.JTextComponent; | |
109 | ||
110 | import org.stackoverflowusers.file.WindowsShortcut; | |
111 | ||
112 | import jalview.api.AlignViewportI; | |
113 | import jalview.api.AlignmentViewPanel; | |
114 | import jalview.api.structures.JalviewStructureDisplayI; | |
115 | import jalview.bin.Cache; | |
116 | import jalview.bin.Jalview; | |
117 | import jalview.bin.Jalview.ExitCode; | |
118 | import jalview.bin.argparser.Arg; | |
119 | import jalview.bin.groovy.JalviewObject; | |
120 | import jalview.bin.groovy.JalviewObjectI; | |
121 | import jalview.datamodel.Alignment; | |
122 | import jalview.datamodel.HiddenColumns; | |
123 | import jalview.datamodel.Sequence; | |
124 | import jalview.datamodel.SequenceI; | |
125 | import jalview.gui.ImageExporter.ImageWriterI; | |
126 | import jalview.gui.QuitHandler.QResponse; | |
127 | import jalview.io.AppletFormatAdapter; | |
128 | import jalview.io.BackupFiles; | |
129 | import jalview.io.DataSourceType; | |
130 | import jalview.io.FileFormat; | |
131 | import jalview.io.FileFormatException; | |
132 | import jalview.io.FileFormatI; | |
133 | import jalview.io.FileFormats; | |
134 | import jalview.io.FileLoader; | |
135 | import jalview.io.FormatAdapter; | |
136 | import jalview.io.IdentifyFile; | |
137 | import jalview.io.JalviewFileChooser; | |
138 | import jalview.io.JalviewFileView; | |
139 | import jalview.io.NewickFile; | |
140 | import jalview.io.exceptions.ImageOutputException; | |
141 | import jalview.jbgui.GSplitFrame; | |
142 | import jalview.jbgui.GStructureViewer; | |
143 | import jalview.project.Jalview2XML; | |
144 | import jalview.structure.StructureSelectionManager; | |
145 | import jalview.urls.IdOrgSettings; | |
146 | import jalview.util.ArgParserUtils; | |
147 | import jalview.util.ArgParserUtils.BaseInfo; | |
148 | import jalview.util.BrowserLauncher; | |
149 | import jalview.util.ChannelProperties; | |
150 | import jalview.util.FileUtils; | |
151 | import jalview.util.ImageMaker.TYPE; | |
152 | import jalview.util.LaunchUtils; | |
153 | import jalview.util.MessageManager; | |
154 | import jalview.util.Platform; | |
155 | import jalview.util.ShortcutKeyMaskExWrapper; | |
156 | import jalview.util.UrlConstants; | |
157 | import jalview.viewmodel.AlignmentViewport; | |
158 | import jalview.ws.params.ParamManager; | |
159 | import jalview.ws.utils.UrlDownloadClient; | |
160 | ||
161 | /** | |
162 | * Jalview Desktop | |
163 | * | |
164 | * | |
165 | * @author $author$ | |
166 | * @version $Revision: 1.155 $ | |
167 | */ | |
168 | public class Desktop extends jalview.jbgui.GDesktop | |
169 | implements DropTargetListener, ClipboardOwner, IProgressIndicator, | |
170 | jalview.api.StructureSelectionManagerProvider, JalviewObjectI | |
171 | { | |
172 | private static final String CITATION; | |
173 | 54 | static |
174 | { | |
175 | 54 | URL bg_logo_url = ChannelProperties.getImageURL( |
176 | "bg_logo." + String.valueOf(SplashScreen.logoSize)); | |
177 | 54 | URL uod_logo_url = ChannelProperties.getImageURL( |
178 | "uod_banner." + String.valueOf(SplashScreen.logoSize)); | |
179 | 54 | boolean logo = (bg_logo_url != null || uod_logo_url != null); |
180 | 54 | StringBuilder sb = new StringBuilder(); |
181 | 54 | sb.append( |
182 | "<br><br>Jalview is free software released under GPLv3.<br><br>Development is managed by The Barton Group, University of Dundee, Scotland, UK."); | |
183 | 54 | if (logo) |
184 | { | |
185 | 54 | sb.append("<br>"); |
186 | } | |
187 | 54 | sb.append(bg_logo_url == null ? "" |
188 | : "<img alt=\"Barton Group logo\" src=\"" | |
189 | + bg_logo_url.toString() + "\">"); | |
190 | 54 | sb.append(uod_logo_url == null ? "" |
191 | : " <img alt=\"University of Dundee shield\" src=\"" | |
192 | + uod_logo_url.toString() + "\">"); | |
193 | 54 | sb.append( |
194 | "<br><br>For help, see <a href=\"https://www.jalview.org/help/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>"); | |
195 | 54 | sb.append("<br><br>If you use Jalview, please cite:" |
196 | + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" | |
197 | + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" | |
198 | + "<br>Bioinformatics <a href=\"https://doi.org/10.1093/bioinformatics/btp033\">doi: 10.1093/bioinformatics/btp033</a>"); | |
199 | 54 | CITATION = sb.toString(); |
200 | } | |
201 | ||
202 | private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)"; | |
203 | ||
204 | private static int DEFAULT_MIN_WIDTH = 300; | |
205 | ||
206 | private static int DEFAULT_MIN_HEIGHT = 250; | |
207 | ||
208 | private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; | |
209 | ||
210 | private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; | |
211 | ||
212 | private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; | |
213 | ||
214 | public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; | |
215 | ||
216 | public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>(); | |
217 | ||
218 | private static int DRAG_MODE = JDesktopPane.OUTLINE_DRAG_MODE; | |
219 | ||
220 | 150 | public static void setLiveDragMode(boolean b) |
221 | { | |
222 | 150 | DRAG_MODE = b ? JDesktopPane.LIVE_DRAG_MODE |
223 | : JDesktopPane.OUTLINE_DRAG_MODE; | |
224 | 150 | if (desktop != null) |
225 | 130 | desktop.setDragMode(DRAG_MODE); |
226 | } | |
227 | ||
228 | private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); | |
229 | ||
230 | public static boolean nosplash = false; | |
231 | ||
232 | /** | |
233 | * news reader - null if it was never started. | |
234 | */ | |
235 | private BlogReader jvnews = null; | |
236 | ||
237 | private File projectFile; | |
238 | ||
239 | /** | |
240 | * @param listener | |
241 | * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) | |
242 | */ | |
243 | 0 | public void addJalviewPropertyChangeListener( |
244 | PropertyChangeListener listener) | |
245 | { | |
246 | 0 | changeSupport.addJalviewPropertyChangeListener(listener); |
247 | } | |
248 | ||
249 | /** | |
250 | * @param propertyName | |
251 | * @param listener | |
252 | * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, | |
253 | * java.beans.PropertyChangeListener) | |
254 | */ | |
255 | 397 | public void addJalviewPropertyChangeListener(String propertyName, |
256 | PropertyChangeListener listener) | |
257 | { | |
258 | 397 | changeSupport.addJalviewPropertyChangeListener(propertyName, listener); |
259 | } | |
260 | ||
261 | /** | |
262 | * @param propertyName | |
263 | * @param listener | |
264 | * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, | |
265 | * java.beans.PropertyChangeListener) | |
266 | */ | |
267 | 260 | public void removeJalviewPropertyChangeListener(String propertyName, |
268 | PropertyChangeListener listener) | |
269 | { | |
270 | 260 | changeSupport.removeJalviewPropertyChangeListener(propertyName, |
271 | listener); | |
272 | } | |
273 | ||
274 | /** Singleton Desktop instance */ | |
275 | public static Desktop instance; | |
276 | ||
277 | public static MyDesktopPane desktop; | |
278 | ||
279 | 2520 | public static MyDesktopPane getDesktop() |
280 | { | |
281 | // BH 2018 could use currentThread() here as a reference to a | |
282 | // Hashtable<Thread, MyDesktopPane> in JavaScript | |
283 | 2520 | return desktop; |
284 | } | |
285 | ||
286 | static int openFrameCount = 0; | |
287 | ||
288 | static final int xOffset = 30; | |
289 | ||
290 | static final int yOffset = 30; | |
291 | ||
292 | public static jalview.ws.jws1.Discoverer discoverer; | |
293 | ||
294 | public static Object[] jalviewClipboard; | |
295 | ||
296 | public static boolean internalCopy = false; | |
297 | ||
298 | static int fileLoadingCount = 0; | |
299 | ||
300 | class MyDesktopManager implements DesktopManager | |
301 | { | |
302 | ||
303 | private DesktopManager delegate; | |
304 | ||
305 | 75 | public MyDesktopManager(DesktopManager delegate) |
306 | { | |
307 | 75 | this.delegate = delegate; |
308 | } | |
309 | ||
310 | 739 | @Override |
311 | public void activateFrame(JInternalFrame f) | |
312 | { | |
313 | 739 | try |
314 | { | |
315 | 739 | delegate.activateFrame(f); |
316 | } catch (NullPointerException npe) | |
317 | { | |
318 | 0 | Point p = getMousePosition(); |
319 | 0 | instance.showPasteMenu(p.x, p.y); |
320 | } | |
321 | } | |
322 | ||
323 | 0 | @Override |
324 | public void beginDraggingFrame(JComponent f) | |
325 | { | |
326 | 0 | delegate.beginDraggingFrame(f); |
327 | } | |
328 | ||
329 | 0 | @Override |
330 | public void beginResizingFrame(JComponent f, int direction) | |
331 | { | |
332 | 0 | delegate.beginResizingFrame(f, direction); |
333 | } | |
334 | ||
335 | 431 | @Override |
336 | public void closeFrame(JInternalFrame f) | |
337 | { | |
338 | 431 | delegate.closeFrame(f); |
339 | } | |
340 | ||
341 | 718 | @Override |
342 | public void deactivateFrame(JInternalFrame f) | |
343 | { | |
344 | 718 | delegate.deactivateFrame(f); |
345 | } | |
346 | ||
347 | 0 | @Override |
348 | public void deiconifyFrame(JInternalFrame f) | |
349 | { | |
350 | 0 | delegate.deiconifyFrame(f); |
351 | } | |
352 | ||
353 | 0 | @Override |
354 | public void dragFrame(JComponent f, int newX, int newY) | |
355 | { | |
356 | 0 | if (newY < 0) |
357 | { | |
358 | 0 | newY = 0; |
359 | } | |
360 | 0 | delegate.dragFrame(f, newX, newY); |
361 | } | |
362 | ||
363 | 0 | @Override |
364 | public void endDraggingFrame(JComponent f) | |
365 | { | |
366 | 0 | delegate.endDraggingFrame(f); |
367 | 0 | desktop.repaint(); |
368 | } | |
369 | ||
370 | 0 | @Override |
371 | public void endResizingFrame(JComponent f) | |
372 | { | |
373 | 0 | delegate.endResizingFrame(f); |
374 | 0 | desktop.repaint(); |
375 | } | |
376 | ||
377 | 0 | @Override |
378 | public void iconifyFrame(JInternalFrame f) | |
379 | { | |
380 | 0 | delegate.iconifyFrame(f); |
381 | } | |
382 | ||
383 | 0 | @Override |
384 | public void maximizeFrame(JInternalFrame f) | |
385 | { | |
386 | 0 | delegate.maximizeFrame(f); |
387 | } | |
388 | ||
389 | 0 | @Override |
390 | public void minimizeFrame(JInternalFrame f) | |
391 | { | |
392 | 0 | delegate.minimizeFrame(f); |
393 | } | |
394 | ||
395 | 0 | @Override |
396 | public void openFrame(JInternalFrame f) | |
397 | { | |
398 | 0 | delegate.openFrame(f); |
399 | } | |
400 | ||
401 | 0 | @Override |
402 | public void resizeFrame(JComponent f, int newX, int newY, int newWidth, | |
403 | int newHeight) | |
404 | { | |
405 | 0 | if (newY < 0) |
406 | { | |
407 | 0 | newY = 0; |
408 | } | |
409 | 0 | delegate.resizeFrame(f, newX, newY, newWidth, newHeight); |
410 | } | |
411 | ||
412 | 0 | @Override |
413 | public void setBoundsForFrame(JComponent f, int newX, int newY, | |
414 | int newWidth, int newHeight) | |
415 | { | |
416 | 0 | delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight); |
417 | } | |
418 | ||
419 | // All other methods, simply delegate | |
420 | ||
421 | } | |
422 | ||
423 | /** | |
424 | * Creates a new Desktop object. | |
425 | */ | |
426 | 75 | public Desktop() |
427 | { | |
428 | 75 | super(); |
429 | /** | |
430 | * A note to implementors. It is ESSENTIAL that any activities that might | |
431 | * block are spawned off as threads rather than waited for during this | |
432 | * constructor. | |
433 | */ | |
434 | 75 | instance = this; |
435 | ||
436 | 75 | doConfigureStructurePrefs(); |
437 | 75 | setTitle(ChannelProperties.getProperty("app_name") + " " |
438 | + Cache.getProperty("VERSION")); | |
439 | ||
440 | /** | |
441 | * Set taskbar "grouped windows" name for linux desktops (works in GNOME and | |
442 | * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not | |
443 | * officially documented or guaranteed to exist, so we access it via | |
444 | * reflection. There appear to be unfathomable criteria about what this | |
445 | * string can contain, and it if doesn't meet those criteria then "java" | |
446 | * (KDE) or "jalview-bin-Jalview" (GNOME) is used. "Jalview", "Jalview | |
447 | * Develop" and "Jalview Test" seem okay, but "Jalview non-release" does | |
448 | * not. The reflection access may generate a warning: WARNING: An illegal | |
449 | * reflective access operation has occurred WARNING: Illegal reflective | |
450 | * access by jalview.gui.Desktop () to field | |
451 | * sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided. | |
452 | */ | |
453 | 75 | if (Platform.isLinux()) |
454 | { | |
455 | 75 | if (LaunchUtils.getJavaVersion() >= 11) |
456 | { | |
457 | /* | |
458 | * Send this message to stderr as the warning that follows (due to | |
459 | * reflection) also goes to stderr. | |
460 | */ | |
461 | 75 | jalview.bin.Console.errPrintln( |
462 | "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that."); | |
463 | } | |
464 | 75 | final String awtAppClassName = "awtAppClassName"; |
465 | 75 | try |
466 | { | |
467 | 75 | Toolkit xToolkit = Toolkit.getDefaultToolkit(); |
468 | 75 | Field[] declaredFields = xToolkit.getClass().getDeclaredFields(); |
469 | 75 | Field awtAppClassNameField = null; |
470 | ||
471 | 75 | if (Arrays.stream(declaredFields) |
472 | .anyMatch(f -> f.getName().equals(awtAppClassName))) | |
473 | { | |
474 | 75 | awtAppClassNameField = xToolkit.getClass() |
475 | .getDeclaredField(awtAppClassName); | |
476 | } | |
477 | ||
478 | 75 | String title = ChannelProperties.getProperty("app_name"); |
479 | 75 | if (awtAppClassNameField != null) |
480 | { | |
481 | 75 | awtAppClassNameField.setAccessible(true); |
482 | 75 | awtAppClassNameField.set(xToolkit, title); |
483 | } | |
484 | else | |
485 | { | |
486 | 0 | jalview.bin.Console |
487 | .debug("XToolkit: " + awtAppClassName + " not found"); | |
488 | } | |
489 | } catch (Exception e) | |
490 | { | |
491 | 0 | jalview.bin.Console.debug("Error setting " + awtAppClassName); |
492 | 0 | jalview.bin.Console.trace(Cache.getStackTraceString(e)); |
493 | } | |
494 | } | |
495 | ||
496 | 75 | setIconImages(ChannelProperties.getIconList()); |
497 | ||
498 | // override quit handling when GUI OS close [X] button pressed | |
499 | 75 | this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); |
500 | 75 | addWindowListener(new WindowAdapter() |
501 | { | |
502 | 0 | @Override |
503 | public void windowClosing(WindowEvent ev) | |
504 | { | |
505 | 0 | QuitHandler.QResponse ret = desktopQuit(true, true); // ui, disposeFlag |
506 | } | |
507 | }); | |
508 | ||
509 | 75 | boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false); |
510 | ||
511 | 75 | boolean showjconsole = Cache.getArgCacheDefault(Arg.JAVACONSOLE, |
512 | "SHOW_JAVA_CONSOLE", false); | |
513 | ||
514 | // start dialogue queue for single dialogues | |
515 | 75 | startDialogQueue(); |
516 | ||
517 | 75 | if (!Platform.isJS()) |
518 | /** | |
519 | * Java only | |
520 | * | |
521 | * @j2sIgnore | |
522 | */ | |
523 | { | |
524 | 75 | Desktop.instance.acquireDialogQueue(); |
525 | ||
526 | 75 | jconsole = new Console(this); |
527 | 75 | jconsole.setHeader(Cache.getVersionDetailsForConsole()); |
528 | 75 | showConsole(showjconsole); |
529 | ||
530 | 75 | Desktop.instance.releaseDialogQueue(); |
531 | } | |
532 | ||
533 | 75 | desktop = new MyDesktopPane(selmemusage); |
534 | ||
535 | 75 | showMemusage.setSelected(selmemusage); |
536 | 75 | desktop.setBackground(Color.white); |
537 | ||
538 | 75 | getContentPane().setLayout(new BorderLayout()); |
539 | // alternate config - have scrollbars - see notes in JAL-153 | |
540 | // JScrollPane sp = new JScrollPane(); | |
541 | // sp.getViewport().setView(desktop); | |
542 | // getContentPane().add(sp, BorderLayout.CENTER); | |
543 | ||
544 | // BH 2018 - just an experiment to try unclipped JInternalFrames. | |
545 | 75 | if (Platform.isJS()) |
546 | { | |
547 | 0 | getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); |
548 | } | |
549 | ||
550 | 75 | getContentPane().add(desktop, BorderLayout.CENTER); |
551 | 75 | desktop.setDragMode(DRAG_MODE); |
552 | ||
553 | // This line prevents Windows Look&Feel resizing all new windows to maximum | |
554 | // if previous window was maximised | |
555 | 75 | desktop.setDesktopManager(new MyDesktopManager( |
556 | 75 | Platform.isJS() ? desktop.getDesktopManager() |
557 | : new DefaultDesktopManager())); | |
558 | /* | |
559 | (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() | |
560 | : Platform.isAMacAndNotJS() | |
561 | ? new AquaInternalFrameManager( | |
562 | desktop.getDesktopManager()) | |
563 | : desktop.getDesktopManager()))); | |
564 | */ | |
565 | ||
566 | 75 | Rectangle dims = getLastKnownDimensions(""); |
567 | 75 | if (dims != null) |
568 | { | |
569 | 59 | setBounds(dims); |
570 | } | |
571 | else | |
572 | { | |
573 | 16 | Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); |
574 | 16 | int xPos = Math.max(5, (screenSize.width - 900) / 2); |
575 | 16 | int yPos = Math.max(5, (screenSize.height - 650) / 2); |
576 | 16 | setBounds(xPos, yPos, 900, 650); |
577 | } | |
578 | ||
579 | 75 | if (!Platform.isJS()) |
580 | /** | |
581 | * Java only | |
582 | * | |
583 | * @j2sIgnore | |
584 | */ | |
585 | { | |
586 | 75 | showNews.setVisible(false); |
587 | ||
588 | 75 | experimentalFeatures.setSelected(showExperimental()); |
589 | ||
590 | 75 | getIdentifiersOrgData(); |
591 | ||
592 | 75 | checkURLLinks(); |
593 | ||
594 | // Spawn a thread that shows the splashscreen | |
595 | 75 | if (!nosplash) |
596 | { | |
597 | 50 | SwingUtilities.invokeLater(new Runnable() |
598 | { | |
599 | 50 | @Override |
600 | public void run() | |
601 | { | |
602 | 50 | new SplashScreen(true); |
603 | } | |
604 | }); | |
605 | } | |
606 | ||
607 | // Thread off a new instance of the file chooser - this reduces the time | |
608 | // it takes to open it later on. | |
609 | 75 | new Thread(new Runnable() |
610 | { | |
611 | 75 | @Override |
612 | public void run() | |
613 | { | |
614 | 75 | jalview.bin.Console.debug("Filechooser init thread started."); |
615 | // default file format now determined by JalviewFileChooser | |
616 | 75 | JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), |
617 | null); | |
618 | 75 | jalview.bin.Console.debug("Filechooser init thread finished."); |
619 | } | |
620 | }).start(); | |
621 | // Add the service change listener | |
622 | 75 | changeSupport.addJalviewPropertyChangeListener("services", |
623 | new PropertyChangeListener() | |
624 | { | |
625 | ||
626 | 2043 | @Override |
627 | public void propertyChange(PropertyChangeEvent evt) | |
628 | { | |
629 | 2043 | jalview.bin.Console |
630 | .debug("Firing service changed event for " | |
631 | + evt.getNewValue()); | |
632 | 2043 | JalviewServicesChanged(evt); |
633 | } | |
634 | }); | |
635 | } | |
636 | ||
637 | 75 | this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); |
638 | ||
639 | 75 | MouseAdapter ma; |
640 | 75 | this.addMouseListener(ma = new MouseAdapter() |
641 | { | |
642 | 0 | @Override |
643 | public void mousePressed(MouseEvent evt) | |
644 | { | |
645 | 0 | if (evt.isPopupTrigger()) // Mac |
646 | { | |
647 | 0 | showPasteMenu(evt.getX(), evt.getY()); |
648 | } | |
649 | } | |
650 | ||
651 | 0 | @Override |
652 | public void mouseReleased(MouseEvent evt) | |
653 | { | |
654 | 0 | if (evt.isPopupTrigger()) // Windows |
655 | { | |
656 | 0 | showPasteMenu(evt.getX(), evt.getY()); |
657 | } | |
658 | } | |
659 | }); | |
660 | 75 | desktop.addMouseListener(ma); |
661 | ||
662 | // This is important for jalviewjsTest task and also early Getdown | |
663 | // splashscreen removal | |
664 | 75 | jalview.bin.Console.info((Platform.isJS() ? "JALVIEWJS" : "JALVIEW") |
665 | + ": CREATED DESKTOP"); | |
666 | ||
667 | } | |
668 | ||
669 | /** | |
670 | * Answers true if user preferences to enable experimental features is True | |
671 | * (on), else false | |
672 | * | |
673 | * @return | |
674 | */ | |
675 | 75 | public boolean showExperimental() |
676 | { | |
677 | 75 | String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, |
678 | Boolean.FALSE.toString()); | |
679 | 75 | return Boolean.valueOf(experimental).booleanValue(); |
680 | } | |
681 | ||
682 | 75 | public void doConfigureStructurePrefs() |
683 | { | |
684 | // configure services | |
685 | 75 | StructureSelectionManager ssm = StructureSelectionManager |
686 | .getStructureSelectionManager(this); | |
687 | 75 | StructureSelectionManager.doConfigureStructurePrefs(ssm); |
688 | } | |
689 | ||
690 | 42 | public void checkForNews() |
691 | { | |
692 | 42 | final Desktop me = this; |
693 | // Thread off the news reader, in case there are connection problems. | |
694 | 42 | new Thread(new Runnable() |
695 | { | |
696 | 42 | @Override |
697 | public void run() | |
698 | { | |
699 | 42 | jalview.bin.Console.debug("Starting news thread."); |
700 | 42 | jvnews = new BlogReader(me); |
701 | 42 | showNews.setVisible(true); |
702 | 42 | jalview.bin.Console.debug("Completed news thread."); |
703 | } | |
704 | }).start(); | |
705 | } | |
706 | ||
707 | 75 | public void getIdentifiersOrgData() |
708 | { | |
709 | 75 | if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) |
710 | {// Thread off the identifiers fetcher | |
711 | 75 | new Thread(new Runnable() |
712 | { | |
713 | 75 | @Override |
714 | public void run() | |
715 | { | |
716 | 75 | jalview.bin.Console |
717 | .debug("Downloading data from identifiers.org"); | |
718 | 75 | try |
719 | { | |
720 | 75 | UrlDownloadClient.download(IdOrgSettings.getUrl(), |
721 | IdOrgSettings.getDownloadLocation()); | |
722 | } catch (IOException e) | |
723 | { | |
724 | 0 | jalview.bin.Console |
725 | .debug("Exception downloading identifiers.org data" | |
726 | + e.getMessage()); | |
727 | } | |
728 | } | |
729 | }).start(); | |
730 | 75 | ; |
731 | } | |
732 | } | |
733 | ||
734 | 0 | @Override |
735 | protected void showNews_actionPerformed(ActionEvent e) | |
736 | { | |
737 | 0 | showNews(showNews.isSelected()); |
738 | } | |
739 | ||
740 | 0 | void showNews(boolean visible) |
741 | { | |
742 | 0 | jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news."); |
743 | 0 | showNews.setSelected(visible); |
744 | 0 | if (visible && !jvnews.isVisible()) |
745 | { | |
746 | 0 | new Thread(new Runnable() |
747 | { | |
748 | 0 | @Override |
749 | public void run() | |
750 | { | |
751 | 0 | long now = System.currentTimeMillis(); |
752 | 0 | Desktop.instance.setProgressBar( |
753 | MessageManager.getString("status.refreshing_news"), now); | |
754 | 0 | jvnews.refreshNews(); |
755 | 0 | Desktop.instance.setProgressBar(null, now); |
756 | 0 | jvnews.showNews(); |
757 | } | |
758 | }).start(); | |
759 | } | |
760 | } | |
761 | ||
762 | /** | |
763 | * recover the last known dimensions for a jalview window | |
764 | * | |
765 | * @param windowName | |
766 | * - empty string is desktop, all other windows have unique prefix | |
767 | * @return null or last known dimensions scaled to current geometry (if last | |
768 | * window geom was known) | |
769 | */ | |
770 | 150 | Rectangle getLastKnownDimensions(String windowName) |
771 | { | |
772 | // TODO: lock aspect ratio for scaling desktop Bug #0058199 | |
773 | 150 | Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); |
774 | 150 | String x = Cache.getProperty(windowName + "SCREEN_X"); |
775 | 150 | String y = Cache.getProperty(windowName + "SCREEN_Y"); |
776 | 150 | String width = Cache.getProperty(windowName + "SCREEN_WIDTH"); |
777 | 150 | String height = Cache.getProperty(windowName + "SCREEN_HEIGHT"); |
778 | 150 | if ((x != null) && (y != null) && (width != null) && (height != null)) |
779 | { | |
780 | 118 | int ix = Integer.parseInt(x), iy = Integer.parseInt(y), |
781 | iw = Integer.parseInt(width), ih = Integer.parseInt(height); | |
782 | 118 | if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null) |
783 | { | |
784 | // attempt #1 - try to cope with change in screen geometry - this | |
785 | // version doesn't preserve original jv aspect ratio. | |
786 | // take ratio of current screen size vs original screen size. | |
787 | 118 | double sw = ((1f * screenSize.width) / (1f * Integer |
788 | .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH")))); | |
789 | 118 | double sh = ((1f * screenSize.height) / (1f * Integer |
790 | .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT")))); | |
791 | // rescale the bounds depending upon the current screen geometry. | |
792 | 118 | ix = (int) (ix * sw); |
793 | 118 | iw = (int) (iw * sw); |
794 | 118 | iy = (int) (iy * sh); |
795 | 118 | ih = (int) (ih * sh); |
796 | 118 | if (ix >= screenSize.width) |
797 | { | |
798 | 0 | jalview.bin.Console.debug( |
799 | "Window geometry location recall error: shifting horizontal to within screenbounds."); | |
800 | 0 | ix = ix % screenSize.width; |
801 | } | |
802 | 118 | if (iy >= screenSize.height) |
803 | { | |
804 | 0 | jalview.bin.Console.debug( |
805 | "Window geometry location recall error: shifting vertical to within screenbounds."); | |
806 | 0 | iy = iy % screenSize.height; |
807 | } | |
808 | 118 | jalview.bin.Console.debug( |
809 | "Got last known dimensions for " + windowName + ": x:" + ix | |
810 | + " y:" + iy + " width:" + iw + " height:" + ih); | |
811 | } | |
812 | // return dimensions for new instance | |
813 | 118 | return new Rectangle(ix, iy, iw, ih); |
814 | } | |
815 | 32 | return null; |
816 | } | |
817 | ||
818 | 0 | void showPasteMenu(int x, int y) |
819 | { | |
820 | 0 | JPopupMenu popup = new JPopupMenu(); |
821 | 0 | JMenuItem item = new JMenuItem( |
822 | MessageManager.getString("label.paste_new_window")); | |
823 | 0 | item.addActionListener(new ActionListener() |
824 | { | |
825 | 0 | @Override |
826 | public void actionPerformed(ActionEvent evt) | |
827 | { | |
828 | 0 | paste(); |
829 | } | |
830 | }); | |
831 | ||
832 | 0 | popup.add(item); |
833 | 0 | popup.show(this, x, y); |
834 | } | |
835 | ||
836 | 1 | public void paste() |
837 | { | |
838 | // quick patch for JAL-4150 - needs some more work and test coverage | |
839 | // TODO - unify below and AlignFrame.paste() | |
840 | // TODO - write tests and fix AlignFrame.paste() which doesn't track if | |
841 | // clipboard has come from a different alignment window than the one where | |
842 | // paste has been called! JAL-4151 | |
843 | ||
844 | 1 | if (Desktop.jalviewClipboard != null) |
845 | { | |
846 | // The clipboard was filled from within Jalview, we must use the | |
847 | // sequences | |
848 | // And dataset from the copied alignment | |
849 | 1 | SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; |
850 | // be doubly sure that we create *new* sequence objects. | |
851 | 1 | SequenceI[] sequences = new SequenceI[newseq.length]; |
852 | 16 | for (int i = 0; i < newseq.length; i++) |
853 | { | |
854 | 15 | sequences[i] = new Sequence(newseq[i]); |
855 | } | |
856 | 1 | Alignment alignment = new Alignment(sequences); |
857 | // dataset is inherited | |
858 | 1 | alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); |
859 | 1 | AlignFrame af = new AlignFrame(alignment, AlignFrame.DEFAULT_WIDTH, |
860 | AlignFrame.DEFAULT_HEIGHT); | |
861 | 1 | String newtitle = new String("Copied sequences"); |
862 | ||
863 | 1 | if (Desktop.jalviewClipboard[2] != null) |
864 | { | |
865 | 0 | HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; |
866 | 0 | af.viewport.setHiddenColumns(hc); |
867 | } | |
868 | ||
869 | 1 | Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH, |
870 | AlignFrame.DEFAULT_HEIGHT); | |
871 | ||
872 | } | |
873 | else | |
874 | { | |
875 | 0 | try |
876 | { | |
877 | 0 | Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); |
878 | 0 | Transferable contents = c.getContents(this); |
879 | ||
880 | 0 | if (contents != null) |
881 | { | |
882 | 0 | String file = (String) contents |
883 | .getTransferData(DataFlavor.stringFlavor); | |
884 | ||
885 | 0 | FileFormatI format = new IdentifyFile().identify(file, |
886 | DataSourceType.PASTE); | |
887 | ||
888 | 0 | new FileLoader().LoadFile(file, DataSourceType.PASTE, format); |
889 | ||
890 | } | |
891 | } catch (Exception ex) | |
892 | { | |
893 | 0 | jalview.bin.Console.outPrintln( |
894 | "Unable to paste alignment from system clipboard:\n" + ex); | |
895 | } | |
896 | } | |
897 | } | |
898 | ||
899 | /** | |
900 | * Adds and opens the given frame to the desktop | |
901 | * | |
902 | * @param frame | |
903 | * Frame to show | |
904 | * @param title | |
905 | * Visible Title | |
906 | * @param w | |
907 | * width | |
908 | * @param h | |
909 | * height | |
910 | */ | |
911 | 430 | public static synchronized void addInternalFrame( |
912 | final JInternalFrame frame, String title, int w, int h) | |
913 | { | |
914 | 430 | addInternalFrame(frame, title, true, w, h, true, false); |
915 | } | |
916 | ||
917 | /** | |
918 | * Add an internal frame to the Jalview desktop | |
919 | * | |
920 | * @param frame | |
921 | * Frame to show | |
922 | * @param title | |
923 | * Visible Title | |
924 | * @param makeVisible | |
925 | * When true, display frame immediately, otherwise, caller must call | |
926 | * setVisible themselves. | |
927 | * @param w | |
928 | * width | |
929 | * @param h | |
930 | * height | |
931 | */ | |
932 | 0 | public static synchronized void addInternalFrame( |
933 | final JInternalFrame frame, String title, boolean makeVisible, | |
934 | int w, int h) | |
935 | { | |
936 | 0 | addInternalFrame(frame, title, makeVisible, w, h, true, false); |
937 | } | |
938 | ||
939 | /** | |
940 | * Add an internal frame to the Jalview desktop and make it visible | |
941 | * | |
942 | * @param frame | |
943 | * Frame to show | |
944 | * @param title | |
945 | * Visible Title | |
946 | * @param w | |
947 | * width | |
948 | * @param h | |
949 | * height | |
950 | * @param resizable | |
951 | * Allow resize | |
952 | */ | |
953 | 17 | public static synchronized void addInternalFrame( |
954 | final JInternalFrame frame, String title, int w, int h, | |
955 | boolean resizable) | |
956 | { | |
957 | 17 | addInternalFrame(frame, title, true, w, h, resizable, false); |
958 | } | |
959 | ||
960 | /** | |
961 | * Add an internal frame to the Jalview desktop | |
962 | * | |
963 | * @param frame | |
964 | * Frame to show | |
965 | * @param title | |
966 | * Visible Title | |
967 | * @param makeVisible | |
968 | * When true, display frame immediately, otherwise, caller must call | |
969 | * setVisible themselves. | |
970 | * @param w | |
971 | * width | |
972 | * @param h | |
973 | * height | |
974 | * @param resizable | |
975 | * Allow resize | |
976 | * @param ignoreMinSize | |
977 | * Do not set the default minimum size for frame | |
978 | */ | |
979 | 507 | public static synchronized void addInternalFrame( |
980 | final JInternalFrame frame, String title, boolean makeVisible, | |
981 | int w, int h, boolean resizable, boolean ignoreMinSize) | |
982 | { | |
983 | ||
984 | // TODO: allow callers to determine X and Y position of frame (eg. via | |
985 | // bounds object). | |
986 | // TODO: consider fixing method to update entries in the window submenu with | |
987 | // the current window title | |
988 | ||
989 | 507 | frame.setTitle(title); |
990 | 507 | if (frame.getWidth() < 1 || frame.getHeight() < 1) |
991 | { | |
992 | 137 | frame.setSize(w, h); |
993 | } | |
994 | // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN | |
995 | // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN | |
996 | // IF JALVIEW IS RUNNING HEADLESS | |
997 | // /////////////////////////////////////////////// | |
998 | 507 | if (instance == null || (System.getProperty("java.awt.headless") != null |
999 | && System.getProperty("java.awt.headless").equals("true"))) | |
1000 | { | |
1001 | 52 | return; |
1002 | } | |
1003 | ||
1004 | 455 | openFrameCount++; |
1005 | ||
1006 | 455 | if (!ignoreMinSize) |
1007 | { | |
1008 | 395 | frame.setMinimumSize( |
1009 | new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); | |
1010 | ||
1011 | // Set default dimension for Alignment Frame window. | |
1012 | // The Alignment Frame window could be added from a number of places, | |
1013 | // hence, | |
1014 | // I did this here in order not to miss out on any Alignment frame. | |
1015 | 395 | if (frame instanceof AlignFrame) |
1016 | { | |
1017 | 295 | frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, |
1018 | ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); | |
1019 | } | |
1020 | } | |
1021 | ||
1022 | 455 | frame.setVisible(makeVisible); |
1023 | 455 | frame.setClosable(true); |
1024 | 455 | frame.setResizable(resizable); |
1025 | 455 | frame.setMaximizable(resizable); |
1026 | 455 | frame.setIconifiable(resizable); |
1027 | 455 | frame.setOpaque(Platform.isJS()); |
1028 | ||
1029 | 455 | if (frame.getX() < 1 && frame.getY() < 1) |
1030 | { | |
1031 | 345 | frame.setLocation(xOffset * openFrameCount, |
1032 | yOffset * ((openFrameCount - 1) % 10) + yOffset); | |
1033 | } | |
1034 | ||
1035 | /* | |
1036 | * add an entry for the new frame in the Window menu (and remove it when the | |
1037 | * frame is closed) | |
1038 | */ | |
1039 | 455 | final JMenuItem menuItem = new JMenuItem(title); |
1040 | 455 | frame.addInternalFrameListener(new InternalFrameAdapter() |
1041 | { | |
1042 | 636 | @Override |
1043 | public void internalFrameActivated(InternalFrameEvent evt) | |
1044 | { | |
1045 | 636 | JInternalFrame itf = desktop.getSelectedFrame(); |
1046 | 636 | if (itf != null) |
1047 | { | |
1048 | 636 | if (itf instanceof AlignFrame) |
1049 | { | |
1050 | 430 | Jalview.getInstance().setCurrentAlignFrame((AlignFrame) itf); |
1051 | } | |
1052 | 636 | itf.requestFocus(); |
1053 | } | |
1054 | } | |
1055 | ||
1056 | 403 | @Override |
1057 | public void internalFrameClosed(InternalFrameEvent evt) | |
1058 | { | |
1059 | 403 | PaintRefresher.RemoveComponent(frame); |
1060 | ||
1061 | /* | |
1062 | * defensive check to prevent frames being added half off the window | |
1063 | */ | |
1064 | 403 | if (openFrameCount > 0) |
1065 | { | |
1066 | 390 | openFrameCount--; |
1067 | } | |
1068 | ||
1069 | /* | |
1070 | * ensure no reference to alignFrame retained by menu item listener | |
1071 | */ | |
1072 | 403 | if (menuItem.getActionListeners().length > 0) |
1073 | { | |
1074 | 382 | menuItem.removeActionListener(menuItem.getActionListeners()[0]); |
1075 | } | |
1076 | 403 | windowMenu.remove(menuItem); |
1077 | } | |
1078 | }); | |
1079 | ||
1080 | 455 | menuItem.addActionListener(new ActionListener() |
1081 | { | |
1082 | 0 | @Override |
1083 | public void actionPerformed(ActionEvent e) | |
1084 | { | |
1085 | 0 | try |
1086 | { | |
1087 | 0 | frame.setSelected(true); |
1088 | 0 | frame.setIcon(false); |
1089 | } catch (java.beans.PropertyVetoException ex) | |
1090 | { | |
1091 | ||
1092 | } | |
1093 | } | |
1094 | }); | |
1095 | ||
1096 | 455 | setKeyBindings(frame); |
1097 | ||
1098 | // Since the latest FlatLaf patch, we occasionally have problems showing | |
1099 | // structureViewer frames... | |
1100 | 455 | int tries = 3; |
1101 | 455 | boolean shown = false; |
1102 | 455 | Exception last = null; |
1103 | 455 | do |
1104 | { | |
1105 | 455 | try |
1106 | { | |
1107 | 455 | desktop.add(frame); |
1108 | 455 | shown = true; |
1109 | } catch (IllegalArgumentException iaex) | |
1110 | { | |
1111 | 0 | last = iaex; |
1112 | 0 | tries--; |
1113 | 0 | jalview.bin.Console.info("Squashed IllegalArgument Exception (" |
1114 | + tries + " left) for " + frame.getTitle(), iaex); | |
1115 | 0 | try |
1116 | { | |
1117 | 0 | Thread.sleep(5); |
1118 | } catch (InterruptedException iex) | |
1119 | { | |
1120 | } | |
1121 | 0 | ; |
1122 | } | |
1123 | 455 | } while (!shown && tries > 0); |
1124 | 455 | if (!shown) |
1125 | { | |
1126 | 0 | jalview.bin.Console.error( |
1127 | "Serious Problem whilst showing window " + frame.getTitle(), | |
1128 | last); | |
1129 | } | |
1130 | ||
1131 | 455 | windowMenu.add(menuItem); |
1132 | ||
1133 | 455 | frame.toFront(); |
1134 | 455 | try |
1135 | { | |
1136 | 455 | frame.setSelected(true); |
1137 | 455 | frame.requestFocus(); |
1138 | } catch (java.beans.PropertyVetoException ve) | |
1139 | { | |
1140 | } catch (java.lang.ClassCastException cex) | |
1141 | { | |
1142 | 0 | jalview.bin.Console.warn( |
1143 | "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869", | |
1144 | cex); | |
1145 | } | |
1146 | } | |
1147 | ||
1148 | /** | |
1149 | * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close | |
1150 | * the window | |
1151 | * | |
1152 | * @param frame | |
1153 | */ | |
1154 | 455 | private static void setKeyBindings(JInternalFrame frame) |
1155 | { | |
1156 | 455 | @SuppressWarnings("serial") |
1157 | final Action closeAction = new AbstractAction() | |
1158 | { | |
1159 | 0 | @Override |
1160 | public void actionPerformed(ActionEvent e) | |
1161 | { | |
1162 | 0 | frame.dispose(); |
1163 | } | |
1164 | }; | |
1165 | ||
1166 | /* | |
1167 | * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action | |
1168 | */ | |
1169 | 455 | KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
1170 | InputEvent.CTRL_DOWN_MASK); | |
1171 | 455 | KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
1172 | ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); | |
1173 | ||
1174 | 455 | InputMap inputMap = frame |
1175 | .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); | |
1176 | 455 | String ctrlW = ctrlWKey.toString(); |
1177 | 455 | inputMap.put(ctrlWKey, ctrlW); |
1178 | 455 | inputMap.put(cmdWKey, ctrlW); |
1179 | ||
1180 | 455 | ActionMap actionMap = frame.getActionMap(); |
1181 | 455 | actionMap.put(ctrlW, closeAction); |
1182 | } | |
1183 | ||
1184 | 0 | @Override |
1185 | public void lostOwnership(Clipboard clipboard, Transferable contents) | |
1186 | { | |
1187 | 0 | if (!internalCopy) |
1188 | { | |
1189 | 0 | Desktop.jalviewClipboard = null; |
1190 | } | |
1191 | ||
1192 | 0 | internalCopy = false; |
1193 | } | |
1194 | ||
1195 | 0 | @Override |
1196 | public void dragEnter(DropTargetDragEvent evt) | |
1197 | { | |
1198 | } | |
1199 | ||
1200 | 0 | @Override |
1201 | public void dragExit(DropTargetEvent evt) | |
1202 | { | |
1203 | } | |
1204 | ||
1205 | 0 | @Override |
1206 | public void dragOver(DropTargetDragEvent evt) | |
1207 | { | |
1208 | } | |
1209 | ||
1210 | 0 | @Override |
1211 | public void dropActionChanged(DropTargetDragEvent evt) | |
1212 | { | |
1213 | } | |
1214 | ||
1215 | /** | |
1216 | * load all files dropped (2.11.4.0 behaviour) | |
1217 | * | |
1218 | * @return false if any file resulted in an error | |
1219 | */ | |
1220 | 0 | public boolean loadDroppedFiles(List<Object> files, |
1221 | List<DataSourceType> protocols, List<Object> failed, | |
1222 | List<Exception> failed_exceptions) | |
1223 | { | |
1224 | 0 | for (int i = 0; i < files.size(); i++) |
1225 | { | |
1226 | 0 | Object file = files.get(i); |
1227 | 0 | try |
1228 | { | |
1229 | // BH 2018 File or String | |
1230 | 0 | String fileName = file.toString(); |
1231 | 0 | DataSourceType protocol = (protocols == null) ? DataSourceType.FILE |
1232 | : protocols.get(i); | |
1233 | 0 | FileFormatI format = null; |
1234 | ||
1235 | 0 | if (fileName.endsWith(".jar")) |
1236 | { | |
1237 | 0 | format = FileFormat.Jalview; |
1238 | } | |
1239 | else | |
1240 | { | |
1241 | 0 | format = new IdentifyFile().identify(file, protocol); |
1242 | } | |
1243 | 0 | if (file instanceof File) |
1244 | { | |
1245 | 0 | Platform.cacheFileData((File) file); |
1246 | } | |
1247 | 0 | new FileLoader().LoadFile(null, file, protocol, format); |
1248 | } catch (Exception x) | |
1249 | { | |
1250 | 0 | failed.add(file); |
1251 | 0 | failed_exceptions.add(x); |
1252 | 0 | jalview.bin.Console.warn( |
1253 | "Unexpected Exception when handling " + file.toString(), x); | |
1254 | } | |
1255 | } | |
1256 | 0 | return failed.size() == 0; // at least one was loaded. |
1257 | } | |
1258 | ||
1259 | /** | |
1260 | * analyse dropped files and process them according to type: load alignments, | |
1261 | * add annotation, trees or features to alignments with the same basename | |
1262 | * | |
1263 | * @return false if any exception was raised | |
1264 | */ | |
1265 | 0 | public boolean processAndLoadDroppedFiles(List<Object> files, |
1266 | List<DataSourceType> protocols, List<Object> failed, | |
1267 | List<Exception> failed_exceptions) | |
1268 | { | |
1269 | // map list to list of strings | |
1270 | 0 | List<String> filenames = new ArrayList<>(); |
1271 | 0 | for (int i = 0; i < files.size(); i++) |
1272 | { | |
1273 | 0 | filenames.add(files.get(i).toString()); |
1274 | } | |
1275 | ||
1276 | // processFilenames will take likely associated files OUT of the list of | |
1277 | // filenames and return them in a BaseInfo object in the Map | |
1278 | 0 | Map<String, BaseInfo> baseInfoMap = ArgParserUtils |
1279 | .processFilenames(filenames, false, files); | |
1280 | // so we can catch exceptions for this file | |
1281 | 0 | Object file = null; |
1282 | 0 | try |
1283 | { | |
1284 | ||
1285 | 0 | for (int i = 0; i < files.size(); i++) |
1286 | { | |
1287 | // BH 2018 File or String | |
1288 | 0 | file = files.get(i); |
1289 | 0 | String fileName = file.toString(); |
1290 | 0 | DataSourceType protocol = (protocols == null) ? DataSourceType.FILE |
1291 | : protocols.get(i); | |
1292 | 0 | FileFormatI format = null; |
1293 | ||
1294 | 0 | if (fileName.toLowerCase(Locale.ROOT).endsWith(".jar")) |
1295 | { | |
1296 | 0 | format = FileFormat.Jalview; |
1297 | } | |
1298 | else | |
1299 | { | |
1300 | 0 | format = new IdentifyFile().identify(file, protocol); |
1301 | } | |
1302 | // If features/annotations/tree file that hasn't been put into the | |
1303 | // baseInfoMap, look through titles of opened AlignFrames to add. | |
1304 | 0 | String ext = FileUtils.getExtension(fileName); |
1305 | 0 | boolean isFeatures = ArgParserUtils.featuresExtensions |
1306 | .contains(ext); | |
1307 | 0 | boolean isAnnotations = ArgParserUtils.annotationsExtensions |
1308 | .contains(ext); | |
1309 | 0 | boolean isTree = ArgParserUtils.treeExtensions.contains(ext); |
1310 | 0 | if (isFeatures || isAnnotations || isTree) |
1311 | { | |
1312 | 0 | String base = FileUtils.getBase(fileName); |
1313 | 0 | AlignFrame matchingAf = null; |
1314 | 0 | AlignFrame[] afs = Desktop.instance.getAlignFrames(); |
1315 | 0 | boolean dontSkip = false; |
1316 | 0 | for (AlignFrame af : afs) |
1317 | { | |
1318 | 0 | String afFilename = af.fileName; |
1319 | 0 | String afTitle = af.getTitle(); |
1320 | /** | |
1321 | * don't need to check the matching afFilename or afTitle has an | |
1322 | * alignment extenstion. It's obviously an alignment! | |
1323 | */ | |
1324 | /* | |
1325 | if ((base.equals(FileUtils.getBase(afFilename)) | |
1326 | && ArgParserUtils.alignmentExtensions | |
1327 | .contains(FileUtils.getExtension(afFilename))) | |
1328 | || (base.equals(FileUtils.getBase(afTitle)) | |
1329 | && ArgParserUtils.alignmentExtensions | |
1330 | .contains(FileUtils | |
1331 | .getExtension(afTitle)))) | |
1332 | */ | |
1333 | 0 | if (base.equals(FileUtils.getBase(afFilename)) |
1334 | || base.equals(FileUtils.getBase(afTitle))) | |
1335 | { | |
1336 | 0 | matchingAf = af; |
1337 | 0 | break; |
1338 | } | |
1339 | } | |
1340 | 0 | if (matchingAf != null) |
1341 | { | |
1342 | 0 | if (isFeatures) |
1343 | { | |
1344 | 0 | matchingAf.parseFeaturesFile(fileName, |
1345 | AppletFormatAdapter.checkProtocol(fileName)); | |
1346 | } | |
1347 | 0 | else if (isAnnotations) |
1348 | { | |
1349 | 0 | matchingAf.loadJalviewDataFile(fileName, null, null, null); |
1350 | } | |
1351 | 0 | else if (isTree) |
1352 | { | |
1353 | 0 | try |
1354 | { | |
1355 | 0 | NewickFile nf = new NewickFile(fileName, |
1356 | AppletFormatAdapter.checkProtocol(fileName)); | |
1357 | 0 | matchingAf.getViewport().setCurrentTree( |
1358 | matchingAf.showNewickTree(nf, fileName).getTree()); | |
1359 | } catch (IOException e) | |
1360 | { | |
1361 | 0 | jalview.bin.Console.warn( |
1362 | "Couldn't add potential tree '" + fileName + "'"); | |
1363 | 0 | dontSkip = true; |
1364 | } | |
1365 | } | |
1366 | 0 | if (!dontSkip) |
1367 | { | |
1368 | // skip to next file | |
1369 | 0 | continue; |
1370 | } | |
1371 | } | |
1372 | } | |
1373 | ||
1374 | 0 | if (file instanceof File) |
1375 | { | |
1376 | 0 | Platform.cacheFileData((File) file); |
1377 | } | |
1378 | // new FileLoader().LoadFile(null, file, protocol, format); | |
1379 | 0 | AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fileName, |
1380 | protocol, format); | |
1381 | // now we add any associated files to the alignframe | |
1382 | 0 | if (baseInfoMap.containsKey(fileName) && baseInfoMap.get(fileName) |
1383 | .getAssociatedFilesMap() != null) | |
1384 | { | |
1385 | 0 | BaseInfo bi = baseInfoMap.get(fileName); |
1386 | 0 | if (bi.getAssociatedFilesMap().containsKey(Arg.FEATURES)) |
1387 | { | |
1388 | 0 | String featuresfile = bi.getAssociatedFilesMap() |
1389 | .get(Arg.FEATURES); | |
1390 | 0 | af.parseFeaturesFile(featuresfile, |
1391 | AppletFormatAdapter.checkProtocol(featuresfile)); | |
1392 | } | |
1393 | 0 | if (bi.getAssociatedFilesMap().containsKey(Arg.ANNOTATIONS)) |
1394 | { | |
1395 | 0 | String annotationsfile = bi.getAssociatedFilesMap() |
1396 | .get(Arg.ANNOTATIONS); | |
1397 | 0 | af.loadJalviewDataFile(annotationsfile, null, null, null); |
1398 | } | |
1399 | 0 | if (bi.getAssociatedFilesMap().containsKey(Arg.TREE)) |
1400 | { | |
1401 | 0 | String treefile = bi.getAssociatedFilesMap().get(Arg.TREE); |
1402 | 0 | try |
1403 | { | |
1404 | 0 | NewickFile nf = new NewickFile(treefile, |
1405 | AppletFormatAdapter.checkProtocol(treefile)); | |
1406 | 0 | af.getViewport().setCurrentTree( |
1407 | af.showNewickTree(nf, treefile).getTree()); | |
1408 | } catch (IOException e) | |
1409 | { | |
1410 | 0 | jalview.bin.Console.warn( |
1411 | "Couldn't add potential tree '" + treefile + "'"); | |
1412 | } | |
1413 | ||
1414 | } | |
1415 | ||
1416 | } | |
1417 | ||
1418 | } | |
1419 | } catch (Exception ex) | |
1420 | { | |
1421 | ||
1422 | 0 | jalview.bin.Console.warn( |
1423 | "Unexpected exception whilst handling drop to Desktop.", ex); | |
1424 | 0 | failed.add(file); |
1425 | 0 | failed_exceptions.add(ex); |
1426 | 0 | return false; |
1427 | } | |
1428 | 0 | return failed.size() == 0; // redundant for 2.11.4.0 implementation |
1429 | } | |
1430 | ||
1431 | 0 | @Override |
1432 | public void drop(DropTargetDropEvent evt) | |
1433 | { | |
1434 | 0 | boolean success = true; |
1435 | // JAL-1552 - acceptDrop required before getTransferable call for | |
1436 | // Java's Transferable for native dnd | |
1437 | 0 | evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); |
1438 | 0 | Transferable t = evt.getTransferable(); |
1439 | 0 | List<Object> files = new ArrayList<>(); |
1440 | 0 | List<DataSourceType> protocols = new ArrayList<>(); |
1441 | ||
1442 | 0 | try |
1443 | { | |
1444 | 0 | Desktop.transferFromDropTarget(files, protocols, evt, t); |
1445 | } catch (Exception e) | |
1446 | { | |
1447 | 0 | e.printStackTrace(); |
1448 | 0 | success = false; |
1449 | } | |
1450 | 0 | try |
1451 | { | |
1452 | 0 | if (files != null) |
1453 | { | |
1454 | 0 | List<Object> failed = new ArrayList<Object>(); |
1455 | 0 | List<Exception> failed_exceptions = new ArrayList<Exception>(); |
1456 | 0 | if (!showExperimental()) |
1457 | { | |
1458 | 0 | success = loadDroppedFiles(files, protocols, failed, |
1459 | failed_exceptions); | |
1460 | } | |
1461 | else | |
1462 | { | |
1463 | 0 | success = processAndLoadDroppedFiles(files, protocols, failed, |
1464 | failed_exceptions); | |
1465 | } | |
1466 | } | |
1467 | } catch (Throwable ex) | |
1468 | { | |
1469 | 0 | jalview.bin.Console.warn( |
1470 | "Unexpected exception whilst handling drop to Desktop.", ex); | |
1471 | 0 | success = false; |
1472 | } | |
1473 | 0 | evt.dropComplete(success); // need this to ensure input focus is properly |
1474 | // transfered to any new windows created | |
1475 | } | |
1476 | ||
1477 | /** | |
1478 | * DOCUMENT ME! | |
1479 | * | |
1480 | * @param e | |
1481 | * DOCUMENT ME! | |
1482 | */ | |
1483 | 0 | @Override |
1484 | public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) | |
1485 | { | |
1486 | // default file format now determined by JalviewFileChooser | |
1487 | 0 | JalviewFileChooser chooser = JalviewFileChooser.forRead( |
1488 | Cache.getProperty("LAST_DIRECTORY"), null, | |
1489 | BackupFiles.getEnabled()); | |
1490 | ||
1491 | 0 | chooser.setFileView(new JalviewFileView()); |
1492 | 0 | chooser.setDialogTitle( |
1493 | MessageManager.getString("label.open_local_file")); | |
1494 | 0 | chooser.setToolTipText(MessageManager.getString("action.open")); |
1495 | ||
1496 | 0 | chooser.setResponseHandler(0, () -> { |
1497 | 0 | File selectedFile = chooser.getSelectedFile(); |
1498 | 0 | Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); |
1499 | ||
1500 | 0 | FileFormatI format = chooser.getSelectedFormat(); |
1501 | ||
1502 | /* | |
1503 | * Call IdentifyFile to verify the file contains what its extension implies. | |
1504 | * Skip this step for dynamically added file formats, because IdentifyFile does | |
1505 | * not know how to recognise them. | |
1506 | */ | |
1507 | 0 | if (FileFormats.getInstance().isIdentifiable(format)) |
1508 | { | |
1509 | 0 | try |
1510 | { | |
1511 | 0 | format = new IdentifyFile().identify(selectedFile, |
1512 | DataSourceType.FILE); | |
1513 | } catch (FileFormatException e) | |
1514 | { | |
1515 | // format = null; //?? | |
1516 | } | |
1517 | } | |
1518 | ||
1519 | 0 | new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, |
1520 | format); | |
1521 | }); | |
1522 | 0 | chooser.showOpenDialog(this); |
1523 | } | |
1524 | ||
1525 | /** | |
1526 | * Shows a dialog for input of a URL at which to retrieve alignment data | |
1527 | * | |
1528 | * @param viewport | |
1529 | */ | |
1530 | 0 | @Override |
1531 | public void inputURLMenuItem_actionPerformed(AlignViewport viewport) | |
1532 | { | |
1533 | // This construct allows us to have a wider textfield | |
1534 | // for viewing | |
1535 | 0 | JLabel label = new JLabel( |
1536 | MessageManager.getString("label.input_file_url")); | |
1537 | ||
1538 | 0 | JPanel panel = new JPanel(new GridLayout(2, 1)); |
1539 | 0 | panel.add(label); |
1540 | ||
1541 | /* | |
1542 | * the URL to fetch is input in Java: an editable combobox with history JS: | |
1543 | * (pending JAL-3038) a plain text field | |
1544 | */ | |
1545 | 0 | JComponent history; |
1546 | 0 | String urlBase = "https://www."; |
1547 | 0 | if (Platform.isJS()) |
1548 | { | |
1549 | 0 | history = new JTextField(urlBase, 35); |
1550 | } | |
1551 | else | |
1552 | /** | |
1553 | * Java only | |
1554 | * | |
1555 | * @j2sIgnore | |
1556 | */ | |
1557 | { | |
1558 | 0 | JComboBox<String> asCombo = new JComboBox<>(); |
1559 | 0 | asCombo.setPreferredSize(new Dimension(400, 20)); |
1560 | 0 | asCombo.setEditable(true); |
1561 | 0 | asCombo.addItem(urlBase); |
1562 | 0 | String historyItems = Cache.getProperty("RECENT_URL"); |
1563 | 0 | if (historyItems != null) |
1564 | { | |
1565 | 0 | for (String token : historyItems.split("\\t")) |
1566 | { | |
1567 | 0 | asCombo.addItem(token); |
1568 | } | |
1569 | } | |
1570 | 0 | history = asCombo; |
1571 | } | |
1572 | 0 | panel.add(history); |
1573 | ||
1574 | 0 | Object[] options = new Object[] { MessageManager.getString("action.ok"), |
1575 | MessageManager.getString("action.cancel") }; | |
1576 | 0 | Runnable action = () -> { |
1577 | 0 | @SuppressWarnings("unchecked") |
1578 | 0 | String url = (history instanceof JTextField |
1579 | ? ((JTextField) history).getText() | |
1580 | : ((JComboBox<String>) history).getEditor().getItem() | |
1581 | .toString().trim()); | |
1582 | ||
1583 | 0 | if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) |
1584 | { | |
1585 | 0 | if (viewport != null) |
1586 | { | |
1587 | 0 | new FileLoader().LoadFile(viewport, url, DataSourceType.URL, |
1588 | FileFormat.Jalview); | |
1589 | } | |
1590 | else | |
1591 | { | |
1592 | 0 | new FileLoader().LoadFile(url, DataSourceType.URL, |
1593 | FileFormat.Jalview); | |
1594 | } | |
1595 | } | |
1596 | else | |
1597 | { | |
1598 | 0 | FileFormatI format = null; |
1599 | 0 | try |
1600 | { | |
1601 | 0 | format = new IdentifyFile().identify(url, DataSourceType.URL); |
1602 | } catch (FileNotFoundException e) | |
1603 | { | |
1604 | 0 | jalview.bin.Console.error("URL '" + url + "' not found", e); |
1605 | } catch (FileFormatException e) | |
1606 | { | |
1607 | 0 | jalview.bin.Console.error( |
1608 | "File at URL '" + url + "' format not recognised", e); | |
1609 | } | |
1610 | ||
1611 | 0 | if (format == null) |
1612 | { | |
1613 | 0 | String msg = MessageManager.formatMessage("label.couldnt_locate", |
1614 | url); | |
1615 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, |
1616 | MessageManager.getString("label.url_not_found"), | |
1617 | JvOptionPane.WARNING_MESSAGE); | |
1618 | 0 | return; |
1619 | } | |
1620 | ||
1621 | 0 | if (viewport != null) |
1622 | { | |
1623 | 0 | new FileLoader().LoadFile(viewport, url, DataSourceType.URL, |
1624 | format); | |
1625 | } | |
1626 | else | |
1627 | { | |
1628 | 0 | new FileLoader().LoadFile(url, DataSourceType.URL, format); |
1629 | } | |
1630 | } | |
1631 | }; | |
1632 | 0 | String dialogOption = MessageManager |
1633 | .getString("label.input_alignment_from_url"); | |
1634 | 0 | JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action) |
1635 | .showInternalDialog(panel, dialogOption, | |
1636 | JvOptionPane.YES_NO_CANCEL_OPTION, | |
1637 | JvOptionPane.PLAIN_MESSAGE, null, options, | |
1638 | MessageManager.getString("action.ok")); | |
1639 | } | |
1640 | ||
1641 | /** | |
1642 | * Opens the CutAndPaste window for the user to paste an alignment in to | |
1643 | * | |
1644 | * @param viewPanel | |
1645 | * - if not null, the pasted alignment is added to the current | |
1646 | * alignment; if null, to a new alignment window | |
1647 | */ | |
1648 | 0 | @Override |
1649 | public void inputTextboxMenuItem_actionPerformed( | |
1650 | AlignmentViewPanel viewPanel) | |
1651 | { | |
1652 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
1653 | 0 | cap.setForInput(viewPanel); |
1654 | 0 | Desktop.addInternalFrame(cap, |
1655 | MessageManager.getString("label.cut_paste_alignmen_file"), true, | |
1656 | 600, 500); | |
1657 | } | |
1658 | ||
1659 | /* | |
1660 | * Check with user and saving files before actually quitting | |
1661 | */ | |
1662 | 0 | public void desktopQuit() |
1663 | { | |
1664 | 0 | desktopQuit(true, false); |
1665 | } | |
1666 | ||
1667 | /** | |
1668 | * close everything, stash window geometries, and shut down all associated | |
1669 | * threads/workers | |
1670 | * | |
1671 | * @param dispose | |
1672 | * - sets the dispose on close flag - JVM may terminate when set | |
1673 | * @param terminateJvm | |
1674 | * - quit with prejudice - stops the JVM. | |
1675 | */ | |
1676 | 81 | public void quitTheDesktop(boolean dispose, boolean terminateJvm) |
1677 | { | |
1678 | 81 | Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); |
1679 | 81 | Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); |
1680 | 81 | Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); |
1681 | 81 | storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, |
1682 | getWidth(), getHeight())); | |
1683 | ||
1684 | 81 | if (jconsole != null) |
1685 | { | |
1686 | 81 | storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); |
1687 | 81 | jconsole.stopConsole(); |
1688 | } | |
1689 | ||
1690 | 81 | if (jvnews != null) |
1691 | { | |
1692 | 70 | storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); |
1693 | } | |
1694 | ||
1695 | // Frames should all close automatically. Keeping external | |
1696 | // viewers open should already be decided by user. | |
1697 | 81 | closeAll_actionPerformed(null); |
1698 | ||
1699 | 81 | if (dialogExecutor != null) |
1700 | { | |
1701 | 43 | dialogExecutor.shutdownNow(); |
1702 | } | |
1703 | ||
1704 | 81 | if (groovyConsole != null) |
1705 | { | |
1706 | // suppress a possible repeat prompt to save script | |
1707 | 0 | groovyConsole.setDirty(false); |
1708 | ||
1709 | // and tidy up | |
1710 | 0 | if (((Window) groovyConsole.getFrame()) != null |
1711 | && ((Window) groovyConsole.getFrame()).isVisible()) | |
1712 | { | |
1713 | // console is visible -- FIXME JAL-4327 | |
1714 | 0 | groovyConsole.exit(); |
1715 | } | |
1716 | else | |
1717 | { | |
1718 | // console is not, so just let it dispose itself when we shutdown | |
1719 | // we don't call groovyConsole.exit() because it calls the shutdown | |
1720 | // handler with invokeAndWait() causing deadlock | |
1721 | 0 | groovyConsole = null; |
1722 | } | |
1723 | } | |
1724 | ||
1725 | 81 | if (terminateJvm) |
1726 | { | |
1727 | // note that shutdown hook will not be run | |
1728 | 0 | jalview.bin.Console.debug("Force Quit selected by user"); |
1729 | 0 | Runtime.getRuntime().halt(0); |
1730 | } | |
1731 | ||
1732 | 81 | jalview.bin.Console.debug("Quit selected by user"); |
1733 | 81 | if (dispose) |
1734 | { | |
1735 | 0 | instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); |
1736 | // instance.dispose(); | |
1737 | } | |
1738 | } | |
1739 | ||
1740 | 0 | public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag) |
1741 | { | |
1742 | 0 | final Runnable doDesktopQuit = () -> { |
1743 | ||
1744 | // FIRST !! check for aborted quit | |
1745 | 0 | if (QuitHandler.quitCancelled()) |
1746 | { | |
1747 | 0 | jalview.bin.Console |
1748 | .debug("Quit was cancelled - Desktop aborting quit"); | |
1749 | 0 | return; |
1750 | } | |
1751 | ||
1752 | // Proceed with quitting | |
1753 | 0 | quitTheDesktop(disposeFlag, |
1754 | QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT); | |
1755 | // and exit the JVM | |
1756 | 0 | instance.quit(); |
1757 | }; | |
1758 | ||
1759 | 0 | return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit, |
1760 | QuitHandler.defaultCancelQuit); | |
1761 | } | |
1762 | ||
1763 | /** | |
1764 | * Exits the program and the JVM. | |
1765 | * | |
1766 | * Don't call this directly | |
1767 | * | |
1768 | * - use desktopQuit() above to tidy up first. | |
1769 | * | |
1770 | * - use closeDesktop() to shutdown Jalview without shutting down the JVM | |
1771 | * | |
1772 | */ | |
1773 | 0 | @Override |
1774 | public void quit() | |
1775 | { | |
1776 | // this will run the shutdownHook but QuitHandler.getQuitResponse() should | |
1777 | // not run a second time if gotQuitResponse flag has been set (i.e. user | |
1778 | // confirmed quit of some kind). | |
1779 | 0 | Jalview.exit("Desktop exiting.", ExitCode.OK); |
1780 | } | |
1781 | ||
1782 | 232 | private void storeLastKnownDimensions(String string, Rectangle jc) |
1783 | { | |
1784 | 232 | jalview.bin.Console.debug("Storing last known dimensions for " + string |
1785 | + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width | |
1786 | + " height:" + jc.height); | |
1787 | ||
1788 | 232 | Cache.setProperty(string + "SCREEN_X", jc.x + ""); |
1789 | 232 | Cache.setProperty(string + "SCREEN_Y", jc.y + ""); |
1790 | 232 | Cache.setProperty(string + "SCREEN_WIDTH", jc.width + ""); |
1791 | 232 | Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + ""); |
1792 | } | |
1793 | ||
1794 | /** | |
1795 | * DOCUMENT ME! | |
1796 | * | |
1797 | * @param e | |
1798 | * DOCUMENT ME! | |
1799 | */ | |
1800 | 0 | @Override |
1801 | public void aboutMenuItem_actionPerformed(ActionEvent e) | |
1802 | { | |
1803 | 0 | new Thread(new Runnable() |
1804 | { | |
1805 | 0 | @Override |
1806 | public void run() | |
1807 | { | |
1808 | 0 | new SplashScreen(false); |
1809 | } | |
1810 | }).start(); | |
1811 | } | |
1812 | ||
1813 | /** | |
1814 | * Returns the html text for the About screen, including any available version | |
1815 | * number, build details, author details and citation reference, but without | |
1816 | * the enclosing {@code html} tags | |
1817 | * | |
1818 | * @return | |
1819 | */ | |
1820 | 551 | public String getAboutMessage() |
1821 | { | |
1822 | 551 | StringBuilder message = new StringBuilder(1024); |
1823 | 551 | message.append("<div style=\"font-family: sans-serif;\">") |
1824 | .append("<h1><strong>Version: ") | |
1825 | .append(Cache.getProperty("VERSION")).append("</strong></h1>") | |
1826 | .append("<strong>Built: <em>") | |
1827 | .append(Cache.getDefault("BUILD_DATE", "unknown")) | |
1828 | .append("</em> from ").append(Cache.getBuildDetailsForSplash()) | |
1829 | .append("</strong>"); | |
1830 | ||
1831 | 550 | String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking"); |
1832 | 550 | if (latestVersion.equals("Checking")) |
1833 | { | |
1834 | // JBP removed this message for 2.11: May be reinstated in future version | |
1835 | // message.append("<br>...Checking latest version...</br>"); | |
1836 | } | |
1837 | 324 | else if (!latestVersion.equals(Cache.getProperty("VERSION"))) |
1838 | { | |
1839 | 324 | boolean red = false; |
1840 | 324 | if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT) |
1841 | .indexOf("automated build") == -1) | |
1842 | { | |
1843 | 324 | red = true; |
1844 | // Displayed when code version and jnlp version do not match and code | |
1845 | // version is not a development build | |
1846 | 324 | message.append("<div style=\"color: #FF0000;font-style: bold;\">"); |
1847 | } | |
1848 | ||
1849 | 324 | message.append("<br>!! Version ") |
1850 | .append(Cache.getDefault("LATEST_VERSION", "..Checking..")) | |
1851 | .append(" is available for download from ") | |
1852 | .append(Cache.getDefault("www.jalview.org", | |
1853 | "https://www.jalview.org")) | |
1854 | .append(" !!"); | |
1855 | 324 | if (red) |
1856 | { | |
1857 | 324 | message.append("</div>"); |
1858 | } | |
1859 | } | |
1860 | 551 | message.append("<br>Authors: "); |
1861 | 551 | message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS)); |
1862 | 550 | message.append(CITATION); |
1863 | ||
1864 | 550 | message.append("</div>"); |
1865 | ||
1866 | 551 | return message.toString(); |
1867 | } | |
1868 | ||
1869 | /** | |
1870 | * Action on requesting Help documentation | |
1871 | */ | |
1872 | 0 | @Override |
1873 | public void documentationMenuItem_actionPerformed() | |
1874 | { | |
1875 | 0 | try |
1876 | { | |
1877 | 0 | if (Platform.isJS()) |
1878 | { | |
1879 | 0 | BrowserLauncher.openURL("https://www.jalview.org/help.html"); |
1880 | } | |
1881 | else | |
1882 | /** | |
1883 | * Java only | |
1884 | * | |
1885 | * @j2sIgnore | |
1886 | */ | |
1887 | { | |
1888 | 0 | Help.showHelpWindow(); |
1889 | } | |
1890 | } catch (Exception ex) | |
1891 | { | |
1892 | 0 | jalview.bin.Console |
1893 | .errPrintln("Error opening help: " + ex.getMessage()); | |
1894 | } | |
1895 | } | |
1896 | ||
1897 | 233 | @Override |
1898 | public void closeAll_actionPerformed(ActionEvent e) | |
1899 | { | |
1900 | // TODO show a progress bar while closing? | |
1901 | 233 | JInternalFrame[] frames = desktop.getAllFrames(); |
1902 | 467 | for (int i = 0; i < frames.length; i++) |
1903 | { | |
1904 | 234 | try |
1905 | { | |
1906 | 234 | frames[i].setClosed(true); |
1907 | } catch (java.beans.PropertyVetoException ex) | |
1908 | { | |
1909 | } | |
1910 | } | |
1911 | 233 | Jalview.getInstance().setCurrentAlignFrame(null); |
1912 | 233 | jalview.bin.Console.info("ALL CLOSED"); |
1913 | ||
1914 | /* | |
1915 | * reset state of singleton objects as appropriate (clear down session state | |
1916 | * when all windows are closed) | |
1917 | */ | |
1918 | 233 | StructureSelectionManager ssm = StructureSelectionManager |
1919 | .getStructureSelectionManager(this); | |
1920 | 233 | if (ssm != null) |
1921 | { | |
1922 | 233 | ssm.resetAll(); |
1923 | } | |
1924 | } | |
1925 | ||
1926 | 6 | public int structureViewersStillRunningCount() |
1927 | { | |
1928 | 6 | int count = 0; |
1929 | 6 | JInternalFrame[] frames = desktop.getAllFrames(); |
1930 | 12 | for (int i = 0; i < frames.length; i++) |
1931 | { | |
1932 | 6 | if (frames[i] != null |
1933 | && frames[i] instanceof JalviewStructureDisplayI) | |
1934 | { | |
1935 | 0 | if (((JalviewStructureDisplayI) frames[i]).stillRunning()) |
1936 | 0 | count++; |
1937 | } | |
1938 | } | |
1939 | 6 | return count; |
1940 | } | |
1941 | ||
1942 | 0 | @Override |
1943 | public void raiseRelated_actionPerformed(ActionEvent e) | |
1944 | { | |
1945 | 0 | reorderAssociatedWindows(false, false); |
1946 | } | |
1947 | ||
1948 | 0 | @Override |
1949 | public void minimizeAssociated_actionPerformed(ActionEvent e) | |
1950 | { | |
1951 | 0 | reorderAssociatedWindows(true, false); |
1952 | } | |
1953 | ||
1954 | 0 | void closeAssociatedWindows() |
1955 | { | |
1956 | 0 | reorderAssociatedWindows(false, true); |
1957 | } | |
1958 | ||
1959 | /* | |
1960 | * (non-Javadoc) | |
1961 | * | |
1962 | * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event. | |
1963 | * ActionEvent) | |
1964 | */ | |
1965 | 0 | @Override |
1966 | protected void garbageCollect_actionPerformed(ActionEvent e) | |
1967 | { | |
1968 | // We simply collect the garbage | |
1969 | 0 | jalview.bin.Console.debug("Collecting garbage..."); |
1970 | 0 | System.gc(); |
1971 | 0 | jalview.bin.Console.debug("Finished garbage collection."); |
1972 | } | |
1973 | ||
1974 | /* | |
1975 | * (non-Javadoc) | |
1976 | * | |
1977 | * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event. | |
1978 | * ActionEvent ) | |
1979 | */ | |
1980 | 0 | @Override |
1981 | protected void showMemusage_actionPerformed(ActionEvent e) | |
1982 | { | |
1983 | 0 | desktop.showMemoryUsage(showMemusage.isSelected()); |
1984 | } | |
1985 | ||
1986 | /* | |
1987 | * (non-Javadoc) | |
1988 | * | |
1989 | * @see | |
1990 | * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent | |
1991 | * ) | |
1992 | */ | |
1993 | 0 | @Override |
1994 | protected void showConsole_actionPerformed(ActionEvent e) | |
1995 | { | |
1996 | 0 | showConsole(showConsole.isSelected()); |
1997 | } | |
1998 | ||
1999 | Console jconsole = null; | |
2000 | ||
2001 | /** | |
2002 | * control whether the java console is visible or not | |
2003 | * | |
2004 | * @param selected | |
2005 | */ | |
2006 | 75 | void showConsole(boolean selected) |
2007 | { | |
2008 | // TODO: decide if we should update properties file | |
2009 | 75 | if (jconsole != null) // BH 2018 |
2010 | { | |
2011 | 75 | showConsole.setSelected(selected); |
2012 | 75 | Cache.setProperty("SHOW_JAVA_CONSOLE", |
2013 | Boolean.valueOf(selected).toString()); | |
2014 | 75 | jconsole.setVisible(selected); |
2015 | } | |
2016 | } | |
2017 | ||
2018 | 0 | void reorderAssociatedWindows(boolean minimize, boolean close) |
2019 | { | |
2020 | 0 | JInternalFrame[] frames = desktop.getAllFrames(); |
2021 | 0 | if (frames == null || frames.length < 1) |
2022 | { | |
2023 | 0 | return; |
2024 | } | |
2025 | ||
2026 | 0 | AlignmentViewport source = null, target = null; |
2027 | 0 | if (frames[0] instanceof AlignFrame) |
2028 | { | |
2029 | 0 | source = ((AlignFrame) frames[0]).getCurrentView(); |
2030 | } | |
2031 | 0 | else if (frames[0] instanceof TreePanel) |
2032 | { | |
2033 | 0 | source = ((TreePanel) frames[0]).getViewPort(); |
2034 | } | |
2035 | 0 | else if (frames[0] instanceof PCAPanel) |
2036 | { | |
2037 | 0 | source = ((PCAPanel) frames[0]).av; |
2038 | } | |
2039 | 0 | else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) |
2040 | { | |
2041 | 0 | source = ((PairwiseAlignPanel) frames[0].getContentPane()).av; |
2042 | } | |
2043 | ||
2044 | 0 | if (source != null) |
2045 | { | |
2046 | 0 | for (int i = 0; i < frames.length; i++) |
2047 | { | |
2048 | 0 | target = null; |
2049 | 0 | if (frames[i] == null) |
2050 | { | |
2051 | 0 | continue; |
2052 | } | |
2053 | 0 | if (frames[i] instanceof AlignFrame) |
2054 | { | |
2055 | 0 | target = ((AlignFrame) frames[i]).getCurrentView(); |
2056 | } | |
2057 | 0 | else if (frames[i] instanceof TreePanel) |
2058 | { | |
2059 | 0 | target = ((TreePanel) frames[i]).getViewPort(); |
2060 | } | |
2061 | 0 | else if (frames[i] instanceof PCAPanel) |
2062 | { | |
2063 | 0 | target = ((PCAPanel) frames[i]).av; |
2064 | } | |
2065 | 0 | else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) |
2066 | { | |
2067 | 0 | target = ((PairwiseAlignPanel) frames[i].getContentPane()).av; |
2068 | } | |
2069 | ||
2070 | 0 | if (source == target) |
2071 | { | |
2072 | 0 | try |
2073 | { | |
2074 | 0 | if (close) |
2075 | { | |
2076 | 0 | frames[i].setClosed(true); |
2077 | } | |
2078 | else | |
2079 | { | |
2080 | 0 | frames[i].setIcon(minimize); |
2081 | 0 | if (!minimize) |
2082 | { | |
2083 | 0 | frames[i].toFront(); |
2084 | } | |
2085 | } | |
2086 | ||
2087 | } catch (java.beans.PropertyVetoException ex) | |
2088 | { | |
2089 | } | |
2090 | } | |
2091 | } | |
2092 | } | |
2093 | } | |
2094 | ||
2095 | /** | |
2096 | * DOCUMENT ME! | |
2097 | * | |
2098 | * @param e | |
2099 | * DOCUMENT ME! | |
2100 | */ | |
2101 | 0 | @Override |
2102 | protected void preferences_actionPerformed(ActionEvent e) | |
2103 | { | |
2104 | 0 | Preferences.openPreferences(); |
2105 | } | |
2106 | ||
2107 | /** | |
2108 | * Prompts the user to choose a file and then saves the Jalview state as a | |
2109 | * Jalview project file | |
2110 | */ | |
2111 | 0 | @Override |
2112 | public void saveState_actionPerformed() | |
2113 | { | |
2114 | 0 | saveState_actionPerformed(false); |
2115 | } | |
2116 | ||
2117 | 2 | public void saveState_actionPerformed(boolean saveAs) |
2118 | { | |
2119 | 2 | java.io.File projectFile = getProjectFile(); |
2120 | // autoSave indicates we already have a file and don't need to ask | |
2121 | 2 | boolean autoSave = projectFile != null && !saveAs |
2122 | && BackupFiles.getEnabled(); | |
2123 | ||
2124 | // jalview.bin.Console.outPrintln("autoSave="+autoSave+", | |
2125 | // projectFile='"+projectFile+"', | |
2126 | // saveAs="+saveAs+", Backups | |
2127 | // "+(BackupFiles.getEnabled()?"enabled":"disabled")); | |
2128 | ||
2129 | 2 | boolean approveSave = false; |
2130 | 2 | if (!autoSave) |
2131 | { | |
2132 | 0 | JalviewFileChooser chooser = new JalviewFileChooser("jvp", |
2133 | "Jalview Project"); | |
2134 | ||
2135 | 0 | chooser.setFileView(new JalviewFileView()); |
2136 | 0 | chooser.setDialogTitle(MessageManager.getString("label.save_state")); |
2137 | ||
2138 | 0 | int value = chooser.showSaveDialog(this); |
2139 | ||
2140 | 0 | if (value == JalviewFileChooser.APPROVE_OPTION) |
2141 | { | |
2142 | 0 | projectFile = chooser.getSelectedFile(); |
2143 | 0 | setProjectFile(projectFile); |
2144 | 0 | approveSave = true; |
2145 | } | |
2146 | } | |
2147 | ||
2148 | 2 | if (approveSave || autoSave) |
2149 | { | |
2150 | 2 | final Desktop me = this; |
2151 | 2 | final java.io.File chosenFile = projectFile; |
2152 | 2 | new Thread(new Runnable() |
2153 | { | |
2154 | 2 | @Override |
2155 | public void run() | |
2156 | { | |
2157 | // TODO: refactor to Jalview desktop session controller action. | |
2158 | 2 | setProgressBar(MessageManager.formatMessage( |
2159 | "label.saving_jalview_project", new Object[] | |
2160 | { chosenFile.getName() }), chosenFile.hashCode()); | |
2161 | 2 | Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent()); |
2162 | // TODO catch and handle errors for savestate | |
2163 | // TODO prevent user from messing with the Desktop whilst we're saving | |
2164 | 2 | try |
2165 | { | |
2166 | 2 | boolean doBackup = BackupFiles.getEnabled(); |
2167 | 2 | BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) |
2168 | : null; | |
2169 | ||
2170 | 2 | new Jalview2XML().saveState( |
2171 | 2 | doBackup ? backupfiles.getTempFile() : chosenFile); |
2172 | ||
2173 | 2 | if (doBackup) |
2174 | { | |
2175 | 2 | backupfiles.setWriteSuccess(true); |
2176 | 2 | backupfiles.rollBackupsAndRenameTempFile(); |
2177 | } | |
2178 | } catch (OutOfMemoryError oom) | |
2179 | { | |
2180 | 0 | new OOMWarning("Whilst saving current state to " |
2181 | + chosenFile.getName(), oom); | |
2182 | } catch (Exception ex) | |
2183 | { | |
2184 | 0 | jalview.bin.Console.error("Problems whilst trying to save to " |
2185 | + chosenFile.getName(), ex); | |
2186 | 0 | JvOptionPane.showMessageDialog(me, |
2187 | MessageManager.formatMessage( | |
2188 | "label.error_whilst_saving_current_state_to", | |
2189 | new Object[] | |
2190 | { chosenFile.getName() }), | |
2191 | MessageManager.getString("label.couldnt_save_project"), | |
2192 | JvOptionPane.WARNING_MESSAGE); | |
2193 | } | |
2194 | 2 | setProgressBar(null, chosenFile.hashCode()); |
2195 | } | |
2196 | }).start(); | |
2197 | } | |
2198 | } | |
2199 | ||
2200 | 0 | @Override |
2201 | public void saveAsState_actionPerformed(ActionEvent e) | |
2202 | { | |
2203 | 0 | saveState_actionPerformed(true); |
2204 | } | |
2205 | ||
2206 | 7 | protected void setProjectFile(File choice) |
2207 | { | |
2208 | 7 | this.projectFile = choice; |
2209 | } | |
2210 | ||
2211 | 2 | public File getProjectFile() |
2212 | { | |
2213 | 2 | return this.projectFile; |
2214 | } | |
2215 | ||
2216 | /** | |
2217 | * Shows a file chooser dialog and tries to read in the selected file as a | |
2218 | * Jalview project | |
2219 | */ | |
2220 | 0 | @Override |
2221 | public void loadState_actionPerformed() | |
2222 | { | |
2223 | 0 | final String[] suffix = new String[] { "jvp", "jar" }; |
2224 | 0 | final String[] desc = new String[] { "Jalview Project", |
2225 | "Jalview Project (old)" }; | |
2226 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
2227 | Cache.getProperty("LAST_DIRECTORY"), suffix, desc, | |
2228 | "Jalview Project", true, BackupFiles.getEnabled()); // last two | |
2229 | // booleans: | |
2230 | // allFiles, | |
2231 | // allowBackupFiles | |
2232 | 0 | chooser.setFileView(new JalviewFileView()); |
2233 | 0 | chooser.setDialogTitle(MessageManager.getString("label.restore_state")); |
2234 | 0 | chooser.setResponseHandler(0, () -> { |
2235 | 0 | File selectedFile = chooser.getSelectedFile(); |
2236 | 0 | setProjectFile(selectedFile); |
2237 | 0 | String choice = selectedFile.getAbsolutePath(); |
2238 | 0 | Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); |
2239 | 0 | new Thread(new Runnable() |
2240 | { | |
2241 | 0 | @Override |
2242 | public void run() | |
2243 | { | |
2244 | 0 | try |
2245 | { | |
2246 | 0 | new Jalview2XML().loadJalviewAlign(selectedFile); |
2247 | } catch (OutOfMemoryError oom) | |
2248 | { | |
2249 | 0 | new OOMWarning("Whilst loading project from " + choice, oom); |
2250 | } catch (Exception ex) | |
2251 | { | |
2252 | 0 | jalview.bin.Console.error( |
2253 | "Problems whilst loading project from " + choice, ex); | |
2254 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
2255 | MessageManager.formatMessage( | |
2256 | "label.error_whilst_loading_project_from", | |
2257 | new Object[] | |
2258 | { choice }), | |
2259 | MessageManager.getString("label.couldnt_load_project"), | |
2260 | JvOptionPane.WARNING_MESSAGE); | |
2261 | } | |
2262 | } | |
2263 | }, "Project Loader").start(); | |
2264 | }); | |
2265 | ||
2266 | 0 | chooser.showOpenDialog(this); |
2267 | } | |
2268 | ||
2269 | 0 | @Override |
2270 | public void inputSequence_actionPerformed(ActionEvent e) | |
2271 | { | |
2272 | 0 | new SequenceFetcher(this); |
2273 | } | |
2274 | ||
2275 | JPanel progressPanel; | |
2276 | ||
2277 | ArrayList<JPanel> fileLoadingPanels = new ArrayList<>(); | |
2278 | ||
2279 | 293 | public void startLoading(final Object fileName) |
2280 | { | |
2281 | 293 | if (fileLoadingCount == 0) |
2282 | { | |
2283 | 293 | fileLoadingPanels.add(addProgressPanel(MessageManager |
2284 | .formatMessage("label.loading_file", new Object[] | |
2285 | { fileName }))); | |
2286 | } | |
2287 | 293 | fileLoadingCount++; |
2288 | } | |
2289 | ||
2290 | 412 | private JPanel addProgressPanel(String string) |
2291 | { | |
2292 | 412 | if (progressPanel == null) |
2293 | { | |
2294 | 298 | progressPanel = new JPanel(new GridLayout(1, 1)); |
2295 | 298 | totalProgressCount = 0; |
2296 | 298 | instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); |
2297 | } | |
2298 | 412 | JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); |
2299 | 412 | JProgressBar progressBar = new JProgressBar(); |
2300 | 412 | progressBar.setIndeterminate(true); |
2301 | ||
2302 | 412 | thisprogress.add(new JLabel(string), BorderLayout.WEST); |
2303 | ||
2304 | 412 | thisprogress.add(progressBar, BorderLayout.CENTER); |
2305 | 412 | progressPanel.add(thisprogress); |
2306 | 412 | ((GridLayout) progressPanel.getLayout()).setRows( |
2307 | ((GridLayout) progressPanel.getLayout()).getRows() + 1); | |
2308 | 412 | ++totalProgressCount; |
2309 | 412 | instance.validate(); |
2310 | 412 | return thisprogress; |
2311 | } | |
2312 | ||
2313 | int totalProgressCount = 0; | |
2314 | ||
2315 | 405 | private void removeProgressPanel(JPanel progbar) |
2316 | { | |
2317 | 405 | if (progressPanel != null) |
2318 | { | |
2319 | 395 | synchronized (progressPanel) |
2320 | { | |
2321 | 395 | progressPanel.remove(progbar); |
2322 | 395 | GridLayout gl = (GridLayout) progressPanel.getLayout(); |
2323 | 395 | gl.setRows(gl.getRows() - 1); |
2324 | 395 | if (--totalProgressCount < 1) |
2325 | { | |
2326 | 275 | this.getContentPane().remove(progressPanel); |
2327 | 275 | progressPanel = null; |
2328 | } | |
2329 | } | |
2330 | } | |
2331 | 405 | validate(); |
2332 | } | |
2333 | ||
2334 | 319 | public void stopLoading() |
2335 | { | |
2336 | 319 | fileLoadingCount--; |
2337 | 319 | if (fileLoadingCount < 1) |
2338 | { | |
2339 | 608 | while (fileLoadingPanels.size() > 0) |
2340 | { | |
2341 | 289 | removeProgressPanel(fileLoadingPanels.remove(0)); |
2342 | } | |
2343 | 319 | fileLoadingPanels.clear(); |
2344 | 319 | fileLoadingCount = 0; |
2345 | } | |
2346 | 319 | validate(); |
2347 | } | |
2348 | ||
2349 | 10 | public static int getViewCount(String alignmentId) |
2350 | { | |
2351 | 10 | AlignmentViewport[] aps = getViewports(alignmentId); |
2352 | 10 | return (aps == null) ? 0 : aps.length; |
2353 | } | |
2354 | ||
2355 | /** | |
2356 | * | |
2357 | * @param alignmentId | |
2358 | * - if null, all sets are returned | |
2359 | * @return all AlignmentPanels concerning the alignmentId sequence set | |
2360 | */ | |
2361 | 89 | public static AlignmentPanel[] getAlignmentPanels(String alignmentId) |
2362 | { | |
2363 | 89 | if (Desktop.desktop == null) |
2364 | { | |
2365 | // no frames created and in headless mode | |
2366 | // TODO: verify that frames are recoverable when in headless mode | |
2367 | 0 | return null; |
2368 | } | |
2369 | 89 | List<AlignmentPanel> aps = new ArrayList<>(); |
2370 | 89 | AlignFrame[] frames = Desktop.getDesktopAlignFrames(); |
2371 | 89 | if (frames == null) |
2372 | { | |
2373 | 21 | return null; |
2374 | } | |
2375 | 68 | for (AlignFrame af : frames) |
2376 | { | |
2377 | 178 | for (AlignmentPanel ap : af.alignPanels) |
2378 | { | |
2379 | 228 | if (alignmentId == null |
2380 | || alignmentId.equals(ap.av.getSequenceSetId())) | |
2381 | { | |
2382 | 138 | aps.add(ap); |
2383 | } | |
2384 | } | |
2385 | } | |
2386 | 68 | if (aps.size() == 0) |
2387 | { | |
2388 | 11 | return null; |
2389 | } | |
2390 | 57 | AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); |
2391 | 57 | return vap; |
2392 | } | |
2393 | ||
2394 | /** | |
2395 | * get all the viewports on an alignment. | |
2396 | * | |
2397 | * @param sequenceSetId | |
2398 | * unique alignment id (may be null - all viewports returned in that | |
2399 | * case) | |
2400 | * @return all viewports on the alignment bound to sequenceSetId | |
2401 | */ | |
2402 | 10 | public static AlignmentViewport[] getViewports(String sequenceSetId) |
2403 | { | |
2404 | 10 | List<AlignmentViewport> viewp = new ArrayList<>(); |
2405 | 10 | if (desktop != null) |
2406 | { | |
2407 | 10 | AlignFrame[] frames = Desktop.getDesktopAlignFrames(); |
2408 | ||
2409 | 10 | for (AlignFrame afr : frames) |
2410 | { | |
2411 | 11 | if (sequenceSetId == null || afr.getViewport().getSequenceSetId() |
2412 | .equals(sequenceSetId)) | |
2413 | { | |
2414 | 10 | if (afr.alignPanels != null) |
2415 | { | |
2416 | 10 | for (AlignmentPanel ap : afr.alignPanels) |
2417 | { | |
2418 | 11 | if (sequenceSetId == null |
2419 | || sequenceSetId.equals(ap.av.getSequenceSetId())) | |
2420 | { | |
2421 | 11 | viewp.add(ap.av); |
2422 | } | |
2423 | } | |
2424 | } | |
2425 | else | |
2426 | { | |
2427 | 0 | viewp.add(afr.getViewport()); |
2428 | } | |
2429 | } | |
2430 | } | |
2431 | 10 | if (viewp.size() > 0) |
2432 | { | |
2433 | 10 | return viewp.toArray(new AlignmentViewport[viewp.size()]); |
2434 | } | |
2435 | } | |
2436 | 0 | return null; |
2437 | } | |
2438 | ||
2439 | /** | |
2440 | * Explode the views in the given frame into separate AlignFrame | |
2441 | * | |
2442 | * @param af | |
2443 | */ | |
2444 | 1 | public static void explodeViews(AlignFrame af) |
2445 | { | |
2446 | 1 | int size = af.alignPanels.size(); |
2447 | 1 | if (size < 2) |
2448 | { | |
2449 | 0 | return; |
2450 | } | |
2451 | ||
2452 | // FIXME: ideally should use UI interface API | |
2453 | 1 | FeatureSettings viewFeatureSettings = (af.featureSettings != null |
2454 | && af.featureSettings.isOpen()) ? af.featureSettings : null; | |
2455 | 1 | Rectangle fsBounds = af.getFeatureSettingsGeometry(); |
2456 | 6 | for (int i = 0; i < size; i++) |
2457 | { | |
2458 | 5 | AlignmentPanel ap = af.alignPanels.get(i); |
2459 | ||
2460 | 5 | AlignFrame newaf = new AlignFrame(ap); |
2461 | ||
2462 | // transfer reference for existing feature settings to new alignFrame | |
2463 | 5 | if (ap == af.alignPanel) |
2464 | { | |
2465 | 1 | if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) |
2466 | { | |
2467 | 0 | newaf.featureSettings = viewFeatureSettings; |
2468 | } | |
2469 | 1 | newaf.setFeatureSettingsGeometry(fsBounds); |
2470 | } | |
2471 | ||
2472 | /* | |
2473 | * Restore the view's last exploded frame geometry if known. Multiple views from | |
2474 | * one exploded frame share and restore the same (frame) position and size. | |
2475 | */ | |
2476 | 5 | Rectangle geometry = ap.av.getExplodedGeometry(); |
2477 | 5 | if (geometry != null) |
2478 | { | |
2479 | 5 | newaf.setBounds(geometry); |
2480 | } | |
2481 | ||
2482 | 5 | ap.av.setGatherViewsHere(false); |
2483 | ||
2484 | 5 | addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, |
2485 | AlignFrame.DEFAULT_HEIGHT); | |
2486 | // and materialise a new feature settings dialog instance for the new | |
2487 | // alignframe | |
2488 | // (closes the old as if 'OK' was pressed) | |
2489 | 5 | if (ap == af.alignPanel && newaf.featureSettings != null |
2490 | && newaf.featureSettings.isOpen() | |
2491 | && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) | |
2492 | { | |
2493 | 0 | newaf.showFeatureSettingsUI(); |
2494 | } | |
2495 | } | |
2496 | ||
2497 | 1 | af.featureSettings = null; |
2498 | 1 | af.alignPanels.clear(); |
2499 | 1 | af.closeMenuItem_actionPerformed(true); |
2500 | ||
2501 | } | |
2502 | ||
2503 | /** | |
2504 | * Gather expanded views (separate AlignFrame's) with the same sequence set | |
2505 | * identifier back in to this frame as additional views, and close the | |
2506 | * expanded views. Note the expanded frames may themselves have multiple | |
2507 | * views. We take the lot. | |
2508 | * | |
2509 | * @param source | |
2510 | */ | |
2511 | 14 | public void gatherViews(AlignFrame source) |
2512 | { | |
2513 | 14 | source.viewport.setGatherViewsHere(true); |
2514 | 14 | source.viewport.setExplodedGeometry(source.getBounds()); |
2515 | 14 | JInternalFrame[] frames = desktop.getAllFrames(); |
2516 | 14 | String viewId = source.viewport.getSequenceSetId(); |
2517 | 121 | for (int t = 0; t < frames.length; t++) |
2518 | { | |
2519 | 107 | if (frames[t] instanceof AlignFrame && frames[t] != source) |
2520 | { | |
2521 | 54 | AlignFrame af = (AlignFrame) frames[t]; |
2522 | 54 | boolean gatherThis = false; |
2523 | 119 | for (int a = 0; a < af.alignPanels.size(); a++) |
2524 | { | |
2525 | 65 | AlignmentPanel ap = af.alignPanels.get(a); |
2526 | 65 | if (viewId.equals(ap.av.getSequenceSetId())) |
2527 | { | |
2528 | 39 | gatherThis = true; |
2529 | 39 | ap.av.setGatherViewsHere(false); |
2530 | 39 | ap.av.setExplodedGeometry(af.getBounds()); |
2531 | 39 | source.addAlignmentPanel(ap, false); |
2532 | } | |
2533 | } | |
2534 | ||
2535 | 54 | if (gatherThis) |
2536 | { | |
2537 | 39 | if (af.featureSettings != null && af.featureSettings.isOpen()) |
2538 | { | |
2539 | 0 | if (source.featureSettings == null) |
2540 | { | |
2541 | // preserve the feature settings geometry for this frame | |
2542 | 0 | source.featureSettings = af.featureSettings; |
2543 | 0 | source.setFeatureSettingsGeometry( |
2544 | af.getFeatureSettingsGeometry()); | |
2545 | } | |
2546 | else | |
2547 | { | |
2548 | // close it and forget | |
2549 | 0 | af.featureSettings.close(); |
2550 | } | |
2551 | } | |
2552 | 39 | af.alignPanels.clear(); |
2553 | 39 | af.closeMenuItem_actionPerformed(true); |
2554 | } | |
2555 | } | |
2556 | } | |
2557 | ||
2558 | // refresh the feature setting UI for the source frame if it exists | |
2559 | 14 | if (source.featureSettings != null && source.featureSettings.isOpen()) |
2560 | { | |
2561 | 0 | source.showFeatureSettingsUI(); |
2562 | } | |
2563 | ||
2564 | } | |
2565 | ||
2566 | 35 | public JInternalFrame[] getAllFrames() |
2567 | { | |
2568 | 35 | return desktop.getAllFrames(); |
2569 | } | |
2570 | ||
2571 | /** | |
2572 | * Checks the given url to see if it gives a response indicating that the user | |
2573 | * should be informed of a new questionnaire. | |
2574 | * | |
2575 | * @param url | |
2576 | */ | |
2577 | 36 | public void checkForQuestionnaire(String url) |
2578 | { | |
2579 | 36 | UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url); |
2580 | // javax.swing.SwingUtilities.invokeLater(jvq); | |
2581 | 36 | new Thread(jvq).start(); |
2582 | } | |
2583 | ||
2584 | 75 | public void checkURLLinks() |
2585 | { | |
2586 | // Thread off the URL link checker | |
2587 | 75 | addDialogThread(new Runnable() |
2588 | { | |
2589 | 75 | @Override |
2590 | public void run() | |
2591 | { | |
2592 | 75 | if (Cache.getDefault("CHECKURLLINKS", true)) |
2593 | { | |
2594 | // check what the actual links are - if it's just the default don't | |
2595 | // bother with the warning | |
2596 | 75 | List<String> links = Preferences.sequenceUrlLinks |
2597 | .getLinksForMenu(); | |
2598 | ||
2599 | // only need to check links if there is one with a | |
2600 | // SEQUENCE_ID which is not the default EMBL_EBI link | |
2601 | 75 | ListIterator<String> li = links.listIterator(); |
2602 | 75 | boolean check = false; |
2603 | 75 | List<JLabel> urls = new ArrayList<>(); |
2604 | 222 | while (li.hasNext()) |
2605 | { | |
2606 | 147 | String link = li.next(); |
2607 | 147 | if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) |
2608 | && !UrlConstants.isDefaultString(link)) | |
2609 | { | |
2610 | 0 | check = true; |
2611 | 0 | int barPos = link.indexOf("|"); |
2612 | 0 | String urlMsg = barPos == -1 ? link |
2613 | : link.substring(0, barPos) + ": " | |
2614 | + link.substring(barPos + 1); | |
2615 | 0 | urls.add(new JLabel(urlMsg)); |
2616 | } | |
2617 | } | |
2618 | 75 | if (!check) |
2619 | { | |
2620 | 75 | return; |
2621 | } | |
2622 | ||
2623 | // ask user to check in case URL links use old style tokens | |
2624 | // ($SEQUENCE_ID$ for sequence id _or_ accession id) | |
2625 | 0 | JPanel msgPanel = new JPanel(); |
2626 | 0 | msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); |
2627 | 0 | msgPanel.add(Box.createVerticalGlue()); |
2628 | 0 | JLabel msg = new JLabel(MessageManager |
2629 | .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); | |
2630 | 0 | JLabel msg2 = new JLabel(MessageManager |
2631 | .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); | |
2632 | 0 | msgPanel.add(msg); |
2633 | 0 | for (JLabel url : urls) |
2634 | { | |
2635 | 0 | msgPanel.add(url); |
2636 | } | |
2637 | 0 | msgPanel.add(msg2); |
2638 | ||
2639 | 0 | final JCheckBox jcb = new JCheckBox( |
2640 | MessageManager.getString("label.do_not_display_again")); | |
2641 | 0 | jcb.addActionListener(new ActionListener() |
2642 | { | |
2643 | 0 | @Override |
2644 | public void actionPerformed(ActionEvent e) | |
2645 | { | |
2646 | // update Cache settings for "don't show this again" | |
2647 | 0 | boolean showWarningAgain = !jcb.isSelected(); |
2648 | 0 | Cache.setProperty("CHECKURLLINKS", |
2649 | Boolean.valueOf(showWarningAgain).toString()); | |
2650 | } | |
2651 | }); | |
2652 | 0 | msgPanel.add(jcb); |
2653 | ||
2654 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, |
2655 | MessageManager | |
2656 | .getString("label.SEQUENCE_ID_no_longer_used"), | |
2657 | JvOptionPane.WARNING_MESSAGE); | |
2658 | } | |
2659 | } | |
2660 | }); | |
2661 | } | |
2662 | ||
2663 | /** | |
2664 | * Proxy class for JDesktopPane which optionally displays the current memory | |
2665 | * usage and highlights the desktop area with a red bar if free memory runs | |
2666 | * low. | |
2667 | * | |
2668 | * @author AMW | |
2669 | */ | |
2670 | public class MyDesktopPane extends JDesktopPane implements Runnable | |
2671 | { | |
2672 | private static final float ONE_MB = 1048576f; | |
2673 | ||
2674 | boolean showMemoryUsage = false; | |
2675 | ||
2676 | Runtime runtime; | |
2677 | ||
2678 | java.text.NumberFormat df; | |
2679 | ||
2680 | float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, | |
2681 | percentUsage; | |
2682 | ||
2683 | 75 | public MyDesktopPane(boolean showMemoryUsage) |
2684 | { | |
2685 | 75 | showMemoryUsage(showMemoryUsage); |
2686 | } | |
2687 | ||
2688 | 75 | public void showMemoryUsage(boolean showMemory) |
2689 | { | |
2690 | 75 | this.showMemoryUsage = showMemory; |
2691 | 75 | if (showMemory) |
2692 | { | |
2693 | 0 | Thread worker = new Thread(this); |
2694 | 0 | worker.start(); |
2695 | } | |
2696 | 75 | repaint(); |
2697 | } | |
2698 | ||
2699 | 582 | public boolean isShowMemoryUsage() |
2700 | { | |
2701 | 582 | return showMemoryUsage; |
2702 | } | |
2703 | ||
2704 | 0 | @Override |
2705 | public void run() | |
2706 | { | |
2707 | 0 | df = java.text.NumberFormat.getNumberInstance(); |
2708 | 0 | df.setMaximumFractionDigits(2); |
2709 | 0 | runtime = Runtime.getRuntime(); |
2710 | ||
2711 | 0 | while (showMemoryUsage) |
2712 | { | |
2713 | 0 | try |
2714 | { | |
2715 | 0 | maxMemory = runtime.maxMemory() / ONE_MB; |
2716 | 0 | allocatedMemory = runtime.totalMemory() / ONE_MB; |
2717 | 0 | freeMemory = runtime.freeMemory() / ONE_MB; |
2718 | 0 | totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); |
2719 | ||
2720 | 0 | percentUsage = (totalFreeMemory / maxMemory) * 100; |
2721 | ||
2722 | // if (percentUsage < 20) | |
2723 | { | |
2724 | // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, | |
2725 | // Color.red); | |
2726 | // instance.set.setBorder(border1); | |
2727 | } | |
2728 | 0 | repaint(); |
2729 | // sleep after showing usage | |
2730 | 0 | Thread.sleep(3000); |
2731 | } catch (Exception ex) | |
2732 | { | |
2733 | 0 | ex.printStackTrace(); |
2734 | } | |
2735 | } | |
2736 | } | |
2737 | ||
2738 | 2520 | @Override |
2739 | public void paintComponent(Graphics g) | |
2740 | { | |
2741 | 2520 | if (showMemoryUsage && g != null && df != null) |
2742 | { | |
2743 | 0 | if (percentUsage < 20) |
2744 | { | |
2745 | 0 | g.setColor(Color.red); |
2746 | } | |
2747 | 0 | FontMetrics fm = g.getFontMetrics(); |
2748 | 0 | if (fm != null) |
2749 | { | |
2750 | 0 | g.drawString(MessageManager.formatMessage("label.memory_stats", |
2751 | new Object[] | |
2752 | { df.format(totalFreeMemory), df.format(maxMemory), | |
2753 | df.format(percentUsage) }), | |
2754 | 10, getHeight() - fm.getHeight()); | |
2755 | } | |
2756 | } | |
2757 | ||
2758 | // output debug scale message. Important for jalview.bin.HiDPISettingTest2 | |
2759 | 2520 | Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics()); |
2760 | } | |
2761 | } | |
2762 | ||
2763 | /** | |
2764 | * Accessor method to quickly get all the AlignmentFrames loaded. | |
2765 | * | |
2766 | * @return an array of AlignFrame, or null if none found | |
2767 | */ | |
2768 | 305 | @Override |
2769 | public AlignFrame[] getAlignFrames() | |
2770 | { | |
2771 | 305 | if (desktop == null) |
2772 | { | |
2773 | 0 | return null; |
2774 | } | |
2775 | ||
2776 | 305 | JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
2777 | ||
2778 | 305 | if (frames == null) |
2779 | { | |
2780 | 0 | return null; |
2781 | } | |
2782 | 305 | List<AlignFrame> avp = new ArrayList<>(); |
2783 | // REVERSE ORDER | |
2784 | 1005 | for (int i = frames.length - 1; i > -1; i--) |
2785 | { | |
2786 | 700 | if (frames[i] instanceof AlignFrame) |
2787 | { | |
2788 | 419 | avp.add((AlignFrame) frames[i]); |
2789 | } | |
2790 | 281 | else if (frames[i] instanceof SplitFrame) |
2791 | { | |
2792 | /* | |
2793 | * Also check for a split frame containing an AlignFrame | |
2794 | */ | |
2795 | 48 | GSplitFrame sf = (GSplitFrame) frames[i]; |
2796 | 48 | if (sf.getTopFrame() instanceof AlignFrame) |
2797 | { | |
2798 | 48 | avp.add((AlignFrame) sf.getTopFrame()); |
2799 | } | |
2800 | 48 | if (sf.getBottomFrame() instanceof AlignFrame) |
2801 | { | |
2802 | 48 | avp.add((AlignFrame) sf.getBottomFrame()); |
2803 | } | |
2804 | } | |
2805 | } | |
2806 | 305 | if (avp.size() == 0) |
2807 | { | |
2808 | 50 | return null; |
2809 | } | |
2810 | 255 | AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]); |
2811 | 255 | return afs; |
2812 | } | |
2813 | ||
2814 | /** | |
2815 | * static version | |
2816 | */ | |
2817 | 305 | public static AlignFrame[] getDesktopAlignFrames() |
2818 | { | |
2819 | 305 | if (Jalview.isHeadlessMode()) |
2820 | { | |
2821 | // Desktop.desktop is null in headless mode | |
2822 | 0 | return Jalview.getInstance().getAlignFrames(); |
2823 | } | |
2824 | ||
2825 | 305 | if (instance != null && desktop != null) |
2826 | { | |
2827 | 305 | return instance.getAlignFrames(); |
2828 | } | |
2829 | ||
2830 | 0 | return null; |
2831 | } | |
2832 | ||
2833 | /** | |
2834 | * Returns an array of any AppJmol frames in the Desktop (or null if none). | |
2835 | * | |
2836 | * @return | |
2837 | */ | |
2838 | 0 | public GStructureViewer[] getJmols() |
2839 | { | |
2840 | 0 | JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
2841 | ||
2842 | 0 | if (frames == null) |
2843 | { | |
2844 | 0 | return null; |
2845 | } | |
2846 | 0 | List<GStructureViewer> avp = new ArrayList<>(); |
2847 | // REVERSE ORDER | |
2848 | 0 | for (int i = frames.length - 1; i > -1; i--) |
2849 | { | |
2850 | 0 | if (frames[i] instanceof AppJmol) |
2851 | { | |
2852 | 0 | GStructureViewer af = (GStructureViewer) frames[i]; |
2853 | 0 | avp.add(af); |
2854 | } | |
2855 | } | |
2856 | 0 | if (avp.size() == 0) |
2857 | { | |
2858 | 0 | return null; |
2859 | } | |
2860 | 0 | GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]); |
2861 | 0 | return afs; |
2862 | } | |
2863 | ||
2864 | /** | |
2865 | * Add Groovy Support to Jalview | |
2866 | */ | |
2867 | 0 | @Override |
2868 | public void groovyShell_actionPerformed() | |
2869 | { | |
2870 | 0 | try |
2871 | { | |
2872 | 0 | openGroovyConsole(); |
2873 | } catch (Exception ex) | |
2874 | { | |
2875 | 0 | jalview.bin.Console.error("Groovy Console creation failed.", ex); |
2876 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
2877 | ||
2878 | MessageManager.getString("label.couldnt_create_groovy_shell"), | |
2879 | MessageManager.getString("label.groovy_support_failed"), | |
2880 | JvOptionPane.ERROR_MESSAGE); | |
2881 | } | |
2882 | } | |
2883 | ||
2884 | /** | |
2885 | * Open the Groovy console | |
2886 | */ | |
2887 | 0 | void openGroovyConsole() |
2888 | { | |
2889 | 0 | if (groovyConsole == null) |
2890 | { | |
2891 | 0 | JalviewObjectI j = new JalviewObject(this); |
2892 | 0 | groovyConsole = new groovy.console.ui.Console(); |
2893 | 0 | groovyConsole.setVariable(JalviewObjectI.jalviewObjectName, j); |
2894 | 0 | groovyConsole.setVariable(JalviewObjectI.currentAlFrameName, |
2895 | getCurrentAlignFrame()); | |
2896 | 0 | groovyConsole.run(); |
2897 | ||
2898 | /* | |
2899 | * We allow only one console at a time, so that AlignFrame menu option | |
2900 | * 'Calculate | Run Groovy script' is unambiguous. Disable 'Groovy Console', and | |
2901 | * enable 'Run script', when the console is opened, and the reverse when it is | |
2902 | * closed | |
2903 | */ | |
2904 | 0 | Window window = (Window) groovyConsole.getFrame(); |
2905 | 0 | window.addWindowListener(new WindowAdapter() |
2906 | { | |
2907 | 0 | @Override |
2908 | public void windowClosed(WindowEvent e) | |
2909 | { | |
2910 | /* | |
2911 | * rebind CMD-Q from Groovy Console to Jalview Quit | |
2912 | */ | |
2913 | 0 | addQuitHandler(); |
2914 | 0 | enableExecuteGroovy(false); |
2915 | } | |
2916 | }); | |
2917 | } | |
2918 | ||
2919 | /* | |
2920 | * show Groovy console window (after close and reopen) | |
2921 | */ | |
2922 | 0 | ((Window) groovyConsole.getFrame()).setVisible(true); |
2923 | ||
2924 | /* | |
2925 | * if we got this far, enable 'Run Groovy' in AlignFrame menus and disable | |
2926 | * opening a second console | |
2927 | */ | |
2928 | 0 | enableExecuteGroovy(true); |
2929 | } | |
2930 | ||
2931 | /** | |
2932 | * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this | |
2933 | * binding when opened | |
2934 | */ | |
2935 | 0 | protected void addQuitHandler() |
2936 | { | |
2937 | 0 | getRootPane() |
2938 | .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( | |
2939 | KeyStroke | |
2940 | .getKeyStroke(KeyEvent.VK_Q, | |
2941 | jalview.util.ShortcutKeyMaskExWrapper | |
2942 | .getMenuShortcutKeyMaskEx()), | |
2943 | "Quit"); | |
2944 | 0 | getRootPane().getActionMap().put("Quit", new AbstractAction() |
2945 | { | |
2946 | 0 | @Override |
2947 | public void actionPerformed(ActionEvent e) | |
2948 | { | |
2949 | 0 | desktopQuit(); |
2950 | } | |
2951 | }); | |
2952 | } | |
2953 | ||
2954 | /** | |
2955 | * Enable or disable 'Run Groovy script' in AlignFrame calculate menus | |
2956 | * | |
2957 | * @param enabled | |
2958 | * true if Groovy console is open | |
2959 | */ | |
2960 | 0 | public void enableExecuteGroovy(boolean enabled) |
2961 | { | |
2962 | /* | |
2963 | * disable opening a second Groovy console (or re-enable when the console is | |
2964 | * closed) | |
2965 | */ | |
2966 | 0 | groovyShell.setEnabled(!enabled); |
2967 | ||
2968 | 0 | AlignFrame[] alignFrames = getDesktopAlignFrames(); |
2969 | 0 | if (alignFrames != null) |
2970 | { | |
2971 | 0 | for (AlignFrame af : alignFrames) |
2972 | { | |
2973 | 0 | af.setGroovyEnabled(enabled); |
2974 | } | |
2975 | } | |
2976 | } | |
2977 | ||
2978 | /** | |
2979 | * Progress bars managed by the IProgressIndicator method. TODO - delegate to | |
2980 | * jalview.gui.ProgressBar | |
2981 | */ | |
2982 | private Hashtable<Long, JPanel> progressBars; | |
2983 | ||
2984 | private Hashtable<Long, IProgressIndicatorHandler> progressBarHandlers; | |
2985 | ||
2986 | private Hashtable<Long, String> progressBarMessages; | |
2987 | ||
2988 | /* | |
2989 | * (non-Javadoc) | |
2990 | * | |
2991 | * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) | |
2992 | */ | |
2993 | 235 | @Override |
2994 | public void setProgressBar(String message, long id) | |
2995 | { | |
2996 | 235 | if (progressBars == null) |
2997 | { | |
2998 | 45 | progressBars = new Hashtable<>(); |
2999 | 45 | progressBarHandlers = new Hashtable<>(); |
3000 | 45 | progressBarMessages = new Hashtable<>(); |
3001 | } | |
3002 | ||
3003 | 235 | if (progressBars.get(Long.valueOf(id)) != null) |
3004 | { | |
3005 | 116 | JPanel panel = progressBars.remove(Long.valueOf(id)); |
3006 | 116 | if (progressBarHandlers.contains(Long.valueOf(id))) |
3007 | { | |
3008 | 0 | progressBarHandlers.remove(Long.valueOf(id)); |
3009 | } | |
3010 | 116 | removeProgressPanel(panel); |
3011 | } | |
3012 | else | |
3013 | { | |
3014 | 119 | progressBars.put(Long.valueOf(id), addProgressPanel(message)); |
3015 | 119 | if (message != null) |
3016 | { | |
3017 | 117 | progressBarMessages.put(id, message); |
3018 | } | |
3019 | else | |
3020 | { | |
3021 | 2 | progressBarMessages.remove(id); |
3022 | } | |
3023 | } | |
3024 | } | |
3025 | ||
3026 | 0 | @Override |
3027 | public JProgressBar getProgressBar(long id) | |
3028 | { | |
3029 | 0 | if (progressBars == null) |
3030 | 0 | return null; |
3031 | ||
3032 | 0 | if (progressBars.get(Long.valueOf(id)) == null) |
3033 | 0 | return null; |
3034 | ||
3035 | 0 | for (Component c : progressBars.get(Long.valueOf(id)).getComponents()) |
3036 | { | |
3037 | 0 | if (c.getClass() == JProgressBar.class) |
3038 | 0 | return (JProgressBar) c; |
3039 | } | |
3040 | 0 | return null; |
3041 | } | |
3042 | ||
3043 | /* | |
3044 | * (non-Javadoc) | |
3045 | * | |
3046 | * @see jalview.gui.IProgressIndicator#registerHandler(long, | |
3047 | * jalview.gui.IProgressIndicatorHandler) | |
3048 | */ | |
3049 | 0 | @Override |
3050 | public void registerHandler(final long id, | |
3051 | final IProgressIndicatorHandler handler) | |
3052 | { | |
3053 | 0 | if (progressBarHandlers == null |
3054 | || !progressBars.containsKey(Long.valueOf(id))) | |
3055 | { | |
3056 | 0 | throw new Error(MessageManager.getString( |
3057 | "error.call_setprogressbar_before_registering_handler")); | |
3058 | } | |
3059 | 0 | progressBarHandlers.put(Long.valueOf(id), handler); |
3060 | 0 | final JPanel progressPanel = progressBars.get(Long.valueOf(id)); |
3061 | 0 | if (handler.canCancel()) |
3062 | { | |
3063 | 0 | JButton cancel = new JButton( |
3064 | MessageManager.getString("action.cancel")); | |
3065 | 0 | final IProgressIndicator us = this; |
3066 | 0 | cancel.addActionListener(new ActionListener() |
3067 | { | |
3068 | ||
3069 | 0 | @Override |
3070 | public void actionPerformed(ActionEvent e) | |
3071 | { | |
3072 | 0 | handler.cancelActivity(id); |
3073 | 0 | us.setProgressBar(MessageManager |
3074 | .formatMessage("label.cancelled_params", new Object[] | |
3075 | { ((JLabel) progressPanel.getComponent(0)).getText() }), | |
3076 | id); | |
3077 | } | |
3078 | }); | |
3079 | 0 | progressPanel.add(cancel, BorderLayout.EAST); |
3080 | } | |
3081 | } | |
3082 | ||
3083 | 0 | @Override |
3084 | public String getMessage(long id) | |
3085 | { | |
3086 | 0 | return progressBarMessages.get(id); |
3087 | } | |
3088 | ||
3089 | /** | |
3090 | * change the text shown alongside a progress bar | |
3091 | * | |
3092 | * @param id | |
3093 | * @param message | |
3094 | */ | |
3095 | 0 | @Override |
3096 | public void setProgressBarMessage(long id, String message) | |
3097 | { | |
3098 | 0 | Container progBar = progressBars.get(id); |
3099 | 0 | if (progBar == null || progBar.getComponentCount() == 0) |
3100 | { | |
3101 | 0 | return; |
3102 | } | |
3103 | 0 | for (Component component : progBar.getComponents()) |
3104 | { | |
3105 | 0 | if (component.getClass().equals(JLabel.class)) |
3106 | { | |
3107 | 0 | ((JLabel) component).setText(message); |
3108 | 0 | ; |
3109 | 0 | progBar.revalidate(); |
3110 | } | |
3111 | } | |
3112 | } | |
3113 | ||
3114 | /** | |
3115 | * | |
3116 | * @return true if any progress bars are still active | |
3117 | */ | |
3118 | 10 | @Override |
3119 | public boolean operationInProgress() | |
3120 | { | |
3121 | 10 | if (progressBars != null && progressBars.size() > 0) |
3122 | { | |
3123 | 0 | return true; |
3124 | } | |
3125 | 10 | return false; |
3126 | } | |
3127 | ||
3128 | /** | |
3129 | * This will return the first AlignFrame holding the given viewport instance. | |
3130 | * It will break if there are more than one AlignFrames viewing a particular | |
3131 | * av. | |
3132 | * | |
3133 | * @param viewport | |
3134 | * @return alignFrame for viewport | |
3135 | */ | |
3136 | 1 | public static AlignFrame getAlignFrameFor(AlignViewportI viewport) |
3137 | { | |
3138 | 1 | if (desktop != null) |
3139 | { | |
3140 | 1 | AlignmentPanel[] aps = getAlignmentPanels( |
3141 | viewport.getSequenceSetId()); | |
3142 | 1 | for (int panel = 0; aps != null && panel < aps.length; panel++) |
3143 | { | |
3144 | 1 | if (aps[panel] != null && aps[panel].av == viewport) |
3145 | { | |
3146 | 1 | return aps[panel].alignFrame; |
3147 | } | |
3148 | } | |
3149 | } | |
3150 | 0 | return null; |
3151 | } | |
3152 | ||
3153 | 0 | public VamsasApplication getVamsasApplication() |
3154 | { | |
3155 | // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS | |
3156 | 0 | return null; |
3157 | ||
3158 | } | |
3159 | ||
3160 | /** | |
3161 | * flag set if jalview GUI is being operated programmatically | |
3162 | */ | |
3163 | private boolean inBatchMode = false; | |
3164 | ||
3165 | /** | |
3166 | * check if jalview GUI is being operated programmatically | |
3167 | * | |
3168 | * @return inBatchMode | |
3169 | */ | |
3170 | 27 | public boolean isInBatchMode() |
3171 | { | |
3172 | 27 | return inBatchMode; |
3173 | } | |
3174 | ||
3175 | /** | |
3176 | * set flag if jalview GUI is being operated programmatically | |
3177 | * | |
3178 | * @param inBatchMode | |
3179 | */ | |
3180 | 145 | public void setInBatchMode(boolean inBatchMode) |
3181 | { | |
3182 | 145 | this.inBatchMode = inBatchMode; |
3183 | } | |
3184 | ||
3185 | /** | |
3186 | * start service discovery and wait till it is done | |
3187 | */ | |
3188 | 65 | public void startServiceDiscovery() |
3189 | { | |
3190 | 65 | startServiceDiscovery(false); |
3191 | } | |
3192 | ||
3193 | /** | |
3194 | * start service discovery threads - blocking or non-blocking | |
3195 | * | |
3196 | * @param blocking | |
3197 | */ | |
3198 | 65 | public void startServiceDiscovery(boolean blocking) |
3199 | { | |
3200 | 65 | startServiceDiscovery(blocking, false); |
3201 | } | |
3202 | ||
3203 | /** | |
3204 | * start service discovery threads | |
3205 | * | |
3206 | * @param blocking | |
3207 | * - false means call returns immediately | |
3208 | * @param ignore_SHOW_JWS2_SERVICES_preference | |
3209 | * - when true JABA services are discovered regardless of user's JWS2 | |
3210 | * discovery preference setting | |
3211 | */ | |
3212 | 65 | public void startServiceDiscovery(boolean blocking, |
3213 | boolean ignore_SHOW_JWS2_SERVICES_preference) | |
3214 | { | |
3215 | 65 | boolean alive = true; |
3216 | 65 | Thread t0 = null, t1 = null, t2 = null; |
3217 | // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release | |
3218 | 65 | if (true) |
3219 | { | |
3220 | // todo: changesupport handlers need to be transferred | |
3221 | 65 | if (discoverer == null) |
3222 | { | |
3223 | 6 | discoverer = new jalview.ws.jws1.Discoverer(); |
3224 | // register PCS handler for desktop. | |
3225 | 6 | discoverer.addPropertyChangeListener(changeSupport); |
3226 | } | |
3227 | // JAL-940 - disabled JWS1 service configuration - always start discoverer | |
3228 | // until we phase out completely | |
3229 | 65 | (t0 = new Thread(discoverer)).start(); |
3230 | } | |
3231 | ||
3232 | 65 | if (ignore_SHOW_JWS2_SERVICES_preference |
3233 | || Cache.getDefault("SHOW_JWS2_SERVICES", true)) | |
3234 | { | |
3235 | 65 | t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() |
3236 | .startDiscoverer(changeSupport); | |
3237 | } | |
3238 | 65 | Thread t3 = null; |
3239 | { | |
3240 | // TODO: do rest service discovery | |
3241 | } | |
3242 | 65 | if (blocking) |
3243 | { | |
3244 | 0 | while (alive) |
3245 | { | |
3246 | 0 | try |
3247 | { | |
3248 | 0 | Thread.sleep(15); |
3249 | } catch (Exception e) | |
3250 | { | |
3251 | } | |
3252 | 0 | alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) |
3253 | || (t3 != null && t3.isAlive()) | |
3254 | || (t0 != null && t0.isAlive()); | |
3255 | } | |
3256 | } | |
3257 | } | |
3258 | ||
3259 | /** | |
3260 | * called to check if the service discovery process completed successfully. | |
3261 | * | |
3262 | * @param evt | |
3263 | */ | |
3264 | 2043 | protected void JalviewServicesChanged(PropertyChangeEvent evt) |
3265 | { | |
3266 | 2043 | if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) |
3267 | { | |
3268 | 2043 | final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() |
3269 | .getErrorMessages(); | |
3270 | 2043 | if (ermsg != null) |
3271 | { | |
3272 | 0 | if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) |
3273 | { | |
3274 | 0 | if (serviceChangedDialog == null) |
3275 | { | |
3276 | // only run if we aren't already displaying one of these. | |
3277 | 0 | addDialogThread(serviceChangedDialog = new Runnable() |
3278 | { | |
3279 | 0 | @Override |
3280 | public void run() | |
3281 | { | |
3282 | ||
3283 | /* | |
3284 | * JalviewDialog jd =new JalviewDialog() { | |
3285 | * | |
3286 | * @Override protected void cancelPressed() { // TODO Auto-generated method stub | |
3287 | * | |
3288 | * }@Override protected void okPressed() { // TODO Auto-generated method stub | |
3289 | * | |
3290 | * }@Override protected void raiseClosed() { // TODO Auto-generated method stub | |
3291 | * | |
3292 | * } }; jd.initDialogFrame(new JLabel("<html><table width=\"450\"><tr><td>" + | |
3293 | * ermsg + | |
3294 | * "<br/>It may be that you have invalid JABA URLs in your web service preferences," | |
3295 | * + " or mis-configured HTTP proxy settings.<br/>" + | |
3296 | * "Check the <em>Connections</em> and <em>Web services</em> tab of the" + | |
3297 | * " Tools->Preferences dialog box to change them.</td></tr></table></html>" ), | |
3298 | * true, true, "Web Service Configuration Problem", 450, 400); | |
3299 | * | |
3300 | * jd.waitForInput(); | |
3301 | */ | |
3302 | 0 | JvOptionPane.showConfirmDialog(Desktop.desktop, |
3303 | new JLabel("<html><table width=\"450\"><tr><td>" | |
3304 | + ermsg + "</td></tr></table>" | |
3305 | + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences," | |
3306 | + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>" | |
3307 | + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the" | |
3308 | + " Tools->Preferences dialog box to change them.</p></html>"), | |
3309 | "Web Service Configuration Problem", | |
3310 | JvOptionPane.DEFAULT_OPTION, | |
3311 | JvOptionPane.ERROR_MESSAGE); | |
3312 | 0 | serviceChangedDialog = null; |
3313 | ||
3314 | } | |
3315 | }); | |
3316 | } | |
3317 | } | |
3318 | else | |
3319 | { | |
3320 | 0 | jalview.bin.Console.error( |
3321 | "Errors reported by JABA discovery service. Check web services preferences.\n" | |
3322 | + ermsg); | |
3323 | } | |
3324 | } | |
3325 | } | |
3326 | } | |
3327 | ||
3328 | private Runnable serviceChangedDialog = null; | |
3329 | ||
3330 | /** | |
3331 | * start a thread to open a URL in the configured browser. Pops up a warning | |
3332 | * dialog to the user if there is an exception when calling out to the browser | |
3333 | * to open the URL. | |
3334 | * | |
3335 | * @param url | |
3336 | */ | |
3337 | 0 | public static void showUrl(final String url) |
3338 | { | |
3339 | 0 | if (url != null && !url.trim().equals("")) |
3340 | { | |
3341 | 0 | jalview.bin.Console.info("Opening URL: " + url); |
3342 | 0 | showUrl(url, Desktop.instance); |
3343 | } | |
3344 | else | |
3345 | { | |
3346 | 0 | jalview.bin.Console.warn("Ignoring attempt to show an empty URL."); |
3347 | } | |
3348 | ||
3349 | } | |
3350 | ||
3351 | /** | |
3352 | * Like showUrl but allows progress handler to be specified | |
3353 | * | |
3354 | * @param url | |
3355 | * @param progress | |
3356 | * (null) or object implementing IProgressIndicator | |
3357 | */ | |
3358 | 0 | public static void showUrl(final String url, |
3359 | final IProgressIndicator progress) | |
3360 | { | |
3361 | 0 | new Thread(new Runnable() |
3362 | { | |
3363 | 0 | @Override |
3364 | public void run() | |
3365 | { | |
3366 | 0 | try |
3367 | { | |
3368 | 0 | if (progress != null) |
3369 | { | |
3370 | 0 | progress.setProgressBar(MessageManager |
3371 | .formatMessage("status.opening_params", new Object[] | |
3372 | { url }), this.hashCode()); | |
3373 | } | |
3374 | 0 | jalview.util.BrowserLauncher.openURL(url); |
3375 | } catch (Exception ex) | |
3376 | { | |
3377 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
3378 | MessageManager | |
3379 | .getString("label.web_browser_not_found_unix"), | |
3380 | MessageManager.getString("label.web_browser_not_found"), | |
3381 | JvOptionPane.WARNING_MESSAGE); | |
3382 | ||
3383 | 0 | ex.printStackTrace(); |
3384 | } | |
3385 | 0 | if (progress != null) |
3386 | { | |
3387 | 0 | progress.setProgressBar(null, this.hashCode()); |
3388 | } | |
3389 | } | |
3390 | }).start(); | |
3391 | } | |
3392 | ||
3393 | public static WsParamSetManager wsparamManager = null; | |
3394 | ||
3395 | 681 | public static ParamManager getUserParameterStore() |
3396 | { | |
3397 | 681 | if (wsparamManager == null) |
3398 | { | |
3399 | 6 | wsparamManager = new WsParamSetManager(); |
3400 | } | |
3401 | 681 | return wsparamManager; |
3402 | } | |
3403 | ||
3404 | /** | |
3405 | * static hyperlink handler proxy method for use by Jalview's internal windows | |
3406 | * | |
3407 | * @param e | |
3408 | */ | |
3409 | 0 | public static void hyperlinkUpdate(HyperlinkEvent e) |
3410 | { | |
3411 | 0 | if (e.getEventType() == EventType.ACTIVATED) |
3412 | { | |
3413 | 0 | String url = null; |
3414 | 0 | try |
3415 | { | |
3416 | 0 | url = e.getURL().toString(); |
3417 | 0 | Desktop.showUrl(url); |
3418 | } catch (Exception x) | |
3419 | { | |
3420 | 0 | if (url != null) |
3421 | { | |
3422 | 0 | jalview.bin.Console |
3423 | .error("Couldn't handle string " + url + " as a URL."); | |
3424 | } | |
3425 | // ignore any exceptions due to dud links. | |
3426 | } | |
3427 | ||
3428 | } | |
3429 | } | |
3430 | ||
3431 | /** | |
3432 | * single thread that handles display of dialogs to user. | |
3433 | */ | |
3434 | ExecutorService dialogExecutor = Executors.newFixedThreadPool(3); | |
3435 | ||
3436 | /** | |
3437 | * flag indicating if dialogExecutor should try to acquire a permit | |
3438 | */ | |
3439 | private volatile boolean dialogPause = true; | |
3440 | ||
3441 | /** | |
3442 | * pause the queue | |
3443 | */ | |
3444 | private Semaphore block = new Semaphore(0); | |
3445 | ||
3446 | private static groovy.console.ui.Console groovyConsole; | |
3447 | ||
3448 | /** | |
3449 | * add another dialog thread to the queue | |
3450 | * | |
3451 | * @param prompter | |
3452 | */ | |
3453 | 144 | public void addDialogThread(final Runnable prompter) |
3454 | { | |
3455 | 144 | dialogExecutor.submit(new Runnable() |
3456 | { | |
3457 | 144 | @Override |
3458 | public void run() | |
3459 | { | |
3460 | 144 | if (dialogPause) |
3461 | { | |
3462 | 44 | acquireDialogQueue(); |
3463 | } | |
3464 | 137 | if (instance == null) |
3465 | { | |
3466 | 0 | return; |
3467 | } | |
3468 | 137 | try |
3469 | { | |
3470 | 137 | SwingUtilities.invokeAndWait(prompter); |
3471 | } catch (Exception q) | |
3472 | { | |
3473 | 9 | jalview.bin.Console.warn("Unexpected Exception in dialog thread.", |
3474 | q); | |
3475 | } | |
3476 | } | |
3477 | }); | |
3478 | } | |
3479 | ||
3480 | private boolean dialogQueueStarted = false; | |
3481 | ||
3482 | 75 | public void startDialogQueue() |
3483 | { | |
3484 | 75 | if (dialogQueueStarted) |
3485 | { | |
3486 | 0 | return; |
3487 | } | |
3488 | // set the flag so we don't pause waiting for another permit and semaphore | |
3489 | // the current task to begin | |
3490 | 75 | releaseDialogQueue(); |
3491 | 75 | dialogQueueStarted = true; |
3492 | } | |
3493 | ||
3494 | 169 | public void acquireDialogQueue() |
3495 | { | |
3496 | 169 | try |
3497 | { | |
3498 | 169 | block.acquire(); |
3499 | 134 | dialogPause = true; |
3500 | } catch (InterruptedException e) | |
3501 | { | |
3502 | 28 | jalview.bin.Console.debug("Interruption when acquiring DialogueQueue", |
3503 | e); | |
3504 | } | |
3505 | } | |
3506 | ||
3507 | 199 | public void releaseDialogQueue() |
3508 | { | |
3509 | 199 | if (!dialogPause) |
3510 | { | |
3511 | 30 | return; |
3512 | } | |
3513 | 169 | block.release(); |
3514 | 169 | dialogPause = false; |
3515 | } | |
3516 | ||
3517 | /** | |
3518 | * Outputs an image of the desktop to file in EPS format, after prompting the | |
3519 | * user for choice of Text or Lineart character rendering (unless a preference | |
3520 | * has been set). The file name is generated as | |
3521 | * | |
3522 | * <pre> | |
3523 | * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds | |
3524 | * </pre> | |
3525 | */ | |
3526 | 0 | @Override |
3527 | protected void snapShotWindow_actionPerformed(ActionEvent e) | |
3528 | { | |
3529 | // currently the menu option to do this is not shown | |
3530 | 0 | invalidate(); |
3531 | ||
3532 | 0 | int width = getWidth(); |
3533 | 0 | int height = getHeight(); |
3534 | 0 | File of = new File( |
3535 | "Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); | |
3536 | 0 | ImageWriterI writer = new ImageWriterI() |
3537 | { | |
3538 | 0 | @Override |
3539 | public void exportImage(Graphics g) throws Exception | |
3540 | { | |
3541 | 0 | paintAll(g); |
3542 | 0 | jalview.bin.Console.info("Successfully written snapshot to file " |
3543 | + of.getAbsolutePath()); | |
3544 | } | |
3545 | }; | |
3546 | 0 | String title = "View of desktop"; |
3547 | 0 | ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, |
3548 | title); | |
3549 | 0 | try |
3550 | { | |
3551 | 0 | exporter.doExport(of, this, width, height, title); |
3552 | } catch (ImageOutputException ioex) | |
3553 | { | |
3554 | 0 | jalview.bin.Console.error( |
3555 | "Unexpected error whilst writing Jalview desktop snapshot as EPS", | |
3556 | ioex); | |
3557 | } | |
3558 | } | |
3559 | ||
3560 | /** | |
3561 | * Explode the views in the given SplitFrame into separate SplitFrame windows. | |
3562 | * This respects (remembers) any previous 'exploded geometry' i.e. the size | |
3563 | * and location last time the view was expanded (if any). However it does not | |
3564 | * remember the split pane divider location - this is set to match the | |
3565 | * 'exploding' frame. | |
3566 | * | |
3567 | * @param sf | |
3568 | */ | |
3569 | 0 | public void explodeViews(SplitFrame sf) |
3570 | { | |
3571 | 0 | AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame(); |
3572 | 0 | AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame(); |
3573 | 0 | List<? extends AlignmentViewPanel> topPanels = oldTopFrame |
3574 | .getAlignPanels(); | |
3575 | 0 | List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame |
3576 | .getAlignPanels(); | |
3577 | 0 | int viewCount = topPanels.size(); |
3578 | 0 | if (viewCount < 2) |
3579 | { | |
3580 | 0 | return; |
3581 | } | |
3582 | ||
3583 | /* | |
3584 | * Processing in reverse order works, forwards order leaves the first panels not | |
3585 | * visible. I don't know why! | |
3586 | */ | |
3587 | 0 | for (int i = viewCount - 1; i >= 0; i--) |
3588 | { | |
3589 | /* | |
3590 | * Make new top and bottom frames. These take over the respective AlignmentPanel | |
3591 | * objects, including their AlignmentViewports, so the cdna/protein | |
3592 | * relationships between the viewports is carried over to the new split frames. | |
3593 | * | |
3594 | * explodedGeometry holds the (x, y) position of the previously exploded | |
3595 | * SplitFrame, and the (width, height) of the AlignFrame component | |
3596 | */ | |
3597 | 0 | AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); |
3598 | 0 | AlignFrame newTopFrame = new AlignFrame(topPanel); |
3599 | 0 | newTopFrame.setSize(oldTopFrame.getSize()); |
3600 | 0 | newTopFrame.setVisible(true); |
3601 | 0 | Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) |
3602 | .getExplodedGeometry(); | |
3603 | 0 | if (geometry != null) |
3604 | { | |
3605 | 0 | newTopFrame.setSize(geometry.getSize()); |
3606 | } | |
3607 | ||
3608 | 0 | AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); |
3609 | 0 | AlignFrame newBottomFrame = new AlignFrame(bottomPanel); |
3610 | 0 | newBottomFrame.setSize(oldBottomFrame.getSize()); |
3611 | 0 | newBottomFrame.setVisible(true); |
3612 | 0 | geometry = ((AlignViewport) bottomPanel.getAlignViewport()) |
3613 | .getExplodedGeometry(); | |
3614 | 0 | if (geometry != null) |
3615 | { | |
3616 | 0 | newBottomFrame.setSize(geometry.getSize()); |
3617 | } | |
3618 | ||
3619 | 0 | topPanel.av.setGatherViewsHere(false); |
3620 | 0 | bottomPanel.av.setGatherViewsHere(false); |
3621 | 0 | JInternalFrame splitFrame = new SplitFrame(newTopFrame, |
3622 | newBottomFrame); | |
3623 | 0 | if (geometry != null) |
3624 | { | |
3625 | 0 | splitFrame.setLocation(geometry.getLocation()); |
3626 | } | |
3627 | 0 | Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); |
3628 | } | |
3629 | ||
3630 | /* | |
3631 | * Clear references to the panels (now relocated in the new SplitFrames) before | |
3632 | * closing the old SplitFrame. | |
3633 | */ | |
3634 | 0 | topPanels.clear(); |
3635 | 0 | bottomPanels.clear(); |
3636 | 0 | sf.close(); |
3637 | } | |
3638 | ||
3639 | /** | |
3640 | * Gather expanded split frames, sharing the same pairs of sequence set ids, | |
3641 | * back into the given SplitFrame as additional views. Note that the gathered | |
3642 | * frames may themselves have multiple views. | |
3643 | * | |
3644 | * @param source | |
3645 | */ | |
3646 | 0 | public void gatherViews(GSplitFrame source) |
3647 | { | |
3648 | /* | |
3649 | * special handling of explodedGeometry for a view within a SplitFrame: - it | |
3650 | * holds the (x, y) position of the enclosing SplitFrame, and the (width, | |
3651 | * height) of the AlignFrame component | |
3652 | */ | |
3653 | 0 | AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); |
3654 | 0 | AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); |
3655 | 0 | myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), |
3656 | source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); | |
3657 | 0 | myBottomFrame.viewport |
3658 | .setExplodedGeometry(new Rectangle(source.getX(), source.getY(), | |
3659 | myBottomFrame.getWidth(), myBottomFrame.getHeight())); | |
3660 | 0 | myTopFrame.viewport.setGatherViewsHere(true); |
3661 | 0 | myBottomFrame.viewport.setGatherViewsHere(true); |
3662 | 0 | String topViewId = myTopFrame.viewport.getSequenceSetId(); |
3663 | 0 | String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); |
3664 | ||
3665 | 0 | JInternalFrame[] frames = desktop.getAllFrames(); |
3666 | 0 | for (JInternalFrame frame : frames) |
3667 | { | |
3668 | 0 | if (frame instanceof SplitFrame && frame != source) |
3669 | { | |
3670 | 0 | SplitFrame sf = (SplitFrame) frame; |
3671 | 0 | AlignFrame topFrame = (AlignFrame) sf.getTopFrame(); |
3672 | 0 | AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame(); |
3673 | 0 | boolean gatherThis = false; |
3674 | 0 | for (int a = 0; a < topFrame.alignPanels.size(); a++) |
3675 | { | |
3676 | 0 | AlignmentPanel topPanel = topFrame.alignPanels.get(a); |
3677 | 0 | AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a); |
3678 | 0 | if (topViewId.equals(topPanel.av.getSequenceSetId()) |
3679 | && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) | |
3680 | { | |
3681 | 0 | gatherThis = true; |
3682 | 0 | topPanel.av.setGatherViewsHere(false); |
3683 | 0 | bottomPanel.av.setGatherViewsHere(false); |
3684 | 0 | topPanel.av.setExplodedGeometry( |
3685 | new Rectangle(sf.getLocation(), topFrame.getSize())); | |
3686 | 0 | bottomPanel.av.setExplodedGeometry( |
3687 | new Rectangle(sf.getLocation(), bottomFrame.getSize())); | |
3688 | 0 | myTopFrame.addAlignmentPanel(topPanel, false); |
3689 | 0 | myBottomFrame.addAlignmentPanel(bottomPanel, false); |
3690 | } | |
3691 | } | |
3692 | ||
3693 | 0 | if (gatherThis) |
3694 | { | |
3695 | 0 | topFrame.getAlignPanels().clear(); |
3696 | 0 | bottomFrame.getAlignPanels().clear(); |
3697 | 0 | sf.close(); |
3698 | } | |
3699 | } | |
3700 | } | |
3701 | ||
3702 | /* | |
3703 | * The dust settles...give focus to the tab we did this from. | |
3704 | */ | |
3705 | 0 | myTopFrame.setDisplayedView(myTopFrame.alignPanel); |
3706 | } | |
3707 | ||
3708 | 672 | public static groovy.console.ui.Console getGroovyConsole() |
3709 | { | |
3710 | 672 | return groovyConsole; |
3711 | } | |
3712 | ||
3713 | /** | |
3714 | * handles the payload of a drag and drop event. | |
3715 | * | |
3716 | * TODO refactor to desktop utilities class | |
3717 | * | |
3718 | * @param files | |
3719 | * - Data source strings extracted from the drop event | |
3720 | * @param protocols | |
3721 | * - protocol for each data source extracted from the drop event | |
3722 | * @param evt | |
3723 | * - the drop event | |
3724 | * @param t | |
3725 | * - the payload from the drop event | |
3726 | * @throws Exception | |
3727 | */ | |
3728 | 0 | public static void transferFromDropTarget(List<Object> files, |
3729 | List<DataSourceType> protocols, DropTargetDropEvent evt, | |
3730 | Transferable t) throws Exception | |
3731 | { | |
3732 | ||
3733 | 0 | DataFlavor uriListFlavor = new DataFlavor( |
3734 | "text/uri-list;class=java.lang.String"), urlFlavour = null; | |
3735 | 0 | try |
3736 | { | |
3737 | 0 | urlFlavour = new DataFlavor( |
3738 | "application/x-java-url; class=java.net.URL"); | |
3739 | } catch (ClassNotFoundException cfe) | |
3740 | { | |
3741 | 0 | jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", |
3742 | cfe); | |
3743 | } | |
3744 | ||
3745 | 0 | if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) |
3746 | { | |
3747 | ||
3748 | 0 | try |
3749 | { | |
3750 | 0 | java.net.URL url = (URL) t.getTransferData(urlFlavour); |
3751 | // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099 | |
3752 | // means url may be null. | |
3753 | 0 | if (url != null) |
3754 | { | |
3755 | 0 | protocols.add(DataSourceType.URL); |
3756 | 0 | files.add(url.toString()); |
3757 | 0 | jalview.bin.Console.debug("Drop handled as URL dataflavor " |
3758 | + files.get(files.size() - 1)); | |
3759 | 0 | return; |
3760 | } | |
3761 | else | |
3762 | { | |
3763 | 0 | if (Platform.isAMacAndNotJS()) |
3764 | { | |
3765 | 0 | jalview.bin.Console.errPrintln( |
3766 | "Please ignore plist error - occurs due to problem with java 8 on OSX"); | |
3767 | } | |
3768 | } | |
3769 | } catch (Throwable ex) | |
3770 | { | |
3771 | 0 | jalview.bin.Console.debug("URL drop handler failed.", ex); |
3772 | } | |
3773 | } | |
3774 | 0 | if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) |
3775 | { | |
3776 | // Works on Windows and MacOSX | |
3777 | 0 | jalview.bin.Console.debug("Drop handled as javaFileListFlavor"); |
3778 | 0 | for (Object file : (List) t |
3779 | .getTransferData(DataFlavor.javaFileListFlavor)) | |
3780 | { | |
3781 | 0 | files.add(file); |
3782 | 0 | protocols.add(DataSourceType.FILE); |
3783 | } | |
3784 | } | |
3785 | else | |
3786 | { | |
3787 | // Unix like behaviour | |
3788 | 0 | boolean added = false; |
3789 | 0 | String data = null; |
3790 | 0 | if (t.isDataFlavorSupported(uriListFlavor)) |
3791 | { | |
3792 | 0 | jalview.bin.Console.debug("Drop handled as uriListFlavor"); |
3793 | // This is used by Unix drag system | |
3794 | 0 | data = (String) t.getTransferData(uriListFlavor); |
3795 | } | |
3796 | 0 | if (data == null) |
3797 | { | |
3798 | // fallback to text: workaround - on OSX where there's a JVM bug | |
3799 | 0 | jalview.bin.Console |
3800 | .debug("standard URIListFlavor failed. Trying text"); | |
3801 | // try text fallback | |
3802 | 0 | DataFlavor textDf = new DataFlavor( |
3803 | "text/plain;class=java.lang.String"); | |
3804 | 0 | if (t.isDataFlavorSupported(textDf)) |
3805 | { | |
3806 | 0 | data = (String) t.getTransferData(textDf); |
3807 | } | |
3808 | ||
3809 | 0 | jalview.bin.Console.debug("Plain text drop content returned " |
3810 | 0 | + (data == null ? "Null - failed" : data)); |
3811 | ||
3812 | } | |
3813 | 0 | if (data != null) |
3814 | { | |
3815 | 0 | while (protocols.size() < files.size()) |
3816 | { | |
3817 | 0 | jalview.bin.Console.debug("Adding missing FILE protocol for " |
3818 | + files.get(protocols.size())); | |
3819 | 0 | protocols.add(DataSourceType.FILE); |
3820 | } | |
3821 | 0 | for (java.util.StringTokenizer st = new java.util.StringTokenizer( |
3822 | 0 | data, "\r\n"); st.hasMoreTokens();) |
3823 | { | |
3824 | 0 | added = true; |
3825 | 0 | String s = st.nextToken(); |
3826 | 0 | if (s.startsWith("#")) |
3827 | { | |
3828 | // the line is a comment (as per the RFC 2483) | |
3829 | 0 | continue; |
3830 | } | |
3831 | 0 | java.net.URI uri = new java.net.URI(s); |
3832 | 0 | if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) |
3833 | { | |
3834 | 0 | protocols.add(DataSourceType.URL); |
3835 | 0 | files.add(uri.toString()); |
3836 | } | |
3837 | else | |
3838 | { | |
3839 | // otherwise preserve old behaviour: catch all for file objects | |
3840 | 0 | java.io.File file = new java.io.File(uri); |
3841 | 0 | protocols.add(DataSourceType.FILE); |
3842 | 0 | files.add(file.toString()); |
3843 | } | |
3844 | } | |
3845 | } | |
3846 | ||
3847 | 0 | if (jalview.bin.Console.isDebugEnabled()) |
3848 | { | |
3849 | 0 | if (data == null || !added) |
3850 | { | |
3851 | ||
3852 | 0 | if (t.getTransferDataFlavors() != null |
3853 | && t.getTransferDataFlavors().length > 0) | |
3854 | { | |
3855 | 0 | jalview.bin.Console.debug( |
3856 | "Couldn't resolve drop data. Here are the supported flavors:"); | |
3857 | 0 | for (DataFlavor fl : t.getTransferDataFlavors()) |
3858 | { | |
3859 | 0 | jalview.bin.Console.debug( |
3860 | "Supported transfer dataflavor: " + fl.toString()); | |
3861 | 0 | Object df = t.getTransferData(fl); |
3862 | 0 | if (df != null) |
3863 | { | |
3864 | 0 | jalview.bin.Console.debug("Retrieves: " + df); |
3865 | } | |
3866 | else | |
3867 | { | |
3868 | 0 | jalview.bin.Console.debug("Retrieved nothing"); |
3869 | } | |
3870 | } | |
3871 | } | |
3872 | else | |
3873 | { | |
3874 | 0 | jalview.bin.Console |
3875 | .debug("Couldn't resolve dataflavor for drop: " | |
3876 | + t.toString()); | |
3877 | } | |
3878 | } | |
3879 | } | |
3880 | } | |
3881 | 0 | if (Platform.isWindowsAndNotJS()) |
3882 | { | |
3883 | 0 | jalview.bin.Console |
3884 | .debug("Scanning dropped content for Windows Link Files"); | |
3885 | ||
3886 | // resolve any .lnk files in the file drop | |
3887 | 0 | for (int f = 0; f < files.size(); f++) |
3888 | { | |
3889 | 0 | String source = files.get(f).toString().toLowerCase(Locale.ROOT); |
3890 | 0 | if (protocols.get(f).equals(DataSourceType.FILE) |
3891 | && (source.endsWith(".lnk") || source.endsWith(".url") | |
3892 | || source.endsWith(".site"))) | |
3893 | { | |
3894 | 0 | try |
3895 | { | |
3896 | 0 | Object obj = files.get(f); |
3897 | 0 | File lf = (obj instanceof File ? (File) obj |
3898 | : new File((String) obj)); | |
3899 | // process link file to get a URL | |
3900 | 0 | jalview.bin.Console.debug("Found potential link file: " + lf); |
3901 | 0 | WindowsShortcut wscfile = new WindowsShortcut(lf); |
3902 | 0 | String fullname = wscfile.getRealFilename(); |
3903 | 0 | protocols.set(f, FormatAdapter.checkProtocol(fullname)); |
3904 | 0 | files.set(f, fullname); |
3905 | 0 | jalview.bin.Console.debug("Parsed real filename " + fullname |
3906 | + " to extract protocol: " + protocols.get(f)); | |
3907 | } catch (Exception ex) | |
3908 | { | |
3909 | 0 | jalview.bin.Console.error( |
3910 | "Couldn't parse " + files.get(f) + " as a link file.", | |
3911 | ex); | |
3912 | } | |
3913 | } | |
3914 | } | |
3915 | } | |
3916 | } | |
3917 | ||
3918 | /** | |
3919 | * Sets the Preferences property for experimental features to True or False | |
3920 | * depending on the state of the controlling menu item | |
3921 | */ | |
3922 | 0 | @Override |
3923 | protected void showExperimental_actionPerformed(boolean selected) | |
3924 | { | |
3925 | 0 | Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); |
3926 | } | |
3927 | ||
3928 | /** | |
3929 | * Answers a (possibly empty) list of any structure viewer frames (currently | |
3930 | * for either Jmol or Chimera) which are currently open. This may optionally | |
3931 | * be restricted to viewers of a specified class, or viewers linked to a | |
3932 | * specified alignment panel. | |
3933 | * | |
3934 | * @param apanel | |
3935 | * if not null, only return viewers linked to this panel | |
3936 | * @param structureViewerClass | |
3937 | * if not null, only return viewers of this class | |
3938 | * @return | |
3939 | */ | |
3940 | 19 | public List<StructureViewerBase> getStructureViewers( |
3941 | AlignmentPanel apanel, | |
3942 | Class<? extends StructureViewerBase> structureViewerClass) | |
3943 | { | |
3944 | 19 | List<StructureViewerBase> result = new ArrayList<>(); |
3945 | 19 | JInternalFrame[] frames = Desktop.instance.getAllFrames(); |
3946 | ||
3947 | 19 | for (JInternalFrame frame : frames) |
3948 | { | |
3949 | 48 | if (frame instanceof StructureViewerBase) |
3950 | { | |
3951 | 17 | if (structureViewerClass == null |
3952 | || structureViewerClass.isInstance(frame)) | |
3953 | { | |
3954 | 17 | if (apanel == null |
3955 | || ((StructureViewerBase) frame).isLinkedWith(apanel)) | |
3956 | { | |
3957 | 17 | result.add((StructureViewerBase) frame); |
3958 | } | |
3959 | } | |
3960 | } | |
3961 | } | |
3962 | 19 | return result; |
3963 | } | |
3964 | ||
3965 | public static final String debugScaleMessage = "Desktop graphics transform scale="; | |
3966 | ||
3967 | private static boolean debugScaleMessageDone = false; | |
3968 | ||
3969 | 2520 | public static void debugScaleMessage(Graphics g) |
3970 | { | |
3971 | 2520 | if (debugScaleMessageDone) |
3972 | { | |
3973 | 2510 | return; |
3974 | } | |
3975 | // output used by tests to check HiDPI scaling settings in action | |
3976 | 10 | try |
3977 | { | |
3978 | 10 | Graphics2D gg = (Graphics2D) g; |
3979 | 10 | if (gg != null) |
3980 | { | |
3981 | 10 | AffineTransform t = gg.getTransform(); |
3982 | 10 | double scaleX = t.getScaleX(); |
3983 | 10 | double scaleY = t.getScaleY(); |
3984 | 10 | jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)"); |
3985 | 10 | jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)"); |
3986 | 10 | debugScaleMessageDone = true; |
3987 | } | |
3988 | else | |
3989 | { | |
3990 | 0 | jalview.bin.Console.debug("Desktop graphics null"); |
3991 | } | |
3992 | } catch (Exception e) | |
3993 | { | |
3994 | 0 | jalview.bin.Console.debug(Cache.getStackTraceString(e)); |
3995 | } | |
3996 | } | |
3997 | ||
3998 | /** | |
3999 | * closes the current instance window, but leaves the JVM running. Bypasses | |
4000 | * any shutdown prompts, but does not set window dispose on close in case JVM | |
4001 | * terminates. | |
4002 | */ | |
4003 | 81 | public static void closeDesktop() |
4004 | { | |
4005 | 81 | if (Desktop.instance != null) |
4006 | { | |
4007 | 81 | Desktop us = Desktop.instance; |
4008 | 81 | Desktop.instance.quitTheDesktop(false, false); |
4009 | // call dispose in a separate thread - try to avoid indirect deadlocks | |
4010 | 81 | if (us != null) |
4011 | { | |
4012 | 81 | new Thread(new Runnable() |
4013 | { | |
4014 | 81 | @Override |
4015 | public void run() | |
4016 | { | |
4017 | 81 | ExecutorService dex = us.dialogExecutor; |
4018 | 81 | if (dex != null) |
4019 | { | |
4020 | 38 | dex.shutdownNow(); |
4021 | 38 | us.dialogExecutor = null; |
4022 | 38 | us.block.drainPermits(); |
4023 | } | |
4024 | 81 | us.dispose(); |
4025 | } | |
4026 | }).start(); | |
4027 | } | |
4028 | } | |
4029 | } | |
4030 | ||
4031 | /** | |
4032 | * checks if any progress bars are being displayed in any of the windows | |
4033 | * managed by the desktop | |
4034 | * | |
4035 | * @return | |
4036 | */ | |
4037 | 15 | public boolean operationsAreInProgress() |
4038 | { | |
4039 | 15 | JInternalFrame[] frames = getAllFrames(); |
4040 | 15 | for (JInternalFrame frame : frames) |
4041 | { | |
4042 | 33 | if (frame instanceof IProgressIndicator) |
4043 | { | |
4044 | 15 | if (((IProgressIndicator) frame).operationInProgress()) |
4045 | { | |
4046 | 5 | return true; |
4047 | } | |
4048 | } | |
4049 | } | |
4050 | 10 | return operationInProgress(); |
4051 | } | |
4052 | ||
4053 | /** | |
4054 | * keep track of modal JvOptionPanes open as modal dialogs for AlignFrames. | |
4055 | * The way the modal JInternalFrame is made means it cannot be a child of an | |
4056 | * AlignFrame, so closing the AlignFrame might leave the modal open :( | |
4057 | */ | |
4058 | private static Map<AlignFrame, JInternalFrame> alignFrameModalMap = new HashMap<>(); | |
4059 | ||
4060 | 0 | protected static void addModal(AlignFrame af, JInternalFrame jif) |
4061 | { | |
4062 | 0 | alignFrameModalMap.put(af, jif); |
4063 | } | |
4064 | ||
4065 | 386 | protected static void closeModal(AlignFrame af) |
4066 | { | |
4067 | 386 | if (!alignFrameModalMap.containsKey(af)) |
4068 | { | |
4069 | 386 | return; |
4070 | } | |
4071 | 0 | JInternalFrame jif = alignFrameModalMap.get(af); |
4072 | 0 | if (jif != null) |
4073 | { | |
4074 | 0 | try |
4075 | { | |
4076 | 0 | jif.setClosed(true); |
4077 | } catch (PropertyVetoException e) | |
4078 | { | |
4079 | 0 | e.printStackTrace(); |
4080 | } | |
4081 | } | |
4082 | 0 | alignFrameModalMap.remove(af); |
4083 | } | |
4084 | ||
4085 | 0 | public void nonBlockingDialog(String title, String message, String button, |
4086 | int type, boolean scrollable, boolean modal) | |
4087 | { | |
4088 | 0 | nonBlockingDialog(title, message, null, button, type, scrollable, false, |
4089 | modal, -1); | |
4090 | } | |
4091 | ||
4092 | 1 | public void nonBlockingDialog(String title, String message, |
4093 | String boxtext, String button, int type, boolean scrollable, | |
4094 | boolean html, boolean modal, int timeout) | |
4095 | { | |
4096 | 1 | nonBlockingDialog(32, 2, title, message, boxtext, button, type, |
4097 | scrollable, html, modal, timeout); | |
4098 | } | |
4099 | ||
4100 | 1 | public void nonBlockingDialog(int width, int height, String title, |
4101 | String message, String boxtext, String button, int type, | |
4102 | boolean scrollable, boolean html, boolean modal, int timeout) | |
4103 | { | |
4104 | 1 | if (type < 0) |
4105 | { | |
4106 | 0 | type = JvOptionPane.WARNING_MESSAGE; |
4107 | } | |
4108 | 1 | JLabel jl = new JLabel(message); |
4109 | ||
4110 | 1 | JTextComponent jtc = null; |
4111 | 1 | if (html) |
4112 | { | |
4113 | 1 | JTextPane jtp = new JTextPane(); |
4114 | 1 | jtp.setContentType("text/html"); |
4115 | 1 | jtp.setEditable(false); |
4116 | 1 | jtp.setAutoscrolls(true); |
4117 | 1 | jtp.setText(boxtext); |
4118 | ||
4119 | 1 | jtc = jtp; |
4120 | } | |
4121 | else | |
4122 | { | |
4123 | 0 | JTextArea jta = new JTextArea(height, width); |
4124 | // jta.setLineWrap(true); | |
4125 | 0 | jta.setEditable(false); |
4126 | 0 | jta.setWrapStyleWord(true); |
4127 | 0 | jta.setAutoscrolls(true); |
4128 | 0 | jta.setText(boxtext); |
4129 | ||
4130 | 0 | jtc = jta; |
4131 | } | |
4132 | ||
4133 | 1 | JScrollPane jsp = scrollable |
4134 | ? new JScrollPane(jtc, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, | |
4135 | JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED) | |
4136 | : null; | |
4137 | ||
4138 | 1 | JvOptionPane jvp = JvOptionPane.newOptionDialog(this); |
4139 | ||
4140 | 1 | JPanel jp = new JPanel(); |
4141 | 1 | jp.setLayout(new BoxLayout(jp, BoxLayout.Y_AXIS)); |
4142 | ||
4143 | 1 | if (message != null) |
4144 | { | |
4145 | 1 | jl.setAlignmentX(Component.LEFT_ALIGNMENT); |
4146 | 1 | jp.add(jl); |
4147 | } | |
4148 | 1 | if (boxtext != null) |
4149 | { | |
4150 | 1 | if (scrollable) |
4151 | { | |
4152 | 0 | jsp.setAlignmentX(Component.LEFT_ALIGNMENT); |
4153 | 0 | jp.add(jsp); |
4154 | } | |
4155 | else | |
4156 | { | |
4157 | 1 | jtc.setAlignmentX(Component.LEFT_ALIGNMENT); |
4158 | 1 | jp.add(jtc); |
4159 | } | |
4160 | } | |
4161 | ||
4162 | 1 | jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> { |
4163 | }); | |
4164 | 1 | jvp.setTimeout(timeout); |
4165 | 1 | JButton jb = new JButton(button); |
4166 | 1 | jvp.showDialogOnTopAsync(this, jp, title, JOptionPane.YES_OPTION, type, |
4167 | null, new Object[] | |
4168 | { button }, button, modal, new JButton[] { jb }, false); | |
4169 | } | |
4170 | ||
4171 | 0 | @Override |
4172 | public AlignFrame getCurrentAlignFrame() | |
4173 | { | |
4174 | 0 | return Jalview.getInstance().getCurrentAlignFrame(); |
4175 | } | |
4176 | } |