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GAlignFrame | 67 | 772 | 296 |
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.Component; | |
26 | import java.awt.GridLayout; | |
27 | import java.awt.event.ActionEvent; | |
28 | import java.awt.event.ActionListener; | |
29 | import java.awt.event.FocusAdapter; | |
30 | import java.awt.event.FocusEvent; | |
31 | import java.awt.event.KeyEvent; | |
32 | import java.awt.event.MouseAdapter; | |
33 | import java.awt.event.MouseEvent; | |
34 | import java.util.HashMap; | |
35 | import java.util.List; | |
36 | import java.util.Map; | |
37 | ||
38 | import javax.swing.BorderFactory; | |
39 | import javax.swing.ButtonGroup; | |
40 | import javax.swing.JCheckBoxMenuItem; | |
41 | import javax.swing.JInternalFrame; | |
42 | import javax.swing.JLabel; | |
43 | import javax.swing.JMenu; | |
44 | import javax.swing.JMenuBar; | |
45 | import javax.swing.JMenuItem; | |
46 | import javax.swing.JPanel; | |
47 | import javax.swing.JRadioButtonMenuItem; | |
48 | import javax.swing.JTabbedPane; | |
49 | import javax.swing.KeyStroke; | |
50 | import javax.swing.event.ChangeEvent; | |
51 | import javax.swing.event.MenuEvent; | |
52 | import javax.swing.event.MenuListener; | |
53 | ||
54 | import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; | |
55 | import jalview.analysis.GeneticCodeI; | |
56 | import jalview.analysis.GeneticCodes; | |
57 | import jalview.api.SplitContainerI; | |
58 | import jalview.bin.Cache; | |
59 | import jalview.gui.JvSwingUtils; | |
60 | import jalview.gui.Preferences; | |
61 | import jalview.io.FileFormats; | |
62 | import jalview.schemes.ResidueColourScheme; | |
63 | import jalview.util.MessageManager; | |
64 | import jalview.util.Platform; | |
65 | ||
66 | @SuppressWarnings("serial") | |
67 | public class GAlignFrame extends JInternalFrame | |
68 | { | |
69 | protected JMenuBar alignFrameMenuBar = new JMenuBar(); | |
70 | ||
71 | protected JMenuItem closeMenuItem = new JMenuItem(); | |
72 | ||
73 | public JMenu webService = new JMenu();// BH 2019 was protected, but not | |
74 | // sufficient for AlignFrame thread run | |
75 | ||
76 | public JMenuItem webServiceNoServices;// BH 2019 was protected, but not | |
77 | // sufficient for AlignFrame thread run | |
78 | ||
79 | protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); | |
80 | ||
81 | protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); | |
82 | ||
83 | protected JMenu sortByAnnotScore = new JMenu(); | |
84 | ||
85 | public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not | |
86 | // sufficient for | |
87 | // AlignFrame.printWriter | |
88 | ||
89 | protected JMenu outputTextboxMenu = new JMenu(); | |
90 | ||
91 | protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); | |
92 | ||
93 | protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); | |
94 | ||
95 | protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); | |
96 | ||
97 | protected JMenuItem undoMenuItem = new JMenuItem(); | |
98 | ||
99 | protected JMenuItem redoMenuItem = new JMenuItem(); | |
100 | ||
101 | protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); | |
102 | ||
103 | protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); | |
104 | ||
105 | public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); | |
106 | ||
107 | JMenuItem copy = new JMenuItem(); | |
108 | ||
109 | JMenuItem copyHighlighted = new JMenuItem(); | |
110 | ||
111 | JMenuItem cut = new JMenuItem(); | |
112 | ||
113 | JMenu pasteMenu = new JMenu(); | |
114 | ||
115 | protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); | |
116 | ||
117 | protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); | |
118 | ||
119 | protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); | |
120 | ||
121 | protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); | |
122 | ||
123 | protected JCheckBoxMenuItem applyToAllGroups; | |
124 | ||
125 | protected JMenu colourMenu = new JMenu(); | |
126 | ||
127 | protected JMenuItem textColour; | |
128 | ||
129 | protected JCheckBoxMenuItem conservationMenuItem; | |
130 | ||
131 | protected JMenuItem modifyConservation; | |
132 | ||
133 | protected JCheckBoxMenuItem abovePIDThreshold; | |
134 | ||
135 | protected JMenuItem modifyPID; | |
136 | ||
137 | protected JCheckBoxMenuItem byConsensusSecondaryStructureMenuItem; | |
138 | ||
139 | protected JMenuItem modifyConsensusSecondaryStructureThreshold; | |
140 | ||
141 | protected JRadioButtonMenuItem annotationColour; | |
142 | ||
143 | protected JMenu sortByTreeMenu = new JMenu(); | |
144 | ||
145 | protected JMenu sort = new JMenu(); | |
146 | ||
147 | protected JMenuItem calculateTree = new JMenuItem(); | |
148 | ||
149 | protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); | |
150 | ||
151 | protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); | |
152 | ||
153 | protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); | |
154 | ||
155 | protected JMenu showTranslation = new JMenu(); | |
156 | ||
157 | protected JMenuItem showReverse = new JMenuItem(); | |
158 | ||
159 | protected JMenuItem showReverseComplement = new JMenuItem(); | |
160 | ||
161 | protected JMenu showProducts = new JMenu(); | |
162 | ||
163 | protected JMenuItem runGroovy = new JMenuItem(); | |
164 | ||
165 | protected JMenuItem loadVcf; | |
166 | ||
167 | protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); | |
168 | ||
169 | protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); | |
170 | ||
171 | protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem(); | |
172 | ||
173 | protected JPanel statusPanel = new JPanel(); | |
174 | ||
175 | protected JMenuItem showAllSeqAnnotations = new JMenuItem(); | |
176 | ||
177 | protected JMenuItem hideAllSeqAnnotations = new JMenuItem(); | |
178 | ||
179 | protected JMenuItem showAllAlAnnotations = new JMenuItem(); | |
180 | ||
181 | protected JMenuItem hideAllAlAnnotations = new JMenuItem(); | |
182 | ||
183 | protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem(); | |
184 | ||
185 | protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); | |
186 | ||
187 | protected JTabbedPane tabbedPane = new JTabbedPane(); | |
188 | ||
189 | protected JMenuItem reload = new JMenuItem(); | |
190 | ||
191 | protected JMenu formatMenu = new JMenu(); | |
192 | ||
193 | protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem(); | |
194 | ||
195 | protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); | |
196 | ||
197 | protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); | |
198 | ||
199 | protected JMenuItem gatherViews = new JMenuItem(); | |
200 | ||
201 | protected JMenuItem expandViews = new JMenuItem(); | |
202 | ||
203 | protected JCheckBoxMenuItem showStrucProvider = new JCheckBoxMenuItem(); | |
204 | ||
205 | protected JCheckBoxMenuItem showSSConsensus = new JCheckBoxMenuItem(); | |
206 | ||
207 | protected JCheckBoxMenuItem showGroupSSConsensus = new JCheckBoxMenuItem(); | |
208 | ||
209 | protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); | |
210 | ||
211 | protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); | |
212 | ||
213 | protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); | |
214 | ||
215 | protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); | |
216 | ||
217 | protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); | |
218 | ||
219 | protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); | |
220 | ||
221 | protected JMenuItem openFeatureSettings; | |
222 | ||
223 | private SequenceAnnotationOrder annotationSortOrder; | |
224 | ||
225 | private boolean showAutoCalculatedAbove = false; | |
226 | ||
227 | private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>(); | |
228 | ||
229 | private SplitContainerI splitFrame; | |
230 | ||
231 | 452 | public GAlignFrame() |
232 | { | |
233 | 452 | try |
234 | { | |
235 | 452 | setFrameIcon(null); |
236 | ||
237 | // for Web-page embedding using id=align-frame-div | |
238 | 452 | setName("jalview-alignment"); |
239 | ||
240 | 452 | jbInit(); |
241 | 452 | setJMenuBar(alignFrameMenuBar); |
242 | ||
243 | // dynamically fill save as menu with available formats | |
244 | 452 | for (String ff : FileFormats.getInstance().getWritableFormats(true)) |
245 | { | |
246 | 4972 | JMenuItem item = new JMenuItem(ff); |
247 | ||
248 | 4972 | item.addActionListener(new ActionListener() |
249 | { | |
250 | 0 | @Override |
251 | public void actionPerformed(ActionEvent e) | |
252 | { | |
253 | 0 | outputText_actionPerformed(e.getActionCommand()); |
254 | } | |
255 | }); | |
256 | ||
257 | 4972 | outputTextboxMenu.add(item); |
258 | } | |
259 | } catch (Exception e) | |
260 | { | |
261 | 0 | jalview.bin.Console.errPrintln(e.toString()); |
262 | } | |
263 | ||
264 | 452 | if (Platform.allowMnemonics()) // was "not mac and not JS" |
265 | { | |
266 | 452 | closeMenuItem.setMnemonic('C'); |
267 | 452 | outputTextboxMenu.setMnemonic('T'); |
268 | 452 | undoMenuItem.setMnemonic('Z'); |
269 | 452 | redoMenuItem.setMnemonic('0'); |
270 | 452 | copy.setMnemonic('C'); |
271 | 452 | cut.setMnemonic('U'); |
272 | 452 | pasteMenu.setMnemonic('P'); |
273 | 452 | reload.setMnemonic('R'); |
274 | } | |
275 | } | |
276 | ||
277 | 452 | private void jbInit() throws Exception |
278 | { | |
279 | 452 | setFrameIcon(null); |
280 | 452 | initColourMenu(); |
281 | ||
282 | 452 | JMenuItem saveAs = new JMenuItem( |
283 | MessageManager.getString("action.save_as")); | |
284 | 452 | ActionListener al = new ActionListener() |
285 | { | |
286 | 0 | @Override |
287 | public void actionPerformed(ActionEvent e) | |
288 | { | |
289 | 0 | saveAs_actionPerformed(); |
290 | } | |
291 | }; | |
292 | ||
293 | // FIXME getDefaultToolkit throws an exception in Headless mode | |
294 | 452 | KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, |
295 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
296 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
297 | false); | |
298 | 452 | addMenuActionAndAccelerator(keyStroke, saveAs, al); |
299 | ||
300 | 452 | closeMenuItem.setText(MessageManager.getString("action.close")); |
301 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
302 | jalview.util.ShortcutKeyMaskExWrapper | |
303 | .getMenuShortcutKeyMaskEx(), | |
304 | false); | |
305 | 452 | al = new ActionListener() |
306 | { | |
307 | 0 | @Override |
308 | public void actionPerformed(ActionEvent e) | |
309 | { | |
310 | 0 | closeMenuItem_actionPerformed(false); |
311 | } | |
312 | }; | |
313 | 452 | addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); |
314 | ||
315 | 452 | JMenu editMenu = new JMenu(MessageManager.getString("action.edit")); |
316 | 452 | JMenu viewMenu = new JMenu(MessageManager.getString("action.view")); |
317 | 452 | JMenu annotationsMenu = new JMenu( |
318 | MessageManager.getString("action.annotations")); | |
319 | 452 | JMenu showMenu = new JMenu(MessageManager.getString("action.show")); |
320 | 452 | colourMenu.setText(MessageManager.getString("action.colour")); |
321 | 452 | JMenu calculateMenu = new JMenu( |
322 | MessageManager.getString("action.calculate")); | |
323 | 452 | webService.setText(MessageManager.getString("action.web_service")); |
324 | 452 | JMenuItem selectAllSequenceMenuItem = new JMenuItem( |
325 | MessageManager.getString("action.select_all")); | |
326 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, |
327 | jalview.util.ShortcutKeyMaskExWrapper | |
328 | .getMenuShortcutKeyMaskEx(), | |
329 | false); | |
330 | 452 | al = new ActionListener() |
331 | { | |
332 | 0 | @Override |
333 | public void actionPerformed(ActionEvent e) | |
334 | { | |
335 | 0 | selectAllSequenceMenuItem_actionPerformed(e); |
336 | } | |
337 | }; | |
338 | 452 | addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al); |
339 | ||
340 | 452 | JMenuItem deselectAllSequenceMenuItem = new JMenuItem( |
341 | MessageManager.getString("action.deselect_all")); | |
342 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false); |
343 | 452 | al = new ActionListener() |
344 | { | |
345 | 0 | @Override |
346 | public void actionPerformed(ActionEvent e) | |
347 | { | |
348 | 0 | deselectAllSequenceMenuItem_actionPerformed(e); |
349 | } | |
350 | }; | |
351 | 452 | addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al); |
352 | ||
353 | 452 | JMenuItem invertSequenceMenuItem = new JMenuItem( |
354 | MessageManager.getString("action.invert_sequence_selection")); | |
355 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, |
356 | jalview.util.ShortcutKeyMaskExWrapper | |
357 | .getMenuShortcutKeyMaskEx(), | |
358 | false); | |
359 | 452 | al = new ActionListener() |
360 | { | |
361 | 0 | @Override |
362 | public void actionPerformed(ActionEvent e) | |
363 | { | |
364 | 0 | invertSequenceMenuItem_actionPerformed(e); |
365 | } | |
366 | }; | |
367 | 452 | addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al); |
368 | ||
369 | 452 | JMenuItem grpsFromSelection = new JMenuItem( |
370 | MessageManager.getString("action.make_groups_selection")); | |
371 | 452 | grpsFromSelection.addActionListener(new ActionListener() |
372 | { | |
373 | 0 | @Override |
374 | public void actionPerformed(ActionEvent e) | |
375 | { | |
376 | 0 | makeGrpsFromSelection_actionPerformed(e); |
377 | } | |
378 | }); | |
379 | 452 | JMenuItem expandAlignment = new JMenuItem( |
380 | MessageManager.getString("action.view_flanking_regions")); | |
381 | 452 | expandAlignment.setToolTipText( |
382 | MessageManager.getString("label.view_flanking_regions")); | |
383 | 452 | expandAlignment.addActionListener(new ActionListener() |
384 | { | |
385 | 0 | @Override |
386 | public void actionPerformed(ActionEvent e) | |
387 | { | |
388 | 0 | expand_newalign(e); |
389 | } | |
390 | }); | |
391 | 452 | JMenuItem remove2LeftMenuItem = new JMenuItem( |
392 | MessageManager.getString("action.remove_left")); | |
393 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, |
394 | jalview.util.ShortcutKeyMaskExWrapper | |
395 | .getMenuShortcutKeyMaskEx(), | |
396 | false); | |
397 | 452 | al = new ActionListener() |
398 | { | |
399 | 0 | @Override |
400 | public void actionPerformed(ActionEvent e) | |
401 | { | |
402 | 0 | remove2LeftMenuItem_actionPerformed(e); |
403 | } | |
404 | }; | |
405 | 452 | addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); |
406 | ||
407 | 452 | JMenuItem remove2RightMenuItem = new JMenuItem( |
408 | MessageManager.getString("action.remove_right")); | |
409 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, |
410 | jalview.util.ShortcutKeyMaskExWrapper | |
411 | .getMenuShortcutKeyMaskEx(), | |
412 | false); | |
413 | 452 | al = new ActionListener() |
414 | { | |
415 | 0 | @Override |
416 | public void actionPerformed(ActionEvent e) | |
417 | { | |
418 | 0 | remove2RightMenuItem_actionPerformed(e); |
419 | } | |
420 | }; | |
421 | 452 | addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al); |
422 | ||
423 | 452 | JMenuItem removeGappedColumnMenuItem = new JMenuItem( |
424 | MessageManager.getString("action.remove_empty_columns")); | |
425 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, |
426 | jalview.util.ShortcutKeyMaskExWrapper | |
427 | .getMenuShortcutKeyMaskEx(), | |
428 | false); | |
429 | 452 | al = new ActionListener() |
430 | { | |
431 | 0 | @Override |
432 | public void actionPerformed(ActionEvent e) | |
433 | { | |
434 | 0 | removeGappedColumnMenuItem_actionPerformed(e); |
435 | } | |
436 | }; | |
437 | 452 | addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al); |
438 | ||
439 | 452 | JMenuItem removeAllGapsMenuItem = new JMenuItem( |
440 | MessageManager.getString("action.remove_all_gaps")); | |
441 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, |
442 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
443 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
444 | false); | |
445 | 452 | al = new ActionListener() |
446 | { | |
447 | 0 | @Override |
448 | public void actionPerformed(ActionEvent e) | |
449 | { | |
450 | 0 | removeAllGapsMenuItem_actionPerformed(e); |
451 | } | |
452 | }; | |
453 | 452 | addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al); |
454 | ||
455 | 452 | JMenuItem justifyLeftMenuItem = new JMenuItem( |
456 | MessageManager.getString("action.left_justify")); | |
457 | 452 | justifyLeftMenuItem.setToolTipText( |
458 | MessageManager.getString("tooltip.left_justify")); | |
459 | 452 | justifyLeftMenuItem.addActionListener(new ActionListener() |
460 | { | |
461 | 0 | @Override |
462 | public void actionPerformed(ActionEvent e) | |
463 | { | |
464 | 0 | justifyLeftMenuItem_actionPerformed(e); |
465 | } | |
466 | }); | |
467 | 452 | JMenuItem justifyRightMenuItem = new JMenuItem( |
468 | MessageManager.getString("action.right_justify")); | |
469 | 452 | justifyRightMenuItem.setToolTipText( |
470 | MessageManager.getString("action.left_justify")); | |
471 | ||
472 | 452 | justifyRightMenuItem.addActionListener(new ActionListener() |
473 | { | |
474 | 0 | @Override |
475 | public void actionPerformed(ActionEvent e) | |
476 | { | |
477 | 0 | justifyRightMenuItem_actionPerformed(e); |
478 | } | |
479 | }); | |
480 | 452 | viewBoxesMenuItem.setText(MessageManager.getString("action.boxes")); |
481 | 452 | viewBoxesMenuItem.setState(true); |
482 | 452 | viewBoxesMenuItem.addActionListener(new ActionListener() |
483 | { | |
484 | 0 | @Override |
485 | public void actionPerformed(ActionEvent e) | |
486 | { | |
487 | 0 | viewBoxesMenuItem_actionPerformed(e); |
488 | } | |
489 | }); | |
490 | 452 | viewTextMenuItem.setText(MessageManager.getString("action.text")); |
491 | 452 | viewTextMenuItem.setState(true); |
492 | 452 | viewTextMenuItem.addActionListener(new ActionListener() |
493 | { | |
494 | 0 | @Override |
495 | public void actionPerformed(ActionEvent e) | |
496 | { | |
497 | 0 | viewTextMenuItem_actionPerformed(e); |
498 | } | |
499 | }); | |
500 | 452 | showNonconservedMenuItem |
501 | .setText(MessageManager.getString("label.show_non_conserved")); | |
502 | 452 | showNonconservedMenuItem.setState(false); |
503 | 452 | showNonconservedMenuItem.addActionListener(new ActionListener() |
504 | { | |
505 | 0 | @Override |
506 | public void actionPerformed(ActionEvent e) | |
507 | { | |
508 | 0 | showUnconservedMenuItem_actionPerformed(e); |
509 | } | |
510 | }); | |
511 | 452 | JMenuItem sortPairwiseMenuItem = new JMenuItem( |
512 | MessageManager.getString("action.by_pairwise_id")); | |
513 | 452 | sortPairwiseMenuItem.addActionListener(new ActionListener() |
514 | { | |
515 | 0 | @Override |
516 | public void actionPerformed(ActionEvent e) | |
517 | { | |
518 | 0 | sortPairwiseMenuItem_actionPerformed(e); |
519 | } | |
520 | }); | |
521 | 452 | JMenuItem sortIDMenuItem = new JMenuItem( |
522 | MessageManager.getString("action.by_id")); | |
523 | 452 | sortIDMenuItem.addActionListener(new ActionListener() |
524 | { | |
525 | 0 | @Override |
526 | public void actionPerformed(ActionEvent e) | |
527 | { | |
528 | 0 | sortIDMenuItem_actionPerformed(e); |
529 | } | |
530 | }); | |
531 | 452 | JMenuItem sortLengthMenuItem = new JMenuItem( |
532 | MessageManager.getString("action.by_length")); | |
533 | 452 | sortLengthMenuItem.addActionListener(new ActionListener() |
534 | { | |
535 | 0 | @Override |
536 | public void actionPerformed(ActionEvent e) | |
537 | { | |
538 | 0 | sortLengthMenuItem_actionPerformed(e); |
539 | } | |
540 | }); | |
541 | 452 | JMenuItem sortGroupMenuItem = new JMenuItem( |
542 | MessageManager.getString("action.by_group")); | |
543 | 452 | sortGroupMenuItem.addActionListener(new ActionListener() |
544 | { | |
545 | 0 | @Override |
546 | public void actionPerformed(ActionEvent e) | |
547 | { | |
548 | 0 | sortGroupMenuItem_actionPerformed(e); |
549 | } | |
550 | }); | |
551 | ||
552 | 452 | JMenuItem removeRedundancyMenuItem = new JMenuItem( |
553 | MessageManager.getString("action.remove_redundancy")); | |
554 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, |
555 | jalview.util.ShortcutKeyMaskExWrapper | |
556 | .getMenuShortcutKeyMaskEx(), | |
557 | false); | |
558 | 452 | al = new ActionListener() |
559 | { | |
560 | 0 | @Override |
561 | public void actionPerformed(ActionEvent e) | |
562 | { | |
563 | 0 | removeRedundancyMenuItem_actionPerformed(e); |
564 | } | |
565 | }; | |
566 | 452 | addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); |
567 | ||
568 | 452 | JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( |
569 | MessageManager.getString("action.pairwise_alignment")); | |
570 | 452 | pairwiseAlignmentMenuItem.addActionListener(new ActionListener() |
571 | { | |
572 | 0 | @Override |
573 | public void actionPerformed(ActionEvent e) | |
574 | { | |
575 | 0 | pairwiseAlignmentMenuItem_actionPerformed(e); |
576 | } | |
577 | }); | |
578 | ||
579 | 452 | this.getContentPane().setLayout(new BorderLayout()); |
580 | 452 | alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
581 | 452 | statusBar.setBackground(Color.white); |
582 | 452 | statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
583 | 452 | statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); |
584 | 452 | statusBar.setText(MessageManager.getString("label.status_bar")); |
585 | 452 | outputTextboxMenu |
586 | .setText(MessageManager.getString("label.out_to_textbox")); | |
587 | ||
588 | 452 | annotationPanelMenuItem.setActionCommand(""); |
589 | 452 | annotationPanelMenuItem |
590 | .setText(MessageManager.getString("label.show_annotations")); | |
591 | 452 | annotationPanelMenuItem |
592 | .setState(Cache.getDefault("SHOW_ANNOTATIONS", true)); | |
593 | 452 | annotationPanelMenuItem.addActionListener(new ActionListener() |
594 | { | |
595 | 0 | @Override |
596 | public void actionPerformed(ActionEvent e) | |
597 | { | |
598 | 0 | annotationPanelMenuItem_actionPerformed(e); |
599 | } | |
600 | }); | |
601 | 452 | showAllAlAnnotations.setText( |
602 | MessageManager.getString("label.show_all_al_annotations")); | |
603 | 452 | final boolean isAnnotationPanelShown = annotationPanelMenuItem |
604 | .getState(); | |
605 | 452 | showAllAlAnnotations.setEnabled(isAnnotationPanelShown); |
606 | 452 | showAllAlAnnotations.addActionListener(new ActionListener() |
607 | { | |
608 | 0 | @Override |
609 | public void actionPerformed(ActionEvent e) | |
610 | { | |
611 | 0 | showAllAnnotations_actionPerformed(false, true); |
612 | } | |
613 | }); | |
614 | 452 | hideAllAlAnnotations.setText( |
615 | MessageManager.getString("label.hide_all_al_annotations")); | |
616 | 452 | hideAllAlAnnotations.setEnabled(isAnnotationPanelShown); |
617 | 452 | hideAllAlAnnotations.addActionListener(new ActionListener() |
618 | { | |
619 | 0 | @Override |
620 | public void actionPerformed(ActionEvent e) | |
621 | { | |
622 | 0 | hideAllAnnotations_actionPerformed(false, true); |
623 | } | |
624 | }); | |
625 | 452 | showAllSeqAnnotations.setText( |
626 | MessageManager.getString("label.show_all_seq_annotations")); | |
627 | 452 | showAllSeqAnnotations.setEnabled(isAnnotationPanelShown); |
628 | 452 | showAllSeqAnnotations.addActionListener(new ActionListener() |
629 | { | |
630 | 0 | @Override |
631 | public void actionPerformed(ActionEvent e) | |
632 | { | |
633 | 0 | showAllAnnotations_actionPerformed(true, false); |
634 | } | |
635 | }); | |
636 | 452 | hideAllSeqAnnotations.setText( |
637 | MessageManager.getString("label.hide_all_seq_annotations")); | |
638 | 452 | hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown); |
639 | 452 | hideAllSeqAnnotations.addActionListener(new ActionListener() |
640 | { | |
641 | 0 | @Override |
642 | public void actionPerformed(ActionEvent e) | |
643 | { | |
644 | 0 | hideAllAnnotations_actionPerformed(true, false); |
645 | } | |
646 | }); | |
647 | 452 | SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder |
648 | .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, | |
649 | SequenceAnnotationOrder.NONE.name())); | |
650 | 452 | final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem( |
651 | MessageManager.getString("label.sort_annotations_by_sequence")); | |
652 | 452 | final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem( |
653 | MessageManager.getString("label.sort_annotations_by_label")); | |
654 | ||
655 | 452 | sortAnnBySequence.setSelected( |
656 | sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); | |
657 | 452 | sortAnnBySequence.addActionListener(new ActionListener() |
658 | { | |
659 | 0 | @Override |
660 | public void actionPerformed(ActionEvent e) | |
661 | { | |
662 | 0 | boolean newState = sortAnnBySequence.getState(); |
663 | 0 | sortAnnByLabel.setSelected(false); |
664 | 0 | setAnnotationSortOrder( |
665 | 0 | newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL |
666 | : SequenceAnnotationOrder.NONE); | |
667 | 0 | sortAnnotations_actionPerformed(); |
668 | } | |
669 | }); | |
670 | 452 | sortAnnByLabel.setSelected( |
671 | sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); | |
672 | 452 | sortAnnByLabel.addActionListener(new ActionListener() |
673 | { | |
674 | 0 | @Override |
675 | public void actionPerformed(ActionEvent e) | |
676 | { | |
677 | 0 | boolean newState = sortAnnByLabel.getState(); |
678 | 0 | sortAnnBySequence.setSelected(false); |
679 | 0 | setAnnotationSortOrder( |
680 | 0 | newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE |
681 | : SequenceAnnotationOrder.NONE); | |
682 | 0 | sortAnnotations_actionPerformed(); |
683 | } | |
684 | }); | |
685 | 452 | showStrucProvider = new JCheckBoxMenuItem( |
686 | MessageManager.getString("label.show_structure_provider")); | |
687 | 452 | showStrucProvider.addActionListener(new ActionListener() |
688 | { | |
689 | 0 | @Override |
690 | public void actionPerformed(ActionEvent e) | |
691 | { | |
692 | 0 | showStructureProvider_actionPerformed(e); |
693 | } | |
694 | ||
695 | }); | |
696 | 452 | colourTextMenuItem = new JCheckBoxMenuItem( |
697 | MessageManager.getString("label.colour_text")); | |
698 | 452 | colourTextMenuItem.addActionListener(new ActionListener() |
699 | { | |
700 | 0 | @Override |
701 | public void actionPerformed(ActionEvent e) | |
702 | { | |
703 | 0 | colourTextMenuItem_actionPerformed(e); |
704 | } | |
705 | }); | |
706 | ||
707 | 452 | JMenuItem htmlMenuItem = new JMenuItem( |
708 | MessageManager.getString("label.html")); | |
709 | 452 | htmlMenuItem.addActionListener(new ActionListener() |
710 | { | |
711 | 0 | @Override |
712 | public void actionPerformed(ActionEvent e) | |
713 | { | |
714 | 0 | htmlMenuItem_actionPerformed(e); |
715 | } | |
716 | }); | |
717 | ||
718 | 452 | JMenuItem createBioJS = new JMenuItem( |
719 | MessageManager.getString("label.biojs_html_export")); | |
720 | 452 | createBioJS.addActionListener(new java.awt.event.ActionListener() |
721 | { | |
722 | 0 | @Override |
723 | public void actionPerformed(ActionEvent e) | |
724 | { | |
725 | 0 | bioJSMenuItem_actionPerformed(e); |
726 | } | |
727 | }); | |
728 | ||
729 | 452 | JMenuItem overviewMenuItem = new JMenuItem( |
730 | MessageManager.getString("label.overview_window")); | |
731 | 452 | overviewMenuItem.addActionListener(new ActionListener() |
732 | { | |
733 | 0 | @Override |
734 | public void actionPerformed(ActionEvent e) | |
735 | { | |
736 | 0 | overviewMenuItem_actionPerformed(e); |
737 | } | |
738 | }); | |
739 | ||
740 | 452 | undoMenuItem.setEnabled(false); |
741 | 452 | undoMenuItem.setText(MessageManager.getString("action.undo")); |
742 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, |
743 | jalview.util.ShortcutKeyMaskExWrapper | |
744 | .getMenuShortcutKeyMaskEx(), | |
745 | false); | |
746 | 452 | al = new ActionListener() |
747 | { | |
748 | 0 | @Override |
749 | public void actionPerformed(ActionEvent e) | |
750 | { | |
751 | 0 | undoMenuItem_actionPerformed(e); |
752 | } | |
753 | }; | |
754 | 452 | addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); |
755 | ||
756 | 452 | redoMenuItem.setEnabled(false); |
757 | 452 | redoMenuItem.setText(MessageManager.getString("action.redo")); |
758 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, |
759 | jalview.util.ShortcutKeyMaskExWrapper | |
760 | .getMenuShortcutKeyMaskEx(), | |
761 | false); | |
762 | 452 | al = new ActionListener() |
763 | { | |
764 | 0 | @Override |
765 | public void actionPerformed(ActionEvent e) | |
766 | { | |
767 | 0 | redoMenuItem_actionPerformed(e); |
768 | } | |
769 | }; | |
770 | 452 | addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); |
771 | ||
772 | 452 | wrapMenuItem.setText(MessageManager.getString("label.wrap")); |
773 | 452 | wrapMenuItem.addActionListener(new ActionListener() |
774 | { | |
775 | 0 | @Override |
776 | public void actionPerformed(ActionEvent e) | |
777 | { | |
778 | 0 | wrapMenuItem_actionPerformed(e); |
779 | } | |
780 | }); | |
781 | ||
782 | 452 | JMenuItem printMenuItem = new JMenuItem( |
783 | MessageManager.getString("action.print")); | |
784 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, |
785 | jalview.util.ShortcutKeyMaskExWrapper | |
786 | .getMenuShortcutKeyMaskEx(), | |
787 | false); | |
788 | 452 | al = new ActionListener() |
789 | { | |
790 | 0 | @Override |
791 | public void actionPerformed(ActionEvent e) | |
792 | { | |
793 | 0 | printMenuItem_actionPerformed(e); |
794 | } | |
795 | }; | |
796 | 452 | addMenuActionAndAccelerator(keyStroke, printMenuItem, al); |
797 | ||
798 | 452 | renderGapsMenuItem |
799 | .setText(MessageManager.getString("action.show_gaps")); | |
800 | 452 | renderGapsMenuItem.setState(true); |
801 | 452 | renderGapsMenuItem.addActionListener(new ActionListener() |
802 | { | |
803 | 0 | @Override |
804 | public void actionPerformed(ActionEvent e) | |
805 | { | |
806 | 0 | renderGapsMenuItem_actionPerformed(e); |
807 | } | |
808 | }); | |
809 | ||
810 | 452 | JMenuItem findMenuItem = new JMenuItem( |
811 | MessageManager.getString("action.find")); | |
812 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, |
813 | jalview.util.ShortcutKeyMaskExWrapper | |
814 | .getMenuShortcutKeyMaskEx(), | |
815 | false); | |
816 | 452 | findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, |
817 | MessageManager.getString("label.find_tip"))); | |
818 | 452 | al = new ActionListener() |
819 | { | |
820 | 0 | @Override |
821 | public void actionPerformed(ActionEvent e) | |
822 | { | |
823 | 0 | findMenuItem_actionPerformed(e); |
824 | } | |
825 | }; | |
826 | 452 | addMenuActionAndAccelerator(keyStroke, findMenuItem, al); |
827 | ||
828 | 452 | showSeqFeatures.setText( |
829 | MessageManager.getString("label.show_sequence_features")); | |
830 | 452 | showSeqFeatures.addActionListener(new ActionListener() |
831 | { | |
832 | 0 | @Override |
833 | public void actionPerformed(ActionEvent actionEvent) | |
834 | { | |
835 | 0 | showSeqFeatures_actionPerformed(actionEvent); |
836 | } | |
837 | }); | |
838 | /* | |
839 | * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); | |
840 | * showSeqFeaturesHeight.addActionListener(new ActionListener() { public | |
841 | * void actionPerformed(ActionEvent actionEvent) { | |
842 | * showSeqFeaturesHeight_actionPerformed(actionEvent); } }); | |
843 | */ | |
844 | 452 | showDbRefsMenuitem |
845 | .setText(MessageManager.getString("label.show_database_refs")); | |
846 | 452 | showDbRefsMenuitem.addActionListener(new ActionListener() |
847 | { | |
848 | ||
849 | 0 | @Override |
850 | public void actionPerformed(ActionEvent e) | |
851 | { | |
852 | 0 | showDbRefs_actionPerformed(e); |
853 | } | |
854 | ||
855 | }); | |
856 | 452 | showNpFeatsMenuitem.setText( |
857 | MessageManager.getString("label.show_non_positional_features")); | |
858 | 452 | showNpFeatsMenuitem.addActionListener(new ActionListener() |
859 | { | |
860 | ||
861 | 0 | @Override |
862 | public void actionPerformed(ActionEvent e) | |
863 | { | |
864 | 0 | showNpFeats_actionPerformed(e); |
865 | } | |
866 | ||
867 | }); | |
868 | 452 | showGroupConservation |
869 | .setText(MessageManager.getString("label.group_conservation")); | |
870 | 452 | showGroupConservation.addActionListener(new ActionListener() |
871 | { | |
872 | ||
873 | 0 | @Override |
874 | public void actionPerformed(ActionEvent e) | |
875 | { | |
876 | 0 | showGroupConservation_actionPerformed(e); |
877 | } | |
878 | ||
879 | }); | |
880 | ||
881 | 452 | showSSConsensus.setText(MessageManager |
882 | .getString("label.show_secondary_structure_consensus")); | |
883 | 452 | showSSConsensus.addActionListener(new ActionListener() |
884 | { | |
885 | ||
886 | 0 | @Override |
887 | public void actionPerformed(ActionEvent e) | |
888 | { | |
889 | 0 | showSSConsensus_actionPerformed(e); |
890 | } | |
891 | ||
892 | }); | |
893 | ||
894 | 452 | showGroupSSConsensus |
895 | .setText(MessageManager.getString("label.group_ss_consensus")); | |
896 | 452 | showGroupSSConsensus.addActionListener(new ActionListener() |
897 | { | |
898 | ||
899 | 0 | @Override |
900 | public void actionPerformed(ActionEvent e) | |
901 | { | |
902 | 0 | showGroupSSConsensus_actionPerformed(e); |
903 | } | |
904 | ||
905 | }); | |
906 | ||
907 | 452 | showGroupConsensus |
908 | .setText(MessageManager.getString("label.group_consensus")); | |
909 | 452 | showGroupConsensus.addActionListener(new ActionListener() |
910 | { | |
911 | ||
912 | 0 | @Override |
913 | public void actionPerformed(ActionEvent e) | |
914 | { | |
915 | 0 | showGroupConsensus_actionPerformed(e); |
916 | } | |
917 | ||
918 | }); | |
919 | 452 | showConsensusHistogram.setText( |
920 | MessageManager.getString("label.show_consensus_histogram")); | |
921 | 452 | showConsensusHistogram.addActionListener(new ActionListener() |
922 | { | |
923 | ||
924 | 0 | @Override |
925 | public void actionPerformed(ActionEvent e) | |
926 | { | |
927 | 0 | showConsensusHistogram_actionPerformed(e); |
928 | } | |
929 | ||
930 | }); | |
931 | ||
932 | 452 | showSequenceLogo |
933 | .setText(MessageManager.getString("label.show_consensus_logo")); | |
934 | 452 | showSequenceLogo.addActionListener(new ActionListener() |
935 | { | |
936 | ||
937 | 0 | @Override |
938 | public void actionPerformed(ActionEvent e) | |
939 | { | |
940 | 0 | showSequenceLogo_actionPerformed(e); |
941 | } | |
942 | ||
943 | }); | |
944 | 452 | normaliseSequenceLogo |
945 | .setText(MessageManager.getString("label.norm_consensus_logo")); | |
946 | 452 | normaliseSequenceLogo.addActionListener(new ActionListener() |
947 | { | |
948 | ||
949 | 0 | @Override |
950 | public void actionPerformed(ActionEvent e) | |
951 | { | |
952 | 0 | normaliseSequenceLogo_actionPