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GAlignFrame | 66 | 763 | 291 |
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.jbgui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.Color; | |
25 | import java.awt.GridLayout; | |
26 | import java.awt.event.ActionEvent; | |
27 | import java.awt.event.ActionListener; | |
28 | import java.awt.event.FocusAdapter; | |
29 | import java.awt.event.FocusEvent; | |
30 | import java.awt.event.KeyEvent; | |
31 | import java.awt.event.MouseAdapter; | |
32 | import java.awt.event.MouseEvent; | |
33 | import java.util.HashMap; | |
34 | import java.util.List; | |
35 | import java.util.Map; | |
36 | ||
37 | import javax.swing.BorderFactory; | |
38 | import javax.swing.ButtonGroup; | |
39 | import javax.swing.JCheckBoxMenuItem; | |
40 | import javax.swing.JInternalFrame; | |
41 | import javax.swing.JLabel; | |
42 | import javax.swing.JMenu; | |
43 | import javax.swing.JMenuBar; | |
44 | import javax.swing.JMenuItem; | |
45 | import javax.swing.JPanel; | |
46 | import javax.swing.JRadioButtonMenuItem; | |
47 | import javax.swing.JTabbedPane; | |
48 | import javax.swing.KeyStroke; | |
49 | import javax.swing.event.ChangeEvent; | |
50 | import javax.swing.event.MenuEvent; | |
51 | import javax.swing.event.MenuListener; | |
52 | ||
53 | import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; | |
54 | import jalview.analysis.GeneticCodeI; | |
55 | import jalview.analysis.GeneticCodes; | |
56 | import jalview.api.SplitContainerI; | |
57 | import jalview.bin.Cache; | |
58 | import jalview.gui.JvSwingUtils; | |
59 | import jalview.gui.Preferences; | |
60 | import jalview.io.FileFormats; | |
61 | import jalview.schemes.ResidueColourScheme; | |
62 | import jalview.util.MessageManager; | |
63 | import jalview.util.Platform; | |
64 | ||
65 | @SuppressWarnings("serial") | |
66 | public class GAlignFrame extends JInternalFrame | |
67 | { | |
68 | protected JMenuBar alignFrameMenuBar = new JMenuBar(); | |
69 | ||
70 | protected JMenuItem closeMenuItem = new JMenuItem(); | |
71 | ||
72 | public JMenu webService = new JMenu();// BH 2019 was protected, but not | |
73 | // sufficient for AlignFrame thread run | |
74 | ||
75 | public JMenuItem webServiceNoServices;// BH 2019 was protected, but not | |
76 | // sufficient for AlignFrame thread run | |
77 | ||
78 | protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); | |
79 | ||
80 | protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); | |
81 | ||
82 | protected JMenu sortByAnnotScore = new JMenu(); | |
83 | ||
84 | public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not | |
85 | // sufficient for | |
86 | // AlignFrame.printWriter | |
87 | ||
88 | protected JMenu outputTextboxMenu = new JMenu(); | |
89 | ||
90 | protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); | |
91 | ||
92 | protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); | |
93 | ||
94 | protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); | |
95 | ||
96 | protected JMenuItem undoMenuItem = new JMenuItem(); | |
97 | ||
98 | protected JMenuItem redoMenuItem = new JMenuItem(); | |
99 | ||
100 | protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); | |
101 | ||
102 | protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); | |
103 | ||
104 | public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); | |
105 | ||
106 | JMenuItem copy = new JMenuItem(); | |
107 | ||
108 | JMenuItem copyHighlighted = new JMenuItem(); | |
109 | ||
110 | JMenuItem cut = new JMenuItem(); | |
111 | ||
112 | JMenu pasteMenu = new JMenu(); | |
113 | ||
114 | protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); | |
115 | ||
116 | protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); | |
117 | ||
118 | protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); | |
119 | ||
120 | protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); | |
121 | ||
122 | protected JCheckBoxMenuItem applyToAllGroups; | |
123 | ||
124 | protected JMenu colourMenu = new JMenu(); | |
125 | ||
126 | protected JMenuItem textColour; | |
127 | ||
128 | protected JCheckBoxMenuItem conservationMenuItem; | |
129 | ||
130 | protected JMenuItem modifyConservation; | |
131 | ||
132 | protected JCheckBoxMenuItem abovePIDThreshold; | |
133 | ||
134 | protected JMenuItem modifyPID; | |
135 | ||
136 | protected JRadioButtonMenuItem annotationColour; | |
137 | ||
138 | protected JMenu sortByTreeMenu = new JMenu(); | |
139 | ||
140 | protected JMenu sort = new JMenu(); | |
141 | ||
142 | protected JMenuItem calculateTree = new JMenuItem(); | |
143 | ||
144 | protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); | |
145 | ||
146 | protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); | |
147 | ||
148 | protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); | |
149 | ||
150 | protected JMenu showTranslation = new JMenu(); | |
151 | ||
152 | protected JMenuItem showReverse = new JMenuItem(); | |
153 | ||
154 | protected JMenuItem showReverseComplement = new JMenuItem(); | |
155 | ||
156 | protected JMenu showProducts = new JMenu(); | |
157 | ||
158 | protected JMenuItem runGroovy = new JMenuItem(); | |
159 | ||
160 | protected JMenuItem loadVcf; | |
161 | ||
162 | protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); | |
163 | ||
164 | protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); | |
165 | ||
166 | protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem(); | |
167 | ||
168 | protected JPanel statusPanel = new JPanel(); | |
169 | ||
170 | protected JMenuItem showAllSeqAnnotations = new JMenuItem(); | |
171 | ||
172 | protected JMenuItem hideAllSeqAnnotations = new JMenuItem(); | |
173 | ||
174 | protected JMenuItem showAllAlAnnotations = new JMenuItem(); | |
175 | ||
176 | protected JMenuItem hideAllAlAnnotations = new JMenuItem(); | |
177 | ||
178 | protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem(); | |
179 | ||
180 | protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); | |
181 | ||
182 | protected JTabbedPane tabbedPane = new JTabbedPane(); | |
183 | ||
184 | protected JMenuItem reload = new JMenuItem(); | |
185 | ||
186 | protected JMenu formatMenu = new JMenu(); | |
187 | ||
188 | protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem(); | |
189 | ||
190 | protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); | |
191 | ||
192 | protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); | |
193 | ||
194 | protected JMenuItem gatherViews = new JMenuItem(); | |
195 | ||
196 | protected JMenuItem expandViews = new JMenuItem(); | |
197 | ||
198 | protected JCheckBoxMenuItem threeDStructure = new JCheckBoxMenuItem(); | |
199 | ||
200 | protected JCheckBoxMenuItem jPred = new JCheckBoxMenuItem(); | |
201 | ||
202 | protected JCheckBoxMenuItem showSSConsensus = new JCheckBoxMenuItem(); | |
203 | ||
204 | protected JCheckBoxMenuItem showGroupSSConsensus = new JCheckBoxMenuItem(); | |
205 | ||
206 | protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); | |
207 | ||
208 | protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); | |
209 | ||
210 | protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); | |
211 | ||
212 | protected JCheckBoxMenuItem showSSConsensusHistogram = new JCheckBoxMenuItem(); | |
213 | ||
214 | protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); | |
215 | ||
216 | protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); | |
217 | ||
218 | protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); | |
219 | ||
220 | protected JMenuItem openFeatureSettings; | |
221 | ||
222 | private SequenceAnnotationOrder annotationSortOrder; | |
223 | ||
224 | private boolean showAutoCalculatedAbove = false; | |
225 | ||
226 | private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>(); | |
227 | ||
228 | private SplitContainerI splitFrame; | |
229 | ||
230 | 453 | public GAlignFrame() |
231 | { | |
232 | 453 | try |
233 | { | |
234 | 453 | setFrameIcon(null); |
235 | ||
236 | // for Web-page embedding using id=align-frame-div | |
237 | 453 | setName("jalview-alignment"); |
238 | ||
239 | 453 | jbInit(); |
240 | 452 | setJMenuBar(alignFrameMenuBar); |
241 | ||
242 | // dynamically fill save as menu with available formats | |
243 | 452 | for (String ff : FileFormats.getInstance().getWritableFormats(true)) |
244 | { | |
245 | 4972 | JMenuItem item = new JMenuItem(ff); |
246 | ||
247 | 4972 | item.addActionListener(new ActionListener() |
248 | { | |
249 | 0 | @Override |
250 | public void actionPerformed(ActionEvent e) | |
251 | { | |
252 | 0 | outputText_actionPerformed(e.getActionCommand()); |
253 | } | |
254 | }); | |
255 | ||
256 | 4972 | outputTextboxMenu.add(item); |
257 | } | |
258 | } catch (Exception e) | |
259 | { | |
260 | 0 | jalview.bin.Console.errPrintln(e.toString()); |
261 | } | |
262 | ||
263 | 452 | if (Platform.allowMnemonics()) // was "not mac and not JS" |
264 | { | |
265 | 452 | closeMenuItem.setMnemonic('C'); |
266 | 452 | outputTextboxMenu.setMnemonic('T'); |
267 | 452 | undoMenuItem.setMnemonic('Z'); |
268 | 452 | redoMenuItem.setMnemonic('0'); |
269 | 452 | copy.setMnemonic('C'); |
270 | 452 | cut.setMnemonic('U'); |
271 | 452 | pasteMenu.setMnemonic('P'); |
272 | 452 | reload.setMnemonic('R'); |
273 | } | |
274 | } | |
275 | ||
276 | 453 | private void jbInit() throws Exception |
277 | { | |
278 | 453 | setFrameIcon(null); |
279 | 453 | initColourMenu(); |
280 | ||
281 | 453 | JMenuItem saveAs = new JMenuItem( |
282 | MessageManager.getString("action.save_as")); | |
283 | 453 | ActionListener al = new ActionListener() |
284 | { | |
285 | 0 | @Override |
286 | public void actionPerformed(ActionEvent e) | |
287 | { | |
288 | 0 | saveAs_actionPerformed(); |
289 | } | |
290 | }; | |
291 | ||
292 | // FIXME getDefaultToolkit throws an exception in Headless mode | |
293 | 453 | KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, |
294 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
295 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
296 | false); | |
297 | 453 | addMenuActionAndAccelerator(keyStroke, saveAs, al); |
298 | ||
299 | 453 | closeMenuItem.setText(MessageManager.getString("action.close")); |
300 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
301 | jalview.util.ShortcutKeyMaskExWrapper | |
302 | .getMenuShortcutKeyMaskEx(), | |
303 | false); | |
304 | 453 | al = new ActionListener() |
305 | { | |
306 | 0 | @Override |
307 | public void actionPerformed(ActionEvent e) | |
308 | { | |
309 | 0 | closeMenuItem_actionPerformed(false); |
310 | } | |
311 | }; | |
312 | 453 | addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); |
313 | ||
314 | 453 | JMenu editMenu = new JMenu(MessageManager.getString("action.edit")); |
315 | 453 | JMenu viewMenu = new JMenu(MessageManager.getString("action.view")); |
316 | 453 | JMenu annotationsMenu = new JMenu( |
317 | MessageManager.getString("action.annotations")); | |
318 | 453 | JMenu showMenu = new JMenu(MessageManager.getString("action.show")); |
319 | 453 | colourMenu.setText(MessageManager.getString("action.colour")); |
320 | 453 | JMenu calculateMenu = new JMenu( |
321 | MessageManager.getString("action.calculate")); | |
322 | 453 | webService.setText(MessageManager.getString("action.web_service")); |
323 | 453 | JMenuItem selectAllSequenceMenuItem = new JMenuItem( |
324 | MessageManager.getString("action.select_all")); | |
325 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, |
326 | jalview.util.ShortcutKeyMaskExWrapper | |
327 | .getMenuShortcutKeyMaskEx(), | |
328 | false); | |
329 | 453 | al = new ActionListener() |
330 | { | |
331 | 0 | @Override |
332 | public void actionPerformed(ActionEvent e) | |
333 | { | |
334 | 0 | selectAllSequenceMenuItem_actionPerformed(e); |
335 | } | |
336 | }; | |
337 | 453 | addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al); |
338 | ||
339 | 453 | JMenuItem deselectAllSequenceMenuItem = new JMenuItem( |
340 | MessageManager.getString("action.deselect_all")); | |
341 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false); |
342 | 453 | al = new ActionListener() |
343 | { | |
344 | 0 | @Override |
345 | public void actionPerformed(ActionEvent e) | |
346 | { | |
347 | 0 | deselectAllSequenceMenuItem_actionPerformed(e); |
348 | } | |
349 | }; | |
350 | 453 | addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al); |
351 | ||
352 | 453 | JMenuItem invertSequenceMenuItem = new JMenuItem( |
353 | MessageManager.getString("action.invert_sequence_selection")); | |
354 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, |
355 | jalview.util.ShortcutKeyMaskExWrapper | |
356 | .getMenuShortcutKeyMaskEx(), | |
357 | false); | |
358 | 453 | al = new ActionListener() |
359 | { | |
360 | 0 | @Override |
361 | public void actionPerformed(ActionEvent e) | |
362 | { | |
363 | 0 | invertSequenceMenuItem_actionPerformed(e); |
364 | } | |
365 | }; | |
366 | 453 | addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al); |
367 | ||
368 | 453 | JMenuItem grpsFromSelection = new JMenuItem( |
369 | MessageManager.getString("action.make_groups_selection")); | |
370 | 453 | grpsFromSelection.addActionListener(new ActionListener() |
371 | { | |
372 | 0 | @Override |
373 | public void actionPerformed(ActionEvent e) | |
374 | { | |
375 | 0 | makeGrpsFromSelection_actionPerformed(e); |
376 | } | |
377 | }); | |
378 | 453 | JMenuItem expandAlignment = new JMenuItem( |
379 | MessageManager.getString("action.view_flanking_regions")); | |
380 | 453 | expandAlignment.setToolTipText( |
381 | MessageManager.getString("label.view_flanking_regions")); | |
382 | 453 | expandAlignment.addActionListener(new ActionListener() |
383 | { | |
384 | 0 | @Override |
385 | public void actionPerformed(ActionEvent e) | |
386 | { | |
387 | 0 | expand_newalign(e); |
388 | } | |
389 | }); | |
390 | 453 | JMenuItem remove2LeftMenuItem = new JMenuItem( |
391 | MessageManager.getString("action.remove_left")); | |
392 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, |
393 | jalview.util.ShortcutKeyMaskExWrapper | |
394 | .getMenuShortcutKeyMaskEx(), | |
395 | false); | |
396 | 453 | al = new ActionListener() |
397 | { | |
398 | 0 | @Override |
399 | public void actionPerformed(ActionEvent e) | |
400 | { | |
401 | 0 | remove2LeftMenuItem_actionPerformed(e); |
402 | } | |
403 | }; | |
404 | 453 | addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); |
405 | ||
406 | 453 | JMenuItem remove2RightMenuItem = new JMenuItem( |
407 | MessageManager.getString("action.remove_right")); | |
408 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, |
409 | jalview.util.ShortcutKeyMaskExWrapper | |
410 | .getMenuShortcutKeyMaskEx(), | |
411 | false); | |
412 | 453 | al = new ActionListener() |
413 | { | |
414 | 0 | @Override |
415 | public void actionPerformed(ActionEvent e) | |
416 | { | |
417 | 0 | remove2RightMenuItem_actionPerformed(e); |
418 | } | |
419 | }; | |
420 | 453 | addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al); |
421 | ||
422 | 453 | JMenuItem removeGappedColumnMenuItem = new JMenuItem( |
423 | MessageManager.getString("action.remove_empty_columns")); | |
424 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, |
425 | jalview.util.ShortcutKeyMaskExWrapper | |
426 | .getMenuShortcutKeyMaskEx(), | |
427 | false); | |
428 | 453 | al = new ActionListener() |
429 | { | |
430 | 0 | @Override |
431 | public void actionPerformed(ActionEvent e) | |
432 | { | |
433 | 0 | removeGappedColumnMenuItem_actionPerformed(e); |
434 | } | |
435 | }; | |
436 | 453 | addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al); |
437 | ||
438 | 453 | JMenuItem removeAllGapsMenuItem = new JMenuItem( |
439 | MessageManager.getString("action.remove_all_gaps")); | |
440 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, |
441 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
442 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
443 | false); | |
444 | 453 | al = new ActionListener() |
445 | { | |
446 | 0 | @Override |
447 | public void actionPerformed(ActionEvent e) | |
448 | { | |
449 | 0 | removeAllGapsMenuItem_actionPerformed(e); |
450 | } | |
451 | }; | |
452 | 453 | addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al); |
453 | ||
454 | 453 | JMenuItem justifyLeftMenuItem = new JMenuItem( |
455 | MessageManager.getString("action.left_justify")); | |
456 | 453 | justifyLeftMenuItem.setToolTipText( |
457 | MessageManager.getString("tooltip.left_justify")); | |
458 | 453 | justifyLeftMenuItem.addActionListener(new ActionListener() |
459 | { | |
460 | 0 | @Override |
461 | public void actionPerformed(ActionEvent e) | |
462 | { | |
463 | 0 | justifyLeftMenuItem_actionPerformed(e); |
464 | } | |
465 | }); | |
466 | 453 | JMenuItem justifyRightMenuItem = new JMenuItem( |
467 | MessageManager.getString("action.right_justify")); | |
468 | 453 | justifyRightMenuItem.setToolTipText( |
469 | MessageManager.getString("action.left_justify")); | |
470 | ||
471 | 453 | justifyRightMenuItem.addActionListener(new ActionListener() |
472 | { | |
473 | 0 | @Override |
474 | public void actionPerformed(ActionEvent e) | |
475 | { | |
476 | 0 | justifyRightMenuItem_actionPerformed(e); |
477 | } | |
478 | }); | |
479 | 453 | viewBoxesMenuItem.setText(MessageManager.getString("action.boxes")); |
480 | 453 | viewBoxesMenuItem.setState(true); |
481 | 453 | viewBoxesMenuItem.addActionListener(new ActionListener() |
482 | { | |
483 | 0 | @Override |
484 | public void actionPerformed(ActionEvent e) | |
485 | { | |
486 | 0 | viewBoxesMenuItem_actionPerformed(e); |
487 | } | |
488 | }); | |
489 | 453 | viewTextMenuItem.setText(MessageManager.getString("action.text")); |
490 | 453 | viewTextMenuItem.setState(true); |
491 | 453 | viewTextMenuItem.addActionListener(new ActionListener() |
492 | { | |
493 | 0 | @Override |
494 | public void actionPerformed(ActionEvent e) | |
495 | { | |
496 | 0 | viewTextMenuItem_actionPerformed(e); |
497 | } | |
498 | }); | |
499 | 453 | showNonconservedMenuItem |
500 | .setText(MessageManager.getString("label.show_non_conserved")); | |
501 | 453 | showNonconservedMenuItem.setState(false); |
502 | 453 | showNonconservedMenuItem.addActionListener(new ActionListener() |
503 | { | |
504 | 0 | @Override |
505 | public void actionPerformed(ActionEvent e) | |
506 | { | |
507 | 0 | showUnconservedMenuItem_actionPerformed(e); |
508 | } | |
509 | }); | |
510 | 453 | JMenuItem sortPairwiseMenuItem = new JMenuItem( |
511 | MessageManager.getString("action.by_pairwise_id")); | |
512 | 453 | sortPairwiseMenuItem.addActionListener(new ActionListener() |
513 | { | |
514 | 0 | @Override |
515 | public void actionPerformed(ActionEvent e) | |
516 | { | |
517 | 0 | sortPairwiseMenuItem_actionPerformed(e); |
518 | } | |
519 | }); | |
520 | 453 | JMenuItem sortIDMenuItem = new JMenuItem( |
521 | MessageManager.getString("action.by_id")); | |
522 | 453 | sortIDMenuItem.addActionListener(new ActionListener() |
523 | { | |
524 | 0 | @Override |
525 | public void actionPerformed(ActionEvent e) | |
526 | { | |
527 | 0 | sortIDMenuItem_actionPerformed(e); |
528 | } | |
529 | }); | |
530 | 453 | JMenuItem sortLengthMenuItem = new JMenuItem( |
531 | MessageManager.getString("action.by_length")); | |
532 | 453 | sortLengthMenuItem.addActionListener(new ActionListener() |
533 | { | |
534 | 0 | @Override |
535 | public void actionPerformed(ActionEvent e) | |
536 | { | |
537 | 0 | sortLengthMenuItem_actionPerformed(e); |
538 | } | |
539 | }); | |
540 | 453 | JMenuItem sortGroupMenuItem = new JMenuItem( |
541 | MessageManager.getString("action.by_group")); | |
542 | 453 | sortGroupMenuItem.addActionListener(new ActionListener() |
543 | { | |
544 | 0 | @Override |
545 | public void actionPerformed(ActionEvent e) | |
546 | { | |
547 | 0 | sortGroupMenuItem_actionPerformed(e); |
548 | } | |
549 | }); | |
550 | ||
551 | 453 | JMenuItem removeRedundancyMenuItem = new JMenuItem( |
552 | MessageManager.getString("action.remove_redundancy")); | |
553 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, |
554 | jalview.util.ShortcutKeyMaskExWrapper | |
555 | .getMenuShortcutKeyMaskEx(), | |
556 | false); | |
557 | 453 | al = new ActionListener() |
558 | { | |
559 | 0 | @Override |
560 | public void actionPerformed(ActionEvent e) | |
561 | { | |
562 | 0 | removeRedundancyMenuItem_actionPerformed(e); |
563 | } | |
564 | }; | |
565 | 453 | addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); |
566 | ||
567 | 453 | JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( |
568 | MessageManager.getString("action.pairwise_alignment")); | |
569 | 453 | pairwiseAlignmentMenuItem.addActionListener(new ActionListener() |
570 | { | |
571 | 0 | @Override |
572 | public void actionPerformed(ActionEvent e) | |
573 | { | |
574 | 0 | pairwiseAlignmentMenuItem_actionPerformed(e); |
575 | } | |
576 | }); | |
577 | ||
578 | 453 | this.getContentPane().setLayout(new BorderLayout()); |
579 | 453 | alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
580 | 453 | statusBar.setBackground(Color.white); |
581 | 453 | statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
582 | 453 | statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); |
583 | 453 | statusBar.setText(MessageManager.getString("label.status_bar")); |
584 | 453 | outputTextboxMenu |
585 | .setText(MessageManager.getString("label.out_to_textbox")); | |
586 | ||
587 | 453 | annotationPanelMenuItem.setActionCommand(""); |
588 | 453 | annotationPanelMenuItem |
589 | .setText(MessageManager.getString("label.show_annotations")); | |
590 | 453 | annotationPanelMenuItem |
591 | .setState(Cache.getDefault("SHOW_ANNOTATIONS", true)); | |
592 | 453 | annotationPanelMenuItem.addActionListener(new ActionListener() |
593 | { | |
594 | 0 | @Override |
595 | public void actionPerformed(ActionEvent e) | |
596 | { | |
597 | 0 | annotationPanelMenuItem_actionPerformed(e); |
598 | } | |
599 | }); | |
600 | 453 | showAllAlAnnotations.setText( |
601 | MessageManager.getString("label.show_all_al_annotations")); | |
602 | 453 | final boolean isAnnotationPanelShown = annotationPanelMenuItem |
603 | .getState(); | |
604 | 453 | showAllAlAnnotations.setEnabled(isAnnotationPanelShown); |
605 | 453 | showAllAlAnnotations.addActionListener(new ActionListener() |
606 | { | |
607 | 0 | @Override |
608 | public void actionPerformed(ActionEvent e) | |
609 | { | |
610 | 0 | showAllAnnotations_actionPerformed(false, true); |
611 | } | |
612 | }); | |
613 | 453 | hideAllAlAnnotations.setText( |
614 | MessageManager.getString("label.hide_all_al_annotations")); | |
615 | 453 | hideAllAlAnnotations.setEnabled(isAnnotationPanelShown); |
616 | 453 | hideAllAlAnnotations.addActionListener(new ActionListener() |
617 | { | |
618 | 0 | @Override |
619 | public void actionPerformed(ActionEvent e) | |
620 | { | |
621 | 0 | hideAllAnnotations_actionPerformed(false, true); |
622 | } | |
623 | }); | |
624 | 453 | showAllSeqAnnotations.setText( |
625 | MessageManager.getString("label.show_all_seq_annotations")); | |
626 | 453 | showAllSeqAnnotations.setEnabled(isAnnotationPanelShown); |
627 | 453 | showAllSeqAnnotations.addActionListener(new ActionListener() |
628 | { | |
629 | 0 | @Override |
630 | public void actionPerformed(ActionEvent e) | |
631 | { | |
632 | 0 | showAllAnnotations_actionPerformed(true, false); |
633 | } | |
634 | }); | |
635 | 453 | hideAllSeqAnnotations.setText( |
636 | MessageManager.getString("label.hide_all_seq_annotations")); | |
637 | 453 | hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown); |
638 | 453 | hideAllSeqAnnotations.addActionListener(new ActionListener() |
639 | { | |
640 | 0 | @Override |
641 | public void actionPerformed(ActionEvent e) | |
642 | { | |
643 | 0 | hideAllAnnotations_actionPerformed(true, false); |
644 | } | |
645 | }); | |
646 | 453 | SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder |
647 | .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, | |
648 | SequenceAnnotationOrder.NONE.name())); | |
649 | 453 | final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem( |
650 | MessageManager.getString("label.sort_annotations_by_sequence")); | |
651 | 453 | final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem( |
652 | MessageManager.getString("label.sort_annotations_by_label")); | |
653 | ||
654 | 453 | sortAnnBySequence.setSelected( |
655 | sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); | |
656 | 453 | sortAnnBySequence.addActionListener(new ActionListener() |
657 | { | |
658 | 0 | @Override |
659 | public void actionPerformed(ActionEvent e) | |
660 | { | |
661 | 0 | boolean newState = sortAnnBySequence.getState(); |
662 | 0 | sortAnnByLabel.setSelected(false); |
663 | 0 | setAnnotationSortOrder( |
664 | 0 | newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL |
665 | : SequenceAnnotationOrder.NONE); | |
666 | 0 | sortAnnotations_actionPerformed(); |
667 | } | |
668 | }); | |
669 | 453 | sortAnnByLabel.setSelected( |
670 | sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); | |
671 | 453 | sortAnnByLabel.addActionListener(new ActionListener() |
672 | { | |
673 | 0 | @Override |
674 | public void actionPerformed(ActionEvent e) | |
675 | { | |
676 | 0 | boolean newState = sortAnnByLabel.getState(); |
677 | 0 | sortAnnBySequence.setSelected(false); |
678 | 0 | setAnnotationSortOrder( |
679 | 0 | newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE |
680 | : SequenceAnnotationOrder.NONE); | |
681 | 0 | sortAnnotations_actionPerformed(); |
682 | } | |
683 | }); | |
684 | 453 | colourTextMenuItem = new JCheckBoxMenuItem( |
685 | MessageManager.getString("label.colour_text")); | |
686 | 453 | colourTextMenuItem.addActionListener(new ActionListener() |
687 | { | |
688 | 0 | @Override |
689 | public void actionPerformed(ActionEvent e) | |
690 | { | |
691 | 0 | colourTextMenuItem_actionPerformed(e); |
692 | } | |
693 | }); | |
694 | ||
695 | 453 | JMenuItem htmlMenuItem = new JMenuItem( |
696 | MessageManager.getString("label.html")); | |
697 | 453 | htmlMenuItem.addActionListener(new ActionListener() |
698 | { | |
699 | 0 | @Override |
700 | public void actionPerformed(ActionEvent e) | |
701 | { | |
702 | 0 | htmlMenuItem_actionPerformed(e); |
703 | } | |
704 | }); | |
705 | ||
706 | 453 | JMenuItem createBioJS = new JMenuItem( |
707 | MessageManager.getString("label.biojs_html_export")); | |
708 | 453 | createBioJS.addActionListener(new java.awt.event.ActionListener() |
709 | { | |
710 | 0 | @Override |
711 | public void actionPerformed(ActionEvent e) | |
712 | { | |
713 | 0 | bioJSMenuItem_actionPerformed(e); |
714 | } | |
715 | }); | |
716 | ||
717 | 453 | JMenuItem overviewMenuItem = new JMenuItem( |
718 | MessageManager.getString("label.overview_window")); | |
719 | 453 | overviewMenuItem.addActionListener(new ActionListener() |
720 | { | |
721 | 0 | @Override |
722 | public void actionPerformed(ActionEvent e) | |
723 | { | |
724 | 0 | overviewMenuItem_actionPerformed(e); |
725 | } | |
726 | }); | |
727 | ||
728 | 453 | undoMenuItem.setEnabled(false); |
729 | 453 | undoMenuItem.setText(MessageManager.getString("action.undo")); |
730 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, |
731 | jalview.util.ShortcutKeyMaskExWrapper | |
732 | .getMenuShortcutKeyMaskEx(), | |
733 | false); | |
734 | 453 | al = new ActionListener() |
735 | { | |
736 | 0 | @Override |
737 | public void actionPerformed(ActionEvent e) | |
738 | { | |
739 | 0 | undoMenuItem_actionPerformed(e); |
740 | } | |
741 | }; | |
742 | 453 | addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); |
743 | ||
744 | 453 | redoMenuItem.setEnabled(false); |
745 | 453 | redoMenuItem.setText(MessageManager.getString("action.redo")); |
746 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, |
747 | jalview.util.ShortcutKeyMaskExWrapper | |
748 | .getMenuShortcutKeyMaskEx(), | |
749 | false); | |
750 | 453 | al = new ActionListener() |
751 | { | |
752 | 0 | @Override |
753 | public void actionPerformed(ActionEvent e) | |
754 | { | |
755 | 0 | redoMenuItem_actionPerformed(e); |
756 | } | |
757 | }; | |
758 | 453 | addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); |
759 | ||
760 | 453 | wrapMenuItem.setText(MessageManager.getString("label.wrap")); |
761 | 453 | wrapMenuItem.addActionListener(new ActionListener() |
762 | { | |
763 | 0 | @Override |
764 | public void actionPerformed(ActionEvent e) | |
765 | { | |
766 | 0 | wrapMenuItem_actionPerformed(e); |
767 | } | |
768 | }); | |
769 | ||
770 | 453 | JMenuItem printMenuItem = new JMenuItem( |
771 | MessageManager.getString("action.print")); | |
772 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, |
773 | jalview.util.ShortcutKeyMaskExWrapper | |
774 | .getMenuShortcutKeyMaskEx(), | |
775 | false); | |
776 | 453 | al = new ActionListener() |
777 | { | |
778 | 0 | @Override |
779 | public void actionPerformed(ActionEvent e) | |
780 | { | |
781 | 0 | printMenuItem_actionPerformed(e); |
782 | } | |
783 | }; | |
784 | 453 | addMenuActionAndAccelerator(keyStroke, printMenuItem, al); |
785 | ||
786 | 453 | renderGapsMenuItem |
787 | .setText(MessageManager.getString("action.show_gaps")); | |
788 | 453 | renderGapsMenuItem.setState(true); |
789 | 453 | renderGapsMenuItem.addActionListener(new ActionListener() |
790 | { | |
791 | 0 | @Override |
792 | public void actionPerformed(ActionEvent e) | |
793 | { | |
794 | 0 | renderGapsMenuItem_actionPerformed(e); |
795 | } | |
796 | }); | |
797 | ||
798 | 453 | JMenuItem findMenuItem = new JMenuItem( |
799 | MessageManager.getString("action.find")); | |
800 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, |
801 | jalview.util.ShortcutKeyMaskExWrapper | |
802 | .getMenuShortcutKeyMaskEx(), | |
803 | false); | |
804 | 453 | findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, |
805 | MessageManager.getString("label.find_tip"))); | |
806 | 453 | al = new ActionListener() |
807 | { | |
808 | 0 | @Override |
809 | public void actionPerformed(ActionEvent e) | |
810 | { | |
811 | 0 | findMenuItem_actionPerformed(e); |
812 | } | |
813 | }; | |
814 | 453 | addMenuActionAndAccelerator(keyStroke, findMenuItem, al); |
815 | ||
816 | 453 | showSeqFeatures.setText( |
817 | MessageManager.getString("label.show_sequence_features")); | |
818 | 453 | showSeqFeatures.addActionListener(new ActionListener() |
819 | { | |
820 | 0 | @Override |
821 | public void actionPerformed(ActionEvent actionEvent) | |
822 | { | |
823 | 0 | showSeqFeatures_actionPerformed(actionEvent); |
824 | } | |
825 | }); | |
826 | /* | |
827 | * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); | |
828 | * showSeqFeaturesHeight.addActionListener(new ActionListener() { public | |
829 | * void actionPerformed(ActionEvent actionEvent) { | |
830 | * showSeqFeaturesHeight_actionPerformed(actionEvent); } }); | |
831 | */ | |
832 | 453 | showDbRefsMenuitem |
833 | .setText(MessageManager.getString("label.show_database_refs")); | |
834 | 453 | showDbRefsMenuitem.addActionListener(new ActionListener() |
835 | { | |
836 | ||
837 | 0 | @Override |
838 | public void actionPerformed(ActionEvent e) | |
839 | { | |
840 | 0 | showDbRefs_actionPerformed(e); |
841 | } | |
842 | ||
843 | }); | |
844 | 453 | showNpFeatsMenuitem.setText( |
845 | MessageManager.getString("label.show_non_positional_features")); | |
846 | 453 | showNpFeatsMenuitem.addActionListener(new ActionListener() |
847 | { | |
848 | ||
849 | 0 | @Override |
850 | public void actionPerformed(ActionEvent e) | |
851 | { | |
852 | 0 | showNpFeats_actionPerformed(e); |
853 | } | |
854 | ||
855 | }); | |
856 | 453 | showGroupConservation |
857 | .setText(MessageManager.getString("label.group_conservation")); | |
858 | 453 | showGroupConservation.addActionListener(new ActionListener() |
859 | { | |
860 | ||
861 | 0 | @Override |
862 | public void actionPerformed(ActionEvent e) | |
863 | { | |
864 | 0 | showGroupConservation_actionPerformed(e); |
865 | } | |
866 | ||
867 | }); | |
868 | ||
869 | 453 | showSSConsensus.setText(MessageManager |
870 | .getString("label.show_secondary_structure_consensus")); | |
871 | 453 | showSSConsensus.addActionListener(new ActionListener() |
872 | { | |
873 | ||
874 | 0 | @Override |
875 | public void actionPerformed(ActionEvent e) | |
876 | { | |
877 | 0 | showSSConsensus_actionPerformed(e); |
878 | } | |
879 | ||
880 | }); | |
881 | ||
882 | 453 | showGroupSSConsensus |
883 | .setText(MessageManager.getString("label.group_ss_consensus")); | |
884 | 453 | showGroupSSConsensus.addActionListener(new ActionListener() |
885 | { | |
886 | ||
887 | 0 | @Override |
888 | public void actionPerformed(ActionEvent e) | |
889 | { | |
890 | 0 | showGroupSSConsensus_actionPerformed(e); |
891 | } | |
892 | ||
893 | }); | |
894 | ||
895 | 453 | showGroupConsensus |
896 | .setText(MessageManager.getString("label.group_consensus")); | |
897 | 453 | showGroupConsensus.addActionListener(new ActionListener() |
898 | { | |
899 | ||
900 | 0 | @Override |
901 | public void actionPerformed(ActionEvent e) | |
902 | { | |
903 | 0 | showGroupConsensus_actionPerformed(e); |
904 | } | |
905 | ||
906 | }); | |
907 | 453 | showConsensusHistogram.setText( |
908 | MessageManager.getString("label.show_consensus_histogram")); | |
909 | 453 | showConsensusHistogram.addActionListener(new ActionListener() |
910 | { | |
911 | ||
912 | 0 | @Override |
913 | public void actionPerformed(ActionEvent e) | |
914 | { | |
915 | 0 | showConsensusHistogram_actionPerformed(e); |
916 | } | |
917 | ||
918 | }); | |
919 | 453 | showSSConsensusHistogram.setText( |
920 | MessageManager.getString("label.show_ssconsensus_histogram")); | |
921 | 453 | showSSConsensusHistogram.addActionListener(new ActionListener() |
922 | { | |
923 | ||
924 | 0 | @Override |
925 | public void actionPerformed(ActionEvent e) | |
926 | { | |
927 | 0 | showConsensusHistogram_actionPerformed(e); |
928 | } | |
929 | ||
930 | }); | |
931 | 453 | showSequenceLogo |
932 | .setText(MessageManager.getString("label.show_consensus_logo")); | |
933 | 453 | showSequenceLogo.addActionListener(new ActionListener() |
934 | { | |
935 | ||
936 | 0 | @Override |
937 | public void actionPerformed(ActionEvent e) | |
938 | { | |
939 | 0 | showSequenceLogo_actionPerformed(e); |
940 | } | |
941 | ||
942 | }); | |
943 | 453 | normaliseSequenceLogo |
944 | .setText(MessageManager.getString("label.norm_consensus_logo")); | |
945 | 453 | normaliseSequenceLogo.addActionListener(new ActionListener() |
946 | { | |
947 | ||
948 | 0 | @Override |
949 | public void actionPerformed(ActionEvent e) | |
950 | { | |
951 | 0 | normaliseSequenceLogo_actionPerformed(e); |
952 | } | |
953 | ||
954 | }); | |
955 | 453 | applyAutoAnnotationSettings |
956 | .setText(MessageManager.getString("label.apply_all_groups")); | |
957 | 453 | applyAutoAnnotationSettings.setState(false); |
958 | 453 | applyAutoAnnotationSettings.setVisible(true); |
959 | 453 | applyAutoAnnotationSettings.addActionListener(new ActionListener() |
960 | { | |
961 | 0 | @Override |
962 | public void actionPerformed(ActionEvent e) | |
963 | { | |
964 | 0 | applyAutoAnnotationSettings_actionPerformed(e); |
965 | } | |
966 | }); | |
967 | ||
968 | 453 | ButtonGroup buttonGroup = new ButtonGroup(); |
969 | 453 | final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem( |
970 | MessageManager.getString("label.show_first")); | |
971 | 453 | final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem( |
972 | MessageManager.getString("label.show_last")); | |
973 | 453 | buttonGroup.add(showAutoFirst); |
974 | 453 | buttonGroup.add(showAutoLast); |
975 | 453 | final boolean autoFirst = Cache |
976 | .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); | |
977 | 453 | showAutoFirst.setSelected(autoFirst); |
978 | 453 | setShowAutoCalculatedAbove(autoFirst); |
979 | 453 | showAutoFirst.addActionListener(new ActionListener() |
980 | { | |
981 | 0 | @Override |
982 | public void actionPerformed(ActionEvent e) | |
983 | { | |
984 | 0 | setShowAutoCalculatedAbove(showAutoFirst.isSelected()); |
985 | 0 | sortAnnotations_actionPerformed(); |
986 | } | |
987 | }); | |
988 | 453 | showAutoLast.setSelected(!showAutoFirst.isSelected()); |
989 | 453 | showAutoLast.addActionListener(new ActionListener() |
990 | { | |
991 | 0 | @Override |
992 | public void actionPerformed(ActionEvent e) | |
993 | { | |
994 | 0 | setShowAutoCalculatedAbove(!showAutoLast.isSelected()); |
995 | 0 | sortAnnotations_actionPerformed(); |
996 | } | |
997 | }); | |
998 | ||
999 | 453 | JMenuItem deleteGroups = new JMenuItem( |
1000 | MessageManager.getString("action.undefine_groups")); | |
1001 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, |
1002 | jalview.util.ShortcutKeyMaskExWrapper | |
1003 | .getMenuShortcutKeyMaskEx(), | |
1004 | false); | |
1005 | 453 | al = new ActionListener() |
1006 | { | |
1007 | 0 | @Override |
1008 | public void actionPerformed(ActionEvent e) | |
1009 | { | |
1010 | 0 | deleteGroups_actionPerformed(e); |
1011 | } | |
1012 | }; | |
1013 | 453 | addMenuActionAndAccelerator(keyStroke, deleteGroups, al); |
1014 | ||
1015 | 453 | JMenuItem annotationColumn = new JMenuItem( |
1016 | MessageManager.getString("action.select_by_annotation")); | |
1017 | 453 | annotationColumn.addActionListener(new ActionListener() |
1018 | { | |
1019 | 0 | @Override |
1020 | public void actionPerformed(ActionEvent e) | |
1021 | { | |
1022 | 0 | annotationColumn_actionPerformed(e); |
1023 | } | |
1024 | }); | |
1025 | ||
1026 | 453 | JMenuItem createGroup = new JMenuItem( |
1027 | MessageManager.getString("action.create_group")); | |
1028 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, |
1029 | jalview.util.ShortcutKeyMaskExWrapper | |
1030 | .getMenuShortcutKeyMaskEx(), | |
1031 | false); | |
1032 | 453 | al = new ActionListener() |
1033 | { | |
1034 | 0 | @Override |
1035 | public void actionPerformed(ActionEvent e) | |
1036 | { | |
1037 | 0 | createGroup_actionPerformed(e); |
1038 | } | |
1039 | }; | |
1040 | 453 | addMenuActionAndAccelerator(keyStroke, createGroup, al); |
1041 | ||
1042 | 453 | JMenuItem unGroup = new JMenuItem( |
1043 | MessageManager.getString("action.remove_group")); | |
1044 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, |
1045 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1046 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
1047 | false); | |
1048 | 453 | al = new ActionListener() |
1049 | { | |
1050 | 0 | @Override |
1051 | public void actionPerformed(ActionEvent e) | |
1052 | { | |
1053 | 0 | unGroup_actionPerformed(e); |
1054 | } | |
1055 | }; | |
1056 | 453 | addMenuActionAndAccelerator(keyStroke, unGroup, al); |
1057 | ||
1058 | 453 | copy.setText(MessageManager.getString("action.copy")); |
1059 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, |
1060 | jalview.util.ShortcutKeyMaskExWrapper | |
1061 | .getMenuShortcutKeyMaskEx(), | |
1062 | false); | |
1063 | ||
1064 | 453 | al = new ActionListener() |
1065 | { | |
1066 | 0 | @Override |
1067 | public void actionPerformed(ActionEvent e) | |
1068 | { | |
1069 | 0 | copy_actionPerformed(); |
1070 | } | |
1071 | }; | |
1072 | 453 | addMenuActionAndAccelerator(keyStroke, copy, al); |
1073 | ||
1074 | 453 | cut.setText(MessageManager.getString("action.cut")); |
1075 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, |
1076 | jalview.util.ShortcutKeyMaskExWrapper | |
1077 | .getMenuShortcutKeyMaskEx(), | |
1078 | false); | |
1079 | 453 | al = new ActionListener() |
1080 | { | |
1081 | 0 | @Override |
1082 | public void actionPerformed(ActionEvent e) | |
1083 | { | |
1084 | 0 | cut_actionPerformed(); |
1085 | } | |
1086 | }; | |
1087 | 453 | addMenuActionAndAccelerator(keyStroke, cut, al); |
1088 | ||
1089 | 453 | JMenuItem delete = new JMenuItem( |
1090 | MessageManager.getString("action.delete")); | |
1091 | 453 | delete.addActionListener(new ActionListener() |
1092 | { | |
1093 | 0 | @Override |
1094 | public void actionPerformed(ActionEvent e) | |
1095 | { | |
1096 | 0 | delete_actionPerformed(); |
1097 | } | |
1098 | }); | |
1099 | ||
1100 | 453 | pasteMenu.setText(MessageManager.getString("action.paste")); |
1101 | 453 | JMenuItem pasteNew = new JMenuItem( |
1102 | MessageManager.getString("label.to_new_alignment")); | |
1103 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, |
1104 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1105 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
1106 | false); | |
1107 | 453 | al = new ActionListener() |
1108 | { | |
1109 | 0 | @Override |
1110 | public void actionPerformed(ActionEvent e) | |
1111 | { | |
1112 | 0 | pasteNew_actionPerformed(e); |
1113 | } | |
1114 | }; | |
1115 | 453 | addMenuActionAndAccelerator(keyStroke, pasteNew, al); |
1116 | ||
1117 | 453 | JMenuItem pasteThis = new JMenuItem( |
1118 | MessageManager.getString("label.to_this_alignment")); | |
1119 | 453 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, |
1120 | jalview.util.ShortcutKeyMaskExWrapper | |
1121 | .getMenuShortcutKeyMaskEx(), | |
1122 | false); | |
1123 | 453 | al = new ActionListener() |
1124 | { | |
1125 | 0 | @Override |
1126 | public void actionPerformed(ActionEvent e) | |
1127 | { | |
1128 | 0 | pasteThis_actionPerformed(e); |
1129 | } | |
1130 | }; | |
1131 | 453 | addMenuActionAndAccelerator(keyStroke, pasteThis, al); |
1132 | ||
1133 | 453 | JMenuItem createPNG = new JMenuItem("PNG"); |
1134 | 453 | createPNG.addActionListener(new ActionListener() |
1135 | { | |
1136 | 0 | @Override |
1137 | public void actionPerformed(ActionEvent e) | |
1138 | { | |
1139 | 0 | createPNG_actionPerformed(e); |
1140 | } | |
1141 | }); | |
1142 | 453 | createPNG.setActionCommand( |
1143 | MessageManager.getString("label.save_png_image")); | |
1144 | ||
1145 | 453 | JMenuItem font = new JMenuItem(MessageManager.getString("action.font")); |
1146 | 453 | font.addActionListener(new ActionListener() |
1147 | { | |
1148 | 0 | @Override |
1149 | public void actionPerformed(ActionEvent e) | |
1150 | { | |
1151 | 0 | font_actionPerformed(e); |
1152 | } | |
1153 | }); | |
1154 | 453 | seqLimits.setText( |
1155 | MessageManager.getString("label.show_sequence_limits")); | |
1156 | 453 | seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true)); |
1157 | 453 | seqLimits.addActionListener(new ActionListener() |
1158 | { | |
1159 | 0 | @Override |
1160 | public void actionPerformed(ActionEvent e) | |
1161 | { | |
1162 | 0 | seqLimit_actionPerformed(e); |
1163 | } | |
1164 | }); | |
1165 | 453 | JMenuItem epsFile = new JMenuItem("EPS"); |
1166 | 453 | epsFile.addActionListener(new ActionListener() |
1167 | { | |
1168 | 0 | @Override |
1169 | public void actionPerformed(ActionEvent e) | |
1170 | { | |
1171 | 0 | createEPS_actionPerformed(e); |
1172 | } | |
1173 | }); | |
1174 | ||
1175 | 453 | JMenuItem createSVG = new JMenuItem("SVG"); |
1176 | 453 | createSVG.addActionListener(new ActionListener() |
1177 | { | |
1178 | 0 | @Override |
1179 | public void actionPerformed(ActionEvent e) | |
1180 | { | |
1181 | 0 | createSVG_actionPerformed(e); |
1182 | } | |
1183 | }); | |
1184 | ||
1185 | 453 | JMenuItem loadTreeMenuItem = new JMenuItem( |
1186 | MessageManager.getString("label.load_associated_tree")); | |
1187 | 453 | loadTreeMenuItem.setActionCommand( |
1188 | MessageManager.getString("label.load_tree_for_sequence_set")); | |
1189 | 453 | loadTreeMenuItem.addActionListener(new ActionListener() |
1190 | { | |
1191 | 0 | @Override |
1192 | public void actionPerformed(ActionEvent e) | |
1193 | { | |
1194 | 0 | loadTreeMenuItem_actionPerformed(e); |
1195 | } | |
1196 | }); | |
1197 | ||
1198 | 453 | scaleAbove.setVisible(false); |
1199 | 453 | scaleAbove.setText(MessageManager.getString("action.scale_above")); |
1200 | 453 | scaleAbove.addActionListener(new ActionListener() |
1201 | { | |
1202 | 0 | @Override |
1203 | public void actionPerformed(ActionEvent e) | |
1204 | { | |
1205 | 0 | scaleAbove_actionPerformed(e); |
1206 | } | |
1207 | }); | |
1208 | 453 | scaleLeft.setVisible(false); |
1209 | 453 | scaleLeft.setSelected(true); |
1210 | 453 | scaleLeft.setText(MessageManager.getString("action.scale_left")); |
1211 | 453 | scaleLeft.addActionListener(new ActionListener() |
1212 | { | |
1213 | 0 | @Override |
1214 | public void actionPerformed(ActionEvent e) | |
1215 | { | |
1216 | 0 | scaleLeft_actionPerformed(e); |
1217 | } | |
1218 | }); | |
1219 | 453 | scaleRight.setVisible(false); |
1220 | 453 | scaleRight.setSelected(true); |
1221 | 453 | scaleRight.setText(MessageManager.getString("action.scale_right")); |
1222 | 453 | scaleRight.addActionListener(new ActionListener() |
1223 | { | |
1224 | 0 | @Override |
1225 | public void actionPerformed(ActionEvent e) | |
1226 | { | |
1227 | 0 | scaleRight_actionPerformed(e); |
1228 | } | |
1229 | }); | |
1230 | 453 | centreColumnLabelsMenuItem.setVisible(true); |
1231 | 453 | centreColumnLabelsMenuItem.setState(false); |
1232 | 453 | centreColumnLabelsMenuItem.setText( |
1233 | MessageManager.getString("label.centre_column_labels")); | |
1234 | 453 | centreColumnLabelsMenuItem.addActionListener(new ActionListener() |
1235 | { | |
1236 | 0 | @Override |
1237 | public void actionPerformed(ActionEvent e) | |
1238 | { | |
1239 | 0 | centreColumnLabels_actionPerformed(e); |
1240 | } | |
1241 | }); | |
1242 | 453 | followHighlightMenuItem.setVisible(true); |
1243 | 453 | followHighlightMenuItem.setState(true); |
1244 | 453 | followHighlightMenuItem |
1245 | .setText(MessageManager.getString("label.automatic_scrolling")); | |
1246 | 453 | followHighlightMenuItem.addActionListener(new ActionListener() |
1247 | { | |
1248 | ||
1249 | 0 | @Override |
1250 | public void actionPerformed(ActionEvent e) | |
1251 | { | |
1252 | 0 | followHighlight_actionPerformed(); |
1253 | } | |
1254 | ||
1255 | }); | |
1256 | ||
1257 | 453 | sortByTreeMenu |
1258 | .setText(MessageManager.getString("action.by_tree_order")); | |
1259 | 453 | sort.setText(MessageManager.getString("action.sort")); |
1260 | 453 | sort.addMenuListener(new MenuListener() |
1261 | { | |
1262 | 0 | @Override |
1263 | public void menuSelected(MenuEvent e) | |
1264 | { | |
1265 | 0 | buildTreeSortMenu(); |
1266 | } | |
1267 | ||
1268 | 0 | @Override |
1269 | public void menuDeselected(MenuEvent e) | |
1270 | { | |
1271 | } | |
1272 | ||
1273 | 0 | @Override |
1274 | public void menuCanceled(MenuEvent e) | |
1275 | { | |
1276 | } | |
1277 | }); | |
1278 | 453 | sortByAnnotScore |
1279 | .setText(MessageManager.getString("label.sort_by_score")); | |
1280 | 453 | sort.add(sortByAnnotScore); |
1281 | 453 | sort.addMenuListener(new javax.swing.event.MenuListener() |
1282 | { | |
1283 | ||
1284 | 0 | @Override |
1285 | public void menuCanceled(MenuEvent e) | |
1286 | { | |
1287 | } | |
1288 | ||
1289 | 0 | @Override |
1290 | public void menuDeselected(MenuEvent e) | |
1291 | { | |
1292 | } | |
1293 | ||
1294 | 0 | @Override |
1295 | public void menuSelected(MenuEvent e) | |
1296 | { | |
1297 | 0 | buildSortByAnnotationScoresMenu(); |
1298 | } | |
1299 | }); | |
1300 | 453 | sortByAnnotScore.setVisible(false); |
1301 | ||
1302 | 453 | calculateTree |
1303 | .setText(MessageManager.getString("action.calculate_tree_pca")); | |
1304 | ||
1305 | 453 | padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); |
1306 | 453 | padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false)); |
1307 | 453 | padGapsMenuitem.addActionListener(new ActionListener() |
1308 | { | |
1309 | 0 | @Override |
1310 | public void actionPerformed(ActionEvent e) | |
1311 | { | |
1312 | 0 | padGapsMenuitem_actionPerformed(e); |
1313 | } | |
1314 | }); | |
1315 | 453 | JMenuItem vamsasStore = new JMenuItem( |
1316 | MessageManager.getString("label.vamsas_store")); | |
1317 | 453 | vamsasStore.setVisible(false); |
1318 | 453 | vamsasStore.addActionListener(new ActionListener() |
1319 | { | |
1320 | 0 | @Override |
1321 | public void actionPerformed(ActionEvent e) | |
1322 | { | |
1323 | 0 | vamsasStore_actionPerformed(e); |
1324 | } | |
1325 | }); | |
1326 | ||
1327 | /* | |
1328 | * Translate as cDNA with sub-menu of translation tables | |
1329 | */ | |
1330 | 453 | showTranslation |
1331 | .setText(MessageManager.getString("label.translate_cDNA")); | |
1332 | 453 | boolean first = true; |
1333 | 453 | for (final GeneticCodeI table : GeneticCodes.getInstance() |
1334 | .getCodeTables()) | |
1335 | { | |
1336 | 11309 | JMenuItem item = new JMenuItem(table.getId() + " " + table.getName()); |
1337 | 11308 | showTranslation.add(item); |
1338 | 11308 | item.addActionListener(new ActionListener() |
1339 | { | |
1340 | 0 | @Override |
1341 | public void actionPerformed(ActionEvent e) | |
1342 | { | |
1343 | 0 | showTranslation_actionPerformed(table); |
1344 | } | |
1345 | }); | |
1346 | 11308 | if (first) |
1347 | { | |
1348 | 453 | showTranslation.addSeparator(); |
1349 | } | |
1350 | 11308 | first = false; |
1351 | } | |
1352 | ||
1353 | 452 | showReverse.setText(MessageManager.getString("label.reverse")); |
1354 | 452 | showReverse.addActionListener(new ActionListener() |
1355 | { | |
1356 | 0 | @Override |
1357 | public void actionPerformed(ActionEvent e) | |
1358 | { | |
1359 | 0 | showReverse_actionPerformed(false); |
1360 | } | |
1361 | }); | |
1362 | 452 | showReverseComplement |
1363 | .setText(MessageManager.getString("label.reverse_complement")); | |
1364 | 452 | showReverseComplement.addActionListener(new ActionListener() |
1365 | { | |
1366 | 0 | @Override |
1367 | public void actionPerformed(ActionEvent e) | |
1368 | { | |
1369 | 0 | showReverse_actionPerformed(true); |
1370 | } | |
1371 | }); | |
1372 | ||
1373 | 452 | JMenuItem extractScores = new JMenuItem( |
1374 | MessageManager.getString("label.extract_scores")); | |
1375 | 452 | extractScores.addActionListener(new ActionListener() |
1376 | { | |
1377 | 0 | @Override |
1378 | public void actionPerformed(ActionEvent e) | |
1379 | { | |
1380 | 0 | extractScores_actionPerformed(e); |
1381 | } | |
1382 | }); | |
1383 | 452 | extractScores.setVisible(true); |
1384 | // JBPNote: TODO: make gui for regex based score extraction | |
1385 | ||
1386 | // for show products actions see AlignFrame.canShowProducts | |
1387 | 452 | showProducts.setText(MessageManager.getString("label.get_cross_refs")); |
1388 | ||
1389 | 452 | runGroovy.setText(MessageManager.getString("label.run_groovy")); |
1390 | 452 | runGroovy.setToolTipText( |
1391 | MessageManager.getString("label.run_groovy_tip")); | |
1392 | 452 | runGroovy.addActionListener(new ActionListener() |
1393 | { | |
1394 | 0 | @Override |
1395 | public void actionPerformed(ActionEvent e) | |
1396 | { | |
1397 | 0 | runGroovy_actionPerformed(); |
1398 | } | |
1399 | }); | |
1400 | ||
1401 | 452 | openFeatureSettings = new JMenuItem( |
1402 | MessageManager.getString("action.feature_settings")); | |
1403 | 452 | openFeatureSettings.addActionListener(new ActionListener() |
1404 | { | |
1405 | 0 | @Override |
1406 | public void actionPerformed(ActionEvent e) | |
1407 | { | |
1408 | 0 | featureSettings_actionPerformed(e); |
1409 | } | |
1410 | }); | |
1411 | ||
1412 | /* | |
1413 | * add sub-menu of database we can fetch from | |
1414 | */ | |
1415 | 452 | JMenuItem fetchSequence = new JMenuItem( |
1416 | MessageManager.getString("label.fetch_sequences")); | |
1417 | 452 | fetchSequence.addActionListener(new ActionListener() |
1418 | { | |
1419 | 0 | @Override |
1420 | public void actionPerformed(ActionEvent e) | |
1421 | { | |
1422 | 0 | fetchSequence_actionPerformed(); |
1423 | } | |
1424 | }); | |
1425 | ||
1426 | 452 | JMenuItem associatedData = new JMenuItem( |
1427 | MessageManager.getString("label.load_features_annotations")); | |
1428 | 452 | associatedData.addActionListener(new ActionListener() |
1429 | { | |
1430 | 0 | @Override |
1431 | public void actionPerformed(ActionEvent e) | |
1432 | { | |
1433 | 0 | associatedData_actionPerformed(e); |
1434 | } | |
1435 | }); | |
1436 | 452 | loadVcf = new JMenuItem( |
1437 | MessageManager.getString("label.load_vcf_file")); | |
1438 | 452 | loadVcf.setToolTipText(MessageManager.getString("label.load_vcf")); |
1439 | 452 | loadVcf.addActionListener(new ActionListener() |
1440 | { | |
1441 | 0 | @Override |
1442 | public void actionPerformed(ActionEvent e) | |
1443 | { | |
1444 | 0 | loadVcf_actionPerformed(); |
1445 | } | |
1446 | }); | |
1447 | 452 | autoCalculate.setText( |
1448 | MessageManager.getString("label.autocalculate_consensus")); | |
1449 | 452 | autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true)); |
1450 | 452 | autoCalculate.addActionListener(new ActionListener() |
1451 | { | |
1452 | 0 | @Override |
1453 | public void actionPerformed(ActionEvent e) | |
1454 | { | |
1455 | 0 | autoCalculate_actionPerformed(e); |
1456 | } | |
1457 | }); | |
1458 | 452 | sortByTree.setText( |
1459 | MessageManager.getString("label.sort_alignment_new_tree")); | |
1460 | 452 | sortByTree.setToolTipText("<html>" + MessageManager.getString( |
1461 | "label.enable_automatically_sort_alignment_when_open_new_tree")); | |
1462 | 452 | sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false)); |
1463 | 452 | sortByTree.addActionListener(new ActionListener() |
1464 | { | |
1465 | 0 | @Override |
1466 | public void actionPerformed(ActionEvent e) | |
1467 | { | |
1468 | 0 | sortByTreeOption_actionPerformed(e); |
1469 | } | |
1470 | }); | |
1471 | ||
1472 | 452 | listenToViewSelections.setText( |
1473 | MessageManager.getString("label.listen_for_selections")); | |
1474 | 452 | listenToViewSelections |
1475 | .setToolTipText("<html>" + MessageManager.getString( | |
1476 | "label.selections_mirror_selections_made_same_sequences_other_views")); | |
1477 | 452 | listenToViewSelections.setState(false); |
1478 | 452 | listenToViewSelections.addActionListener(new ActionListener() |
1479 | { | |
1480 | 0 | @Override |
1481 | public void actionPerformed(ActionEvent e) | |
1482 | { | |
1483 | 0 | listenToViewSelections_actionPerformed(e); |
1484 | } | |
1485 | }); | |
1486 | ||
1487 | 452 | JMenu addSequenceMenu = new JMenu( |
1488 | MessageManager.getString("label.add_sequences")); | |
1489 | 452 | JMenuItem addFromFile = new JMenuItem( |
1490 | MessageManager.getString("label.from_file")); | |
1491 | 452 | addFromFile.addActionListener(new ActionListener() |
1492 | { | |
1493 | 0 | @Override |
1494 | public void actionPerformed(ActionEvent e) | |
1495 | { | |
1496 | 0 | addFromFile_actionPerformed(e); |
1497 | } | |
1498 | }); | |
1499 | 452 | JMenuItem addFromText = new JMenuItem( |
1500 | MessageManager.getString("label.from_textbox")); | |
1501 | 452 | addFromText.addActionListener(new ActionListener() |
1502 | { | |
1503 | 0 | @Override |
1504 | public void actionPerformed(ActionEvent e) | |
1505 | { | |
1506 | 0 | addFromText_actionPerformed(e); |
1507 | } | |
1508 | }); | |
1509 | 452 | JMenuItem addFromURL = new JMenuItem( |
1510 | MessageManager.getString("label.from_url")); | |
1511 | 452 | addFromURL.addActionListener(new ActionListener() |
1512 | { | |
1513 | 0 | @Override |
1514 | public void actionPerformed(ActionEvent e) | |
1515 | { | |
1516 | 0 | addFromURL_actionPerformed(e); |
1517 | } | |
1518 | }); | |
1519 | 452 | JMenuItem exportFeatures = new JMenuItem( |
1520 | MessageManager.getString("label.export_features")); | |
1521 | 452 | exportFeatures.addActionListener(new ActionListener() |
1522 | { | |
1523 | 0 | @Override |
1524 | public void actionPerformed(ActionEvent e) | |
1525 | { | |
1526 | 0 | exportFeatures_actionPerformed(e); |
1527 | } | |
1528 | }); | |
1529 | 452 | JMenuItem exportAnnotations = new JMenuItem( |
1530 | MessageManager.getString("label.export_annotations")); | |
1531 | 452 | exportAnnotations.addActionListener(new ActionListener() |
1532 | { | |
1533 | 0 | @Override |
1534 | public void actionPerformed(ActionEvent e) | |
1535 | { | |
1536 | 0 | exportAnnotations_actionPerformed(e); |
1537 | } | |
1538 | }); | |
1539 | 452 | statusPanel.setLayout(new GridLayout()); |
1540 | 452 | JMenuItem showAllSeqs = new JMenuItem( |
1541 | MessageManager.getString("label.all_sequences")); | |
1542 | 452 | showAllSeqs.setToolTipText( |
1543 | MessageManager.getString("label.toggle_sequence_visibility")); | |
1544 | 452 | showAllSeqs.addActionListener(new ActionListener() |
1545 | { | |
1546 | 0 | @Override |
1547 | public void actionPerformed(ActionEvent e) | |
1548 | { | |
1549 | 0 | showAllSeqs_actionPerformed(e); |
1550 | } | |
1551 | }); | |
1552 | 452 | JMenuItem showAllColumns = new JMenuItem( |
1553 | MessageManager.getString("label.all_columns")); | |
1554 | 452 | showAllColumns.setToolTipText( |
1555 | MessageManager.getString("label.toggle_columns_visibility")); | |
1556 | 452 | showAllColumns.addActionListener(new ActionListener() |
1557 | { | |
1558 | 0 | @Override |
1559 | public void actionPerformed(ActionEvent e) | |
1560 | { | |
1561 | 0 | showAllColumns_actionPerformed(e); |
1562 | } | |
1563 | }); | |
1564 | 452 | JMenu hideMenu = new JMenu(MessageManager.getString("action.hide")); |
1565 | 452 | JMenuItem hideSelSequences = new JMenuItem( |
1566 | MessageManager.getString("label.selected_sequences")); | |
1567 | 452 | hideSelSequences.setToolTipText( |
1568 | MessageManager.getString("label.toggle_sequence_visibility")); | |
1569 | 452 | hideSelSequences.addActionListener(new ActionListener() |
1570 | { | |
1571 | 0 | @Override |
1572 | public void actionPerformed(ActionEvent e) | |
1573 | { | |
1574 | 0 | hideSelSequences_actionPerformed(e); |
1575 | } | |
1576 | }); | |
1577 | 452 | JMenuItem hideSelColumns = new JMenuItem( |
1578 | MessageManager.getString("label.selected_columns")); | |
1579 | 452 | hideSelColumns.setToolTipText( |
1580 | MessageManager.getString("label.toggle_columns_visibility")); | |
1581 | 452 | hideSelColumns.addActionListener(new ActionListener() |
1582 | { | |
1583 | 0 | @Override |
1584 | public void actionPerformed(ActionEvent e) | |
1585 | { | |
1586 | 0 | hideSelColumns_actionPerformed(e); |
1587 | } | |
1588 | }); | |
1589 | 452 | JMenuItem hideAllSelection = new JMenuItem( |
1590 | MessageManager.getString("label.selected_region")); | |
1591 | 452 | hideAllSelection.addActionListener(new ActionListener() |
1592 | { | |
1593 | 0 | @Override |
1594 | public void actionPerformed(ActionEvent e) | |
1595 | { | |
1596 | 0 | hideAllSelection_actionPerformed(e); |
1597 | } | |
1598 | }); | |
1599 | // TODO: should be hidden if no selection exists. | |
1600 | 452 | JMenuItem hideAllButSelection = new JMenuItem( |
1601 | MessageManager.getString("label.all_but_selected_region")); | |
1602 | 452 | hideAllButSelection.addActionListener(new ActionListener() |
1603 | { | |
1604 | 0 | @Override |
1605 | public void actionPerformed(ActionEvent e) | |
1606 | { | |
1607 | 0 | hideAllButSelection_actionPerformed(e); |
1608 | } | |
1609 | }); | |
1610 | 452 | JMenuItem showAllhidden = new JMenuItem( |
1611 | MessageManager.getString("label.all_sequences_columns")); | |
1612 | 452 | showAllhidden.setToolTipText(MessageManager |
1613 | .getString("label.toggles_visibility_hidden_selected_regions")); | |
1614 | 452 | showAllhidden.addActionListener(new ActionListener() |
1615 | { | |
1616 | 0 | @Override |
1617 | public void actionPerformed(ActionEvent e) | |
1618 | { | |
1619 | 0 | showAllhidden_actionPerformed(e); |
1620 | } | |
1621 | }); | |
1622 | 452 | hiddenMarkers.setText( |
1623 | MessageManager.getString("action.show_hidden_markers")); | |
1624 | 452 | hiddenMarkers.addActionListener(new ActionListener() |
1625 | { | |
1626 | 0 | @Override |
1627 | public void actionPerformed(ActionEvent e) | |
1628 | { | |
1629 | 0 | hiddenMarkers_actionPerformed(e); |
1630 | } | |
1631 | }); | |
1632 | ||
1633 | 452 | JMenuItem invertColSel = new JMenuItem( |
1634 | MessageManager.getString("action.invert_column_selection")); | |
1635 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, |
1636 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1637 | | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK, | |
1638 | false); | |
1639 | 452 | al = new ActionListener() |
1640 | { | |
1641 | 0 | @Override |
1642 | public void actionPerformed(ActionEvent e) | |
1643 | { | |
1644 | 0 | invertColSel_actionPerformed(e); |
1645 | } | |
1646 | }; | |
1647 | 452 | addMenuActionAndAccelerator(keyStroke, invertColSel, al); |
1648 | ||
1649 | 452 | showComplementMenuItem.setVisible(false); |
1650 | 452 | showComplementMenuItem.addActionListener(new ActionListener() |
1651 | { | |
1652 | 0 | @Override |
1653 | public void actionPerformed(ActionEvent e) | |
1654 | { | |
1655 | 0 | showComplement_actionPerformed(showComplementMenuItem.getState()); |
1656 | } | |
1657 | }); | |
1658 | ||
1659 | 452 | tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() |
1660 | { | |
1661 | 157 | @Override |
1662 | public void stateChanged(ChangeEvent evt) | |
1663 | { | |
1664 | 157 | JTabbedPane pane = (JTabbedPane) evt.getSource(); |
1665 | 157 | int sel = pane.getSelectedIndex(); |
1666 | 157 | tabSelectionChanged(sel); |
1667 | } | |
1668 | }); | |
1669 | 452 | tabbedPane.addMouseListener(new MouseAdapter() |
1670 | { | |
1671 | 0 | @Override |
1672 | public void mousePressed(MouseEvent e) | |
1673 | { | |
1674 | 0 | if (e.isPopupTrigger()) // Mac |
1675 | { | |
1676 | 0 | tabbedPane_mousePressed(e); |
1677 | } | |
1678 | } | |
1679 | ||
1680 | 0 | @Override |
1681 | public void mouseReleased(MouseEvent e) | |
1682 | { | |
1683 | 0 | if (e.isPopupTrigger()) // Windows |
1684 | { | |
1685 | 0 | tabbedPane_mousePressed(e); |
1686 | } | |
1687 | } | |
1688 | }); | |
1689 | 452 | tabbedPane.addFocusListener(new FocusAdapter() |
1690 | { | |
1691 | 61 | @Override |
1692 | public void focusGained(FocusEvent e) | |
1693 | { | |
1694 | 61 | tabbedPane_focusGained(e); |
1695 | } | |
1696 | }); | |
1697 | ||
1698 | 452 | JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); |
1699 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, |
1700 | jalview.util.ShortcutKeyMaskExWrapper | |
1701 | .getMenuShortcutKeyMaskEx(), | |
1702 | false); | |
1703 | 452 | al = new ActionListener() |
1704 | { | |
1705 | 0 | @Override |
1706 | public void actionPerformed(ActionEvent e) | |
1707 | { | |
1708 | 0 | save_actionPerformed(e); |
1709 | } | |
1710 | }; | |
1711 | 452 | addMenuActionAndAccelerator(keyStroke, save, al); |
1712 | ||
1713 | 452 | reload.setEnabled(false); |
1714 | 452 | reload.setText(MessageManager.getString("action.reload")); |
1715 | 452 | reload.addActionListener(new ActionListener() |
1716 | { | |
1717 | 0 | @Override |
1718 | public void actionPerformed(ActionEvent e) | |
1719 | { | |
1720 | 0 | reload_actionPerformed(e); |
1721 | } | |
1722 | }); | |
1723 | ||
1724 | 452 | JMenuItem newView = new JMenuItem( |
1725 | MessageManager.getString("action.new_view")); | |
1726 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, |
1727 | jalview.util.ShortcutKeyMaskExWrapper | |
1728 | .getMenuShortcutKeyMaskEx(), | |
1729 | false); | |
1730 | 452 | al = new ActionListener() |
1731 | { | |
1732 | 0 | @Override |
1733 | public void actionPerformed(ActionEvent e) | |
1734 | { | |
1735 | 0 | newView_actionPerformed(e); |
1736 | } | |
1737 | }; | |
1738 | 452 | addMenuActionAndAccelerator(keyStroke, newView, al); |
1739 | ||
1740 | 452 | tabbedPane.setToolTipText("<html><i>" |
1741 | + MessageManager.getString("label.rename_tab_eXpand_reGroup") | |
1742 | + "</i></html>"); | |
1743 | ||
1744 | 452 | formatMenu.setText(MessageManager.getString("action.format")); |
1745 | 452 | JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); |
1746 | ||
1747 | 452 | idRightAlign.setText( |
1748 | MessageManager.getString("label.right_align_sequence_id")); | |
1749 | 452 | idRightAlign.addActionListener(new ActionListener() |
1750 | { | |
1751 | 0 | @Override |
1752 | public void actionPerformed(ActionEvent e) | |
1753 | { | |
1754 | 0 | idRightAlign_actionPerformed(e); |
1755 | } | |
1756 | }); | |
1757 | ||
1758 | 452 | gatherViews.setEnabled(false); |
1759 | 452 | gatherViews.setText(MessageManager.getString("action.gather_views")); |
1760 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); |
1761 | 452 | al = new ActionListener() |
1762 | { | |
1763 | 0 | @Override |
1764 | public void actionPerformed(ActionEvent e) | |
1765 | { | |
1766 | 0 | gatherViews_actionPerformed(e); |
1767 | } | |
1768 | }; | |
1769 | 452 | addMenuActionAndAccelerator(keyStroke, gatherViews, al); |
1770 | ||
1771 | 452 | expandViews.setEnabled(false); |
1772 | 452 | expandViews.setText(MessageManager.getString("action.expand_views")); |
1773 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); |
1774 | 452 | al = new ActionListener() |
1775 | { | |
1776 | 0 | @Override |
1777 | public void actionPerformed(ActionEvent e) | |
1778 | { | |
1779 | 0 | expandViews_actionPerformed(e); |
1780 | } | |
1781 | }; | |
1782 | 452 | addMenuActionAndAccelerator(keyStroke, expandViews, al); |
1783 | ||
1784 | 452 | JMenuItem pageSetup = new JMenuItem( |
1785 | MessageManager.getString("action.page_setup")); | |
1786 | 452 | pageSetup.addActionListener(new ActionListener() |
1787 | { | |
1788 | 0 | @Override |
1789 | public void actionPerformed(ActionEvent e) | |
1790 | { | |
1791 | 0 | pageSetup_actionPerformed(e); |
1792 | } | |
1793 | }); | |
1794 | 452 | JMenuItem alignmentProperties = new JMenuItem( |
1795 | MessageManager.getString("label.alignment_props")); | |
1796 | 452 | alignmentProperties.addActionListener(new ActionListener() |
1797 | { | |
1798 | 0 | @Override |
1799 | public void actionPerformed(ActionEvent actionEvent) | |
1800 | { | |
1801 | 0 | alignmentProperties(); |
1802 | } | |
1803 | }); | |
1804 | 452 | JMenuItem selectHighlighted = new JMenuItem( |
1805 | MessageManager.getString("action.select_highlighted_columns")); | |
1806 | 452 | selectHighlighted.setToolTipText( |
1807 | MessageManager.getString("tooltip.select_highlighted_columns")); | |
1808 | 452 | al = new ActionListener() |
1809 | { | |
1810 | 0 | @Override |
1811 | public void actionPerformed(ActionEvent actionEvent) | |
1812 | { | |
1813 | 0 | selectHighlightedColumns_actionPerformed(actionEvent); |
1814 | } | |
1815 | }; | |
1816 | 452 | selectHighlighted.addActionListener(al); |
1817 | ||
1818 | 452 | copyHighlighted = new JMenuItem( |
1819 | MessageManager.getString("action.copy_highlighted_regions")); | |
1820 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, |
1821 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1822 | + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
1823 | false); | |
1824 | 452 | copyHighlighted.setToolTipText( |
1825 | MessageManager.getString("tooltip.copy_highlighted_regions")); | |
1826 | 452 | al = new ActionListener() |
1827 | { | |
1828 | 0 | @Override |
1829 | public void actionPerformed(ActionEvent actionEvent) | |
1830 | { | |
1831 | 0 | copyHighlightedColumns_actionPerformed(actionEvent); |
1832 | } | |
1833 | }; | |
1834 | 452 | addMenuActionAndAccelerator(keyStroke, copyHighlighted, al); |
1835 | 452 | copyHighlighted.addActionListener(al); |
1836 | ||
1837 | 452 | ButtonGroup ssButtonGroup = new ButtonGroup(); |
1838 | 452 | final JRadioButtonMenuItem showAll = new JRadioButtonMenuItem( |
1839 | MessageManager.getString("label.show_first")); | |
1840 | 452 | final JRadioButtonMenuItem showjPred = new JRadioButtonMenuItem( |
1841 | MessageManager.getString("label.show_last")); | |
1842 | 452 | final JRadioButtonMenuItem show3DSS = new JRadioButtonMenuItem( |
1843 | MessageManager.getString("label.show_last")); | |
1844 | 452 | ssButtonGroup.add(showAll); |
1845 | 452 | ssButtonGroup.add(showjPred); |
1846 | 452 | ssButtonGroup.add(show3DSS); |
1847 | 452 | final boolean autoFirst1 = Cache |
1848 | .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); | |
1849 | 452 | showAll.setSelected(autoFirst1); |
1850 | 452 | setShowAutoCalculatedAbove(autoFirst); |
1851 | 452 | showAutoFirst.addActionListener(new ActionListener() |
1852 | { | |
1853 | 0 | @Override |
1854 | public void actionPerformed(ActionEvent e) | |
1855 | { | |
1856 | 0 | setShowAutoCalculatedAbove(showAutoFirst.isSelected()); |
1857 | 0 | sortAnnotations_actionPerformed(); |
1858 | } | |
1859 | }); | |
1860 | 452 | showAutoLast.setSelected(!showAutoFirst.isSelected()); |
1861 | 452 | showAutoLast.addActionListener(new ActionListener() |
1862 | { | |
1863 | 0 | @Override |
1864 | public void actionPerformed(ActionEvent e) | |
1865 | { | |
1866 | 0 | setShowAutoCalculatedAbove(!showAutoLast.isSelected()); |
1867 | 0 | sortAnnotations_actionPerformed(); |
1868 | } | |
1869 | }); | |
1870 | ||
1871 | 452 | JMenu tooltipSettingsMenu = new JMenu( |
1872 | MessageManager.getString("label.sequence_id_tooltip")); | |
1873 | 452 | JMenu autoAnnMenu = new JMenu( |
1874 | MessageManager.getString("label.autocalculated_annotation")); | |
1875 | ||
1876 | 452 | JMenu showSS = new JMenu( |
1877 | MessageManager.getString("label.show_secondary_structure")); | |
1878 | ||
1879 | 452 | showSS.addMouseListener(new MouseAdapter() |
1880 | { | |
1881 | ||
1882 | 0 | @Override |
1883 | public void mouseEntered(MouseEvent e) | |
1884 | { | |
1885 | ||
1886 | 0 | updateShowSSRadioButtons(showSS, ssButtonGroup); // Update radio buttons |
1887 | // every time the menu | |
1888 | // is clicked | |
1889 | ||
1890 | } | |
1891 | }); | |
1892 | ||
1893 | 452 | JMenu exportImageMenu = new JMenu( |
1894 | MessageManager.getString("label.export_image")); | |
1895 | 452 | JMenu fileMenu = new JMenu(MessageManager.getString("action.file")); |
1896 | 452 | alignFrameMenuBar.add(fileMenu); |
1897 | 452 | alignFrameMenuBar.add(editMenu); |
1898 | 452 | alignFrameMenuBar.add(selectMenu); |
1899 | 452 | alignFrameMenuBar.add(viewMenu); |
1900 | 452 | alignFrameMenuBar.add(annotationsMenu); |
1901 | 452 | alignFrameMenuBar.add(formatMenu); |
1902 | 452 | alignFrameMenuBar.add(colourMenu); |
1903 | 452 | alignFrameMenuBar.add(calculateMenu); |
1904 | 452 | if (!Platform.isJS()) |
1905 | { | |
1906 | 452 | alignFrameMenuBar.add(webService); |
1907 | } | |
1908 | ||
1909 | 452 | fileMenu.add(fetchSequence); |
1910 | 452 | fileMenu.add(addSequenceMenu); |
1911 | 452 | fileMenu.add(reload); |
1912 | 452 | fileMenu.addSeparator(); |
1913 | 452 | fileMenu.add(vamsasStore); |
1914 | 452 | fileMenu.add(save); |
1915 | 452 | fileMenu.add(saveAs); |
1916 | 452 | fileMenu.add(outputTextboxMenu); |
1917 | 452 | fileMenu.add(pageSetup); |
1918 | 452 | fileMenu.add(printMenuItem); |
1919 | 452 | fileMenu.addSeparator(); |
1920 | 452 | fileMenu.add(exportImageMenu); |
1921 | 452 | fileMenu.add(exportFeatures); |
1922 | 452 | fileMenu.add(exportAnnotations); |
1923 | 452 | fileMenu.add(loadTreeMenuItem); |
1924 | 452 | fileMenu.add(associatedData); |
1925 | 452 | if (!Platform.isJS()) |
1926 | { | |
1927 | 452 | fileMenu.add(loadVcf); |
1928 | } | |
1929 | 452 | fileMenu.addSeparator(); |
1930 | 452 | fileMenu.add(closeMenuItem); |
1931 | ||
1932 | 452 | pasteMenu.add(pasteNew); |
1933 | 452 | pasteMenu.add(pasteThis); |
1934 | 452 | editMenu.add(undoMenuItem); |
1935 | 452 | editMenu.add(redoMenuItem); |
1936 | 452 | editMenu.add(cut); |
1937 | 452 | editMenu.add(copy); |
1938 | 452 | editMenu.add(copyHighlighted); |
1939 | 452 | editMenu.add(pasteMenu); |
1940 | 452 | editMenu.add(delete); |
1941 | 452 | editMenu.addSeparator(); |
1942 | 452 | editMenu.add(remove2LeftMenuItem); |
1943 | 452 | editMenu.add(remove2RightMenuItem); |
1944 | 452 | editMenu.add(removeGappedColumnMenuItem); |
1945 | 452 | editMenu.add(removeAllGapsMenuItem); |
1946 | 452 | editMenu.add(removeRedundancyMenuItem); |
1947 | 452 | editMenu.addSeparator(); |
1948 | ||
1949 | 452 | editMenu.add(justifyLeftMenuItem); |
1950 | 452 | editMenu.add(justifyRightMenuItem); |
1951 | ||
1952 | 452 | editMenu.addSeparator(); |
1953 | 452 | editMenu.add(padGapsMenuitem); |
1954 | ||
1955 | 452 | showMenu.add(showAllColumns); |
1956 | 452 | showMenu.add(showAllSeqs); |
1957 | 452 | showMenu.add(showAllhidden); |
1958 | 452 | hideMenu.add(hideSelColumns); |
1959 | 452 | hideMenu.add(hideSelSequences); |
1960 | 452 | hideMenu.add(hideAllSelection); |
1961 | 452 | hideMenu.add(hideAllButSelection); |
1962 | 452 | viewMenu.add(newView); |
1963 | 452 | viewMenu.add(expandViews); |
1964 | 452 | viewMenu.add(gatherViews); |
1965 | 452 | viewMenu.addSeparator(); |
1966 | 452 | viewMenu.add(showMenu); |
1967 | 452 | viewMenu.add(hideMenu); |
1968 | 452 | viewMenu.add(showComplementMenuItem); |
1969 | 452 | viewMenu.addSeparator(); |
1970 | 452 | viewMenu.add(followHighlightMenuItem); |
1971 | 452 | viewMenu.addSeparator(); |
1972 | 452 | viewMenu.add(showSeqFeatures); |
1973 | // viewMenu.add(showSeqFeaturesHeight); | |
1974 | 452 | viewMenu.add(openFeatureSettings); |
1975 | 452 | tooltipSettingsMenu.add(showDbRefsMenuitem); |
1976 | 452 | tooltipSettingsMenu.add(showNpFeatsMenuitem); |
1977 | 452 | viewMenu.add(tooltipSettingsMenu); |
1978 | 452 | viewMenu.addSeparator(); |
1979 | 452 | viewMenu.add(alignmentProperties); |
1980 | 452 | viewMenu.addSeparator(); |
1981 | 452 | viewMenu.add(overviewMenuItem); |
1982 | ||
1983 | 452 | annotationsMenu.add(annotationPanelMenuItem); |
1984 | 452 | annotationsMenu.addSeparator(); |
1985 | 452 | annotationsMenu.add(showAllAlAnnotations); |
1986 | 452 | annotationsMenu.add(hideAllAlAnnotations); |
1987 | 452 | annotationsMenu.addSeparator(); |
1988 | 452 | annotationsMenu.add(showAllSeqAnnotations); |
1989 | 452 | annotationsMenu.add(hideAllSeqAnnotations); |
1990 | 452 | annotationsMenu.add(sortAnnBySequence); |
1991 | 452 | annotationsMenu.add(sortAnnByLabel); |
1992 | 452 | annotationsMenu.addSeparator(); |
1993 | 452 | annotationsMenu.add(showSS); |
1994 | 452 | annotationsMenu.addSeparator(); |
1995 | 452 | autoAnnMenu.add(showAutoFirst); |
1996 | 452 | autoAnnMenu.add(showAutoLast); |
1997 | 452 | autoAnnMenu.addSeparator(); |
1998 | 452 | autoAnnMenu.add(applyAutoAnnotationSettings); |
1999 | 452 | autoAnnMenu.add(showConsensusHistogram); |
2000 | 452 | autoAnnMenu.add(showSSConsensusHistogram); |
2001 | 452 | autoAnnMenu.add(showSequenceLogo); |
2002 | 452 | autoAnnMenu.add(normaliseSequenceLogo); |
2003 | // autoAnnMenu.add(showSSConsensus); | |
2004 | 452 | autoAnnMenu.addSeparator(); |
2005 | 452 | autoAnnMenu.add(showGroupConservation); |
2006 | 452 | autoAnnMenu.add(showGroupConsensus); |
2007 | 452 | autoAnnMenu.add(showGroupSSConsensus); |
2008 | 452 | annotationsMenu.add(autoAnnMenu); |
2009 | ||
2010 | 452 | sort.add(sortIDMenuItem); |
2011 | 452 | sort.add(sortLengthMenuItem); |
2012 | 452 | sort.add(sortGroupMenuItem); |
2013 | 452 | sort.add(sortPairwiseMenuItem); |
2014 | 452 | sort.add(sortByTreeMenu); |
2015 | 452 | calculateMenu.add(sort); |
2016 | 452 | calculateMenu.add(calculateTree); |
2017 | 452 | calculateMenu.addSeparator(); |
2018 | 452 | calculateMenu.add(pairwiseAlignmentMenuItem); |
2019 | 452 | calculateMenu.addSeparator(); |
2020 | 452 | calculateMenu.add(showTranslation); |
2021 | 452 | calculateMenu.add(showReverse); |
2022 | 452 | calculateMenu.add(showReverseComplement); |
2023 | 452 | calculateMenu.add(showProducts); |
2024 | 452 | calculateMenu.add(autoCalculate); |
2025 | 452 | calculateMenu.add(sortByTree); |
2026 | 452 | calculateMenu.addSeparator(); |
2027 | 452 | calculateMenu.add(expandAlignment); |
2028 | 452 | calculateMenu.add(extractScores); |
2029 | 452 | if (!Platform.isJS()) |
2030 | { | |
2031 | 452 | calculateMenu.addSeparator(); |
2032 | 452 | calculateMenu.add(runGroovy); |
2033 | } | |
2034 | ||
2035 | 452 | webServiceNoServices = new JMenuItem( |
2036 | MessageManager.getString("label.no_services")); | |
2037 | 452 | webService.add(webServiceNoServices); |
2038 | 452 | if (!Platform.isJS()) |
2039 | { | |
2040 | 452 | exportImageMenu.add(htmlMenuItem); |
2041 | } | |
2042 | 452 | exportImageMenu.add(epsFile); |
2043 | 452 | exportImageMenu.add(createPNG); |
2044 | 452 | if (!Platform.isJS()) |
2045 | { | |
2046 | 452 | exportImageMenu.add(createBioJS); |
2047 | 452 | exportImageMenu.add(createSVG); |
2048 | } | |
2049 | 452 | addSequenceMenu.add(addFromFile); |
2050 | 452 | addSequenceMenu.add(addFromText); |
2051 | 452 | addSequenceMenu.add(addFromURL); |
2052 | 452 | this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); |
2053 | 452 | statusPanel.add(statusBar, null); |
2054 | 452 | this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); |
2055 | ||
2056 | 452 | formatMenu.add(font); |
2057 | 452 | formatMenu.addSeparator(); |
2058 | 452 | formatMenu.add(wrapMenuItem); |
2059 | 452 | formatMenu.add(scaleAbove); |
2060 | 452 | formatMenu.add(scaleLeft); |
2061 | 452 | formatMenu.add(scaleRight); |
2062 | 452 | formatMenu.add(seqLimits); |
2063 | 452 | formatMenu.add(idRightAlign); |
2064 | 452 | formatMenu.add(hiddenMarkers); |
2065 | 452 | formatMenu.add(viewBoxesMenuItem); |
2066 | 452 | formatMenu.add(viewTextMenuItem); |
2067 | 452 | formatMenu.add(colourTextMenuItem); |
2068 | 452 | formatMenu.add(renderGapsMenuItem); |
2069 | 452 | formatMenu.add(centreColumnLabelsMenuItem); |
2070 | 452 | formatMenu.add(showNonconservedMenuItem); |
2071 | 452 | selectMenu.add(findMenuItem); |
2072 | 452 | selectMenu.addSeparator(); |
2073 | 452 | selectMenu.add(selectAllSequenceMenuItem); |
2074 | 452 | selectMenu.add(deselectAllSequenceMenuItem); |
2075 | 452 | selectMenu.add(invertSequenceMenuItem); |
2076 | 452 | selectMenu.add(invertColSel); |
2077 | 452 | selectMenu.add(createGroup); |
2078 | 452 | selectMenu.add(unGroup); |
2079 | 452 | selectMenu.add(grpsFromSelection); |
2080 | 452 | selectMenu.add(deleteGroups); |
2081 | 452 | selectMenu.add(annotationColumn); |
2082 | 452 | selectMenu.add(selectHighlighted); |
2083 | // TODO - determine if the listenToViewSelections button is needed : see bug | |
2084 | // JAL-574 | |
2085 | // selectMenu.addSeparator(); | |
2086 | // selectMenu.add(listenToViewSelections); | |
2087 | } | |
2088 | ||
2089 | ||
2090 | 0 | protected void showSSConsensus_actionPerformed(ActionEvent e) |
2091 | { | |
2092 | // TODO Auto-generated method stub | |
2093 | ||
2094 | } | |
2095 | ||
2096 | 0 | protected void createPNG_actionPerformed(ActionEvent object) |
2097 | { | |
2098 | // TODO Auto-generated method stub | |
2099 | ||
2100 | } | |
2101 | ||
2102 | 0 | protected void createEPS_actionPerformed(ActionEvent object) |
2103 | { | |
2104 | // TODO Auto-generated method stub | |
2105 | ||
2106 | } | |
2107 | ||
2108 | 0 | protected void createSVG_actionPerformed(ActionEvent object) |
2109 | { | |
2110 | // TODO Auto-generated method stub | |
2111 | ||
2112 | } | |
2113 | ||
2114 | 0 | protected void copyHighlightedColumns_actionPerformed( |
2115 | ActionEvent actionEvent) | |
2116 | { | |
2117 | ||
2118 | } | |
2119 | ||
2120 | 0 | protected void loadVcf_actionPerformed() |
2121 | { | |
2122 | } | |
2123 | ||
2124 | /** | |
2125 | * Constructs the entries on the Colour menu (but does not add them to the | |
2126 | * menu). | |
2127 | */ | |
2128 | 453 | protected void initColourMenu() |
2129 | { | |
2130 | 453 | applyToAllGroups = new JCheckBoxMenuItem( |
2131 | MessageManager.getString("label.apply_colour_to_all_groups")); | |
2132 | 453 | applyToAllGroups.addActionListener(new ActionListener() |
2133 | { | |
2134 | 0 | @Override |
2135 | public void actionPerformed(ActionEvent e) | |
2136 | { | |
2137 | 0 | applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); |
2138 | } | |
2139 | }); | |
2140 | ||
2141 | 453 | textColour = new JMenuItem( |
2142 | MessageManager.getString("label.text_colour")); | |
2143 | 453 | textColour.addActionListener(new ActionListener() |
2144 | { | |
2145 | 0 | @Override |
2146 | public void actionPerformed(ActionEvent e) | |
2147 | { | |
2148 | 0 | textColour_actionPerformed(); |
2149 | } | |
2150 | }); | |
2151 | ||
2152 | 453 | conservationMenuItem = new JCheckBoxMenuItem( |
2153 | MessageManager.getString("action.by_conservation")); | |
2154 | 453 | conservationMenuItem.addActionListener(new ActionListener() |
2155 | { | |
2156 | 0 | @Override |
2157 | public void actionPerformed(ActionEvent e) | |
2158 | { | |
2159 | 0 | conservationMenuItem_actionPerformed( |
2160 | conservationMenuItem.isSelected()); | |
2161 | } | |
2162 | }); | |
2163 | ||
2164 | 453 | abovePIDThreshold = new JCheckBoxMenuItem( |
2165 | MessageManager.getString("label.above_identity_threshold")); | |
2166 | 453 | abovePIDThreshold.addActionListener(new ActionListener() |
2167 | { | |
2168 | 0 | @Override |
2169 | public void actionPerformed(ActionEvent e) | |
2170 | { | |
2171 | 0 | abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); |
2172 | } | |
2173 | }); | |
2174 | 453 | modifyPID = new JMenuItem( |
2175 | MessageManager.getString("label.modify_identity_threshold")); | |
2176 | 453 | modifyPID.addActionListener(new ActionListener() |
2177 | { | |
2178 | 0 | @Override |
2179 | public void actionPerformed(ActionEvent e) | |
2180 | { | |
2181 | 0 | modifyPID_actionPerformed(); |
2182 | } | |
2183 | }); | |
2184 | 453 | modifyConservation = new JMenuItem(MessageManager |
2185 | .getString("label.modify_conservation_threshold")); | |
2186 | 453 | modifyConservation.addActionListener(new ActionListener() |
2187 | { | |
2188 | 0 | @Override |
2189 | public void actionPerformed(ActionEvent e) | |
2190 | { | |
2191 | 0 | modifyConservation_actionPerformed(); |
2192 | } | |
2193 | }); | |
2194 | ||
2195 | 453 | annotationColour = new JRadioButtonMenuItem( |
2196 | MessageManager.getString("action.by_annotation")); | |
2197 | 453 | annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); |
2198 | 453 | annotationColour.addActionListener(new ActionListener() |
2199 | { | |
2200 | 0 | @Override |
2201 | public void actionPerformed(ActionEvent e) | |
2202 | { | |
2203 | 0 | annotationColour_actionPerformed(); |
2204 | } | |
2205 | }); | |
2206 | } | |
2207 | ||
2208 | 0 | protected void selectHighlightedColumns_actionPerformed( |
2209 | ActionEvent actionEvent) | |
2210 | { | |
2211 | // TODO Auto-generated method stub | |
2212 | ||
2213 | } | |
2214 | ||
2215 | /** | |
2216 | * Generate the reverse sequence (or reverse complement if the flag is true) | |
2217 | * and add it to the alignment | |
2218 | * | |
2219 | * @param complement | |
2220 | */ | |
2221 | 0 | protected void showReverse_actionPerformed(boolean complement) |
2222 | { | |
2223 | } | |
2224 | ||
2225 | /** | |
2226 | * Try to run script in a Groovy console, having first ensured that this | |
2227 | * alignframe is set as currentAlignFrame in Desktop | |
2228 | */ | |
2229 | 0 | protected void runGroovy_actionPerformed() |
2230 | { | |
2231 | ||
2232 | } | |
2233 | ||
2234 | /** | |
2235 | * Adds the given action listener and key accelerator to the given menu item. | |
2236 | * Also saves in a lookup table to support lookup of action by key stroke. | |
2237 | * | |
2238 | * @param keyStroke | |
2239 | * @param menuItem | |
2240 | * @param actionListener | |
2241 | */ | |
2242 | 12225 | protected void addMenuActionAndAccelerator(KeyStroke keyStroke, |
2243 | JMenuItem menuItem, ActionListener actionListener) | |
2244 | { | |
2245 | 12225 | menuItem.setAccelerator(keyStroke); |
2246 | 12225 | accelerators.put(keyStroke, menuItem); |
2247 | 12225 | menuItem.addActionListener(actionListener); |
2248 | } | |
2249 | ||
2250 | /** | |
2251 | * Action on clicking sort annotations by type. | |
2252 | * | |
2253 | * @param sortOrder | |
2254 | */ | |
2255 | 0 | protected void sortAnnotations_actionPerformed() |
2256 | { | |
2257 | } | |
2258 | ||
2259 | /** | |
2260 | * Action on clicking Show all annotations. | |
2261 | * | |
2262 | * @param forSequences | |
2263 | * update sequence-related annotations | |
2264 | * @param forAlignment | |
2265 | * update non-sequence-related annotations | |
2266 | */ | |
2267 | 0 | protected void showAllAnnotations_actionPerformed(boolean forSequences, |
2268 | boolean forAlignment) | |
2269 | { | |
2270 | 0 | setAnnotationsVisibility(true, forSequences, forAlignment); |
2271 | } | |
2272 | ||
2273 | /** | |
2274 | * Action on clicking Hide all annotations. | |
2275 | * | |
2276 | * @param forSequences | |
2277 | * update sequence-related annotations | |
2278 | * @param forAlignment | |
2279 | * update non-sequence-related annotations | |
2280 | */ | |
2281 | 0 | protected void hideAllAnnotations_actionPerformed(boolean forSequences, |
2282 | boolean forAlignment) | |
2283 | { | |
2284 | 0 | setAnnotationsVisibility(false, forSequences, forAlignment); |
2285 | } | |
2286 | ||
2287 | /** | |
2288 | * Set the visibility of annotations to true or false. Can act on | |
2289 | * sequence-related annotations, or alignment-related, or both. | |
2290 | * | |
2291 | * @param visible | |
2292 | * @param forSequences | |
2293 | * update sequence-related annotations | |
2294 | * @param forAlignment | |
2295 | * update non-sequence-related annotations | |
2296 | */ | |
2297 | 0 | public void setAnnotationsVisibility(boolean visible, |
2298 | boolean forSequences, boolean forAlignment) | |
2299 | { | |
2300 | ||
2301 | } | |
2302 | ||
2303 | 0 | protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) |
2304 | { | |
2305 | // TODO Auto-generated method stub | |
2306 | ||
2307 | } | |
2308 | ||
2309 | 0 | protected void listenToViewSelections_actionPerformed(ActionEvent e) |
2310 | { | |
2311 | // TODO Auto-generated method stub | |
2312 | ||
2313 | } | |
2314 | ||
2315 | 0 | protected void showAllhidden_actionPerformed(ActionEvent e) |
2316 | { | |
2317 | // TODO Auto-generated method stub | |
2318 | ||
2319 | } | |
2320 | ||
2321 | 0 | protected void hideAllButSelection_actionPerformed(ActionEvent e) |
2322 | { | |
2323 | // TODO Auto-generated method stub | |
2324 | ||
2325 | } | |
2326 | ||
2327 | 0 | protected void hideAllSelection_actionPerformed(ActionEvent e) |
2328 | { | |
2329 | // TODO Auto-generated method stub | |
2330 | ||
2331 | } | |
2332 | ||
2333 | 0 | protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) |
2334 | { | |
2335 | // TODO Auto-generated method stub | |
2336 | ||
2337 | } | |
2338 | ||
2339 | 0 | protected void showConsensusHistogram_actionPerformed(ActionEvent e) |
2340 | { | |
2341 | // TODO Auto-generated method stub | |
2342 | ||
2343 | } | |
2344 | ||
2345 | 0 | protected void showSSConsensusHistogram_actionPerformed(ActionEvent e) |
2346 | { | |
2347 | // TODO Auto-generated method stub | |
2348 | ||
2349 | } | |
2350 | ||
2351 | 0 | protected void showSequenceLogo_actionPerformed(ActionEvent e) |
2352 | { | |
2353 | // TODO Auto-generated method stub | |
2354 | ||
2355 | } | |
2356 | ||
2357 | 0 | protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) |
2358 | { | |
2359 | // TODO Auto-generated method stub | |
2360 | ||
2361 | } | |
2362 | 0 | protected void showGroupConsensus_actionPerformed(ActionEvent e) |
2363 | { | |
2364 | // TODO Auto-generated method stub | |
2365 | ||
2366 | } | |
2367 | ||
2368 | 0 | protected void showGroupSSConsensus_actionPerformed(ActionEvent e) |
2369 | { | |
2370 | // TODO Auto-generated method stub | |
2371 | ||
2372 | } | |
2373 | ||
2374 | 0 | protected void showGroupConservation_actionPerformed(ActionEvent e) |
2375 | { | |
2376 | // TODO Auto-generated method stub | |
2377 | ||
2378 | } | |
2379 | ||
2380 | 0 | protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) |
2381 | { | |
2382 | // TODO Auto-generated method stub | |
2383 | ||
2384 | } | |
2385 | ||
2386 | 0 | protected void justifyRightMenuItem_actionPerformed(ActionEvent e) |
2387 | { | |
2388 | // TODO Auto-generated method stub | |
2389 | ||
2390 | } | |
2391 | ||
2392 | 0 | protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) |
2393 | { | |
2394 | // TODO Auto-generated method stub | |
2395 | ||
2396 | } | |
2397 | ||
2398 | 0 | protected void followHighlight_actionPerformed() |
2399 | { | |
2400 | // TODO Auto-generated method stub | |
2401 | ||
2402 | } | |
2403 | ||
2404 | 0 | protected void showNpFeats_actionPerformed(ActionEvent e) |
2405 | { | |
2406 | // TODO Auto-generated method stub | |
2407 | ||
2408 | } | |
2409 | ||
2410 | 0 | protected void showDbRefs_actionPerformed(ActionEvent e) |
2411 | { | |
2412 | // TODO Auto-generated method stub | |
2413 | ||
2414 | } | |
2415 | ||
2416 | 0 | protected void centreColumnLabels_actionPerformed(ActionEvent e) |
2417 | { | |
2418 | } | |
2419 | ||
2420 | 0 | protected void buildSortByAnnotationScoresMenu() |
2421 | { | |
2422 | } | |
2423 | ||
2424 | 0 | protected void extractScores_actionPerformed(ActionEvent e) |
2425 | { | |
2426 | } | |
2427 | ||
2428 | 0 | protected void outputText_actionPerformed(String formatName) |
2429 | { | |
2430 | } | |
2431 | ||
2432 | 0 | public void addFromFile_actionPerformed(ActionEvent e) |
2433 | { | |
2434 | ||
2435 | } | |
2436 | ||
2437 | 0 | public void addFromText_actionPerformed(ActionEvent e) |
2438 | { | |
2439 | ||
2440 | } | |
2441 | ||
2442 | 0 | public void addFromURL_actionPerformed(ActionEvent e) |
2443 | { | |
2444 | ||
2445 | } | |
2446 | ||
2447 | 0 | public void exportFeatures_actionPerformed(ActionEvent e) |
2448 | { | |
2449 | ||
2450 | } | |
2451 | ||
2452 | 0 | public void exportAnnotations_actionPerformed(ActionEvent e) |
2453 | { | |
2454 | ||
2455 | } | |
2456 | ||
2457 | 0 | protected void htmlMenuItem_actionPerformed(ActionEvent e) |
2458 | { | |
2459 | } | |
2460 | ||
2461 | 0 | protected void bioJSMenuItem_actionPerformed(ActionEvent e) |
2462 | { | |
2463 | ||
2464 | } | |
2465 | ||
2466 | 0 | protected void closeMenuItem_actionPerformed(boolean b) |
2467 | { | |
2468 | } | |
2469 | ||
2470 | 0 | protected void redoMenuItem_actionPerformed(ActionEvent e) |
2471 | { | |
2472 | } | |
2473 | ||
2474 | 0 | protected void undoMenuItem_actionPerformed(ActionEvent e) |
2475 | { | |
2476 | } | |
2477 | ||
2478 | 0 | protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) |
2479 | { | |
2480 | } | |
2481 | ||
2482 | 0 | protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) |
2483 | { | |
2484 | } | |
2485 | ||
2486 | 0 | protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) |
2487 | { | |
2488 | } | |
2489 | ||
2490 | 0 | protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) |
2491 | { | |
2492 | } | |
2493 | ||
2494 | 0 | protected void remove2RightMenuItem_actionPerformed(ActionEvent e) |
2495 | { | |
2496 | } | |
2497 | ||
2498 | 0 | protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) |
2499 | { | |
2500 | } | |
2501 | ||
2502 | 0 | protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) |
2503 | { | |
2504 | } | |
2505 | ||
2506 | 0 | protected void wrapMenuItem_actionPerformed(ActionEvent e) |
2507 | { | |
2508 | } | |
2509 | ||
2510 | 0 | protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) |
2511 | { | |
2512 | } | |
2513 | ||
2514 | 0 | protected void viewTextMenuItem_actionPerformed(ActionEvent e) |
2515 | { | |
2516 | } | |
2517 | ||
2518 | 0 | protected void colourTextMenuItem_actionPerformed(ActionEvent e) |
2519 | { | |
2520 | } | |
2521 | ||
2522 | 0 | protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) |
2523 | { | |
2524 | } | |
2525 | ||
2526 | 0 | protected void overviewMenuItem_actionPerformed(ActionEvent e) |
2527 | { | |
2528 | } | |
2529 | ||
2530 | 0 | protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) |
2531 | { | |
2532 | } | |
2533 | ||
2534 | 0 | protected void sortIDMenuItem_actionPerformed(ActionEvent e) |
2535 | { | |
2536 | } | |
2537 | ||
2538 | 0 | protected void sortLengthMenuItem_actionPerformed(ActionEvent e) |
2539 | { | |
2540 | } | |
2541 | ||
2542 | 0 | protected void sortGroupMenuItem_actionPerformed(ActionEvent e) |
2543 | { | |
2544 | } | |
2545 | ||
2546 | 0 | protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) |
2547 | { | |
2548 | } | |
2549 | ||
2550 | 0 | protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) |
2551 | { | |
2552 | } | |
2553 | ||
2554 | 0 | protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) |
2555 | { | |
2556 | } | |
2557 | ||
2558 | 0 | protected void conservationMenuItem_actionPerformed(boolean selected) |
2559 | { | |
2560 | } | |
2561 | ||
2562 | 0 | protected void printMenuItem_actionPerformed(ActionEvent e) |
2563 | { | |
2564 | } | |
2565 | ||
2566 | 0 | protected void renderGapsMenuItem_actionPerformed(ActionEvent e) |
2567 | { | |
2568 | } | |
2569 | ||
2570 | 0 | protected void findMenuItem_actionPerformed(ActionEvent e) |
2571 | { | |
2572 | } | |
2573 | ||
2574 | 0 | protected void abovePIDThreshold_actionPerformed(boolean selected) |
2575 | { | |
2576 | } | |
2577 | ||
2578 | 0 | public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) |
2579 | { | |
2580 | } | |
2581 | ||
2582 | 0 | protected void deleteGroups_actionPerformed(ActionEvent e) |
2583 | { | |
2584 | } | |
2585 | ||
2586 | 0 | protected void createGroup_actionPerformed(ActionEvent e) |
2587 | { | |
2588 | } | |
2589 | ||
2590 | 0 | protected void unGroup_actionPerformed(ActionEvent e) |
2591 | { | |
2592 | } | |
2593 | ||
2594 | 0 | protected void copy_actionPerformed() |
2595 | { | |
2596 | } | |
2597 | ||
2598 | 0 | protected void cut_actionPerformed() |
2599 | { | |
2600 | } | |
2601 | ||
2602 | 0 | protected void delete_actionPerformed() |
2603 | { | |
2604 | } | |
2605 | ||
2606 | 0 | protected void pasteNew_actionPerformed(ActionEvent e) |
2607 | { | |
2608 | } | |
2609 | ||
2610 | 0 | protected void pasteThis_actionPerformed(ActionEvent e) |
2611 | { | |
2612 | } | |
2613 | ||
2614 | 0 | protected void applyToAllGroups_actionPerformed(boolean selected) |
2615 | { | |
2616 | } | |
2617 | ||
2618 | 0 | protected void font_actionPerformed(ActionEvent e) |
2619 | { | |
2620 | } | |
2621 | ||
2622 | 0 | protected void seqLimit_actionPerformed(ActionEvent e) |
2623 | { | |
2624 | } | |
2625 | ||
2626 | 0 | public void seqDBRef_actionPerformed(ActionEvent e) |
2627 | { | |
2628 | ||
2629 | } | |
2630 | ||
2631 | 0 | protected void loadTreeMenuItem_actionPerformed(ActionEvent e) |
2632 | { | |
2633 | ||
2634 | } | |
2635 | ||
2636 | /** | |
2637 | * Template method to handle the 'load T-Coffee scores' menu event. | |
2638 | * <p> | |
2639 | * Subclasses override this method to provide a custom action. | |
2640 | * | |
2641 | * @param event | |
2642 | * The raised event | |
2643 | */ | |
2644 | 0 | protected void loadScores_actionPerformed(ActionEvent event) |
2645 | { | |
2646 | ||
2647 | } | |
2648 | ||
2649 | 0 | protected void jpred_actionPerformed(ActionEvent e) |
2650 | { | |
2651 | } | |
2652 | ||
2653 | 0 | protected void scaleAbove_actionPerformed(ActionEvent e) |
2654 | { | |
2655 | } | |
2656 | ||
2657 | 0 | protected void scaleLeft_actionPerformed(ActionEvent e) |
2658 | { | |
2659 | } | |
2660 | ||
2661 | 0 | protected void scaleRight_actionPerformed(ActionEvent e) |
2662 | { | |
2663 | } | |
2664 | ||
2665 | 0 | protected void modifyPID_actionPerformed() |
2666 | { | |
2667 | } | |
2668 | ||
2669 | 0 | protected void modifyConservation_actionPerformed() |
2670 | { | |
2671 | } | |
2672 | ||
2673 | 0 | protected void saveAs_actionPerformed() |
2674 | { | |
2675 | } | |
2676 | ||
2677 | 0 | protected void padGapsMenuitem_actionPerformed(ActionEvent e) |
2678 | { | |
2679 | } | |
2680 | ||
2681 | 0 | public void vamsasStore_actionPerformed(ActionEvent e) |
2682 | { | |
2683 | ||
2684 | } | |
2685 | ||
2686 | 0 | public void vamsasLoad_actionPerformed(ActionEvent e) |
2687 | { | |
2688 | ||
2689 | } | |
2690 | ||
2691 | 0 | public void showTranslation_actionPerformed(GeneticCodeI codeTable) |
2692 | { | |
2693 | ||
2694 | } | |
2695 | ||
2696 | 0 | public void featureSettings_actionPerformed(ActionEvent e) |
2697 | { | |
2698 | ||
2699 | } | |
2700 | ||
2701 | 0 | public void fetchSequence_actionPerformed() |
2702 | { | |
2703 | ||
2704 | } | |
2705 | ||
2706 | 0 | public void smoothFont_actionPerformed(ActionEvent e) |
2707 | { | |
2708 | ||
2709 | } | |
2710 | ||
2711 | 0 | public void annotationColour_actionPerformed() |
2712 | { | |
2713 | } | |
2714 | ||
2715 | 0 | public void annotationColumn_actionPerformed(ActionEvent e) |
2716 | { | |
2717 | } | |
2718 | ||
2719 | 0 | public void associatedData_actionPerformed(ActionEvent e) |
2720 | { | |
2721 | ||
2722 | } | |
2723 | ||
2724 | 0 | public void autoCalculate_actionPerformed(ActionEvent e) |
2725 | { | |
2726 | ||
2727 | } | |
2728 | ||
2729 | 0 | public void sortByTreeOption_actionPerformed(ActionEvent e) |
2730 | { | |
2731 | ||
2732 | } | |
2733 | ||
2734 | 0 | public void showAllSeqs_actionPerformed(ActionEvent e) |
2735 | { | |
2736 | ||
2737 | } | |
2738 | ||
2739 | 0 | public void showAllColumns_actionPerformed(ActionEvent e) |
2740 | { | |
2741 | ||
2742 | } | |
2743 | ||
2744 | 0 | public void hideSelSequences_actionPerformed(ActionEvent e) |
2745 | { | |
2746 | ||
2747 | } | |
2748 | ||
2749 | 0 | public void hideSelColumns_actionPerformed(ActionEvent e) |
2750 | { | |
2751 | ||
2752 | } | |
2753 | ||
2754 | 0 | public void hiddenMarkers_actionPerformed(ActionEvent e) |
2755 | { | |
2756 | ||
2757 | } | |
2758 | ||
2759 | 0 | public void findPdbId_actionPerformed(ActionEvent e) |
2760 | { | |
2761 | ||
2762 | } | |
2763 | ||
2764 | 0 | public void enterPdbId_actionPerformed(ActionEvent e) |
2765 | { | |
2766 | ||
2767 | } | |
2768 | ||
2769 | 0 | public void pdbFile_actionPerformed(ActionEvent e) |
2770 | { | |
2771 | ||
2772 | } | |
2773 | ||
2774 | 0 | public void invertColSel_actionPerformed(ActionEvent e) |
2775 | { | |
2776 | ||
2777 | } | |
2778 | ||
2779 | 0 | public void tabSelectionChanged(int sel) |
2780 | { | |
2781 | ||
2782 | } | |
2783 | ||
2784 | 0 | public void tabbedPane_mousePressed(MouseEvent e) |
2785 | { | |
2786 | ||
2787 | } | |
2788 | ||
2789 | 61 | public void tabbedPane_focusGained(FocusEvent e) |
2790 | { | |
2791 | 61 | requestFocus(); |
2792 | } | |
2793 | ||
2794 | 0 | public void save_actionPerformed(ActionEvent e) |
2795 | { | |
2796 | ||
2797 | } | |
2798 | ||
2799 | 0 | public void reload_actionPerformed(ActionEvent e) |
2800 | { | |
2801 | ||
2802 | } | |
2803 | ||
2804 | 0 | public void newView_actionPerformed(ActionEvent e) |
2805 | { | |
2806 | ||
2807 | } | |
2808 | ||
2809 | 0 | public void textColour_actionPerformed() |
2810 | { | |
2811 | ||
2812 | } | |
2813 | ||
2814 | 0 | public void idRightAlign_actionPerformed(ActionEvent e) |
2815 | { | |
2816 | ||
2817 | } | |
2818 | ||
2819 | 0 | public void expandViews_actionPerformed(ActionEvent e) |
2820 | { | |
2821 | ||
2822 | } | |
2823 | ||
2824 | 0 | public void gatherViews_actionPerformed(ActionEvent e) |
2825 | { | |
2826 | ||
2827 | } | |
2828 | ||
2829 | 0 | public void buildTreeSortMenu() |
2830 | { | |
2831 | ||
2832 | } | |
2833 | ||
2834 | 0 | public void pageSetup_actionPerformed(ActionEvent e) |
2835 | { | |
2836 | ||
2837 | } | |
2838 | ||
2839 | 0 | public void alignmentProperties() |
2840 | { | |
2841 | ||
2842 | } | |
2843 | ||
2844 | 0 | protected void expand_newalign(ActionEvent e) |
2845 | { | |
2846 | // TODO Auto-generated method stub | |
2847 | ||
2848 | } | |
2849 | ||
2850 | 452 | protected boolean isShowAutoCalculatedAbove() |
2851 | { | |
2852 | 452 | return showAutoCalculatedAbove; |
2853 | } | |
2854 | ||
2855 | 905 | protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove) |
2856 | { | |
2857 | 905 | this.showAutoCalculatedAbove = showAutoCalculatedAbove; |
2858 | } | |
2859 | ||
2860 | 0 | protected SequenceAnnotationOrder getAnnotationSortOrder() |
2861 | { | |
2862 | 0 | return annotationSortOrder; |
2863 | } | |
2864 | ||
2865 | 0 | protected void setAnnotationSortOrder( |
2866 | SequenceAnnotationOrder annotationSortOrder) | |
2867 | { | |
2868 | 0 | this.annotationSortOrder = annotationSortOrder; |
2869 | } | |
2870 | ||
2871 | 33 | public Map<KeyStroke, JMenuItem> getAccelerators() |
2872 | { | |
2873 | 33 | return this.accelerators; |
2874 | } | |
2875 | ||
2876 | /** | |
2877 | * Returns the selected index of the tabbed pane, or -1 if none selected | |
2878 | * (including the case where the tabbed pane has not been made visible). | |
2879 | * | |
2880 | * @return | |
2881 | */ | |
2882 | 0 | public int getTabIndex() |
2883 | { | |
2884 | 0 | return tabbedPane.getSelectedIndex(); |
2885 | } | |
2886 | ||
2887 | 0 | public JPanel getStatusPanel() |
2888 | { | |
2889 | 0 | return statusPanel; |
2890 | } | |
2891 | ||
2892 | /** | |
2893 | * Sets a reference to the containing split frame. Also makes the 'toggle | |
2894 | * split view' menu item visible and checked. | |
2895 | * | |
2896 | * @param sf | |
2897 | */ | |
2898 | 6 | public void setSplitFrame(SplitContainerI sf) |
2899 | { | |
2900 | 6 | this.splitFrame = sf; |
2901 | 6 | if (sf != null) |
2902 | { | |
2903 | 6 | this.showComplementMenuItem.setVisible(true); |
2904 | 6 | this.showComplementMenuItem.setState(true); |
2905 | } | |
2906 | } | |
2907 | ||
2908 | 3 | public SplitContainerI getSplitViewContainer() |
2909 | { | |
2910 | 3 | return this.splitFrame; |
2911 | } | |
2912 | ||
2913 | 0 | protected void showComplement_actionPerformed(boolean complement) |
2914 | { | |
2915 | } | |
2916 | ||
2917 | 0 | protected List<String> updateShowSSRadioButtons() |
2918 | { | |
2919 | // TODO Auto-generated method stub | |
2920 | 0 | return null; |
2921 | } | |
2922 | ||
2923 | 0 | protected void updateShowSSRadioButtons(JMenu showSS, |
2924 | ButtonGroup ssButtonGroup) | |
2925 | { | |
2926 | // TODO Auto-generated method stub | |
2927 | } | |
2928 | ||
2929 | 0 | protected void showSS_actionPerformed(String ssSourceSelection) |
2930 | { | |
2931 | // TODO Auto-generated method stub | |
2932 | ||
2933 | } | |
2934 | } |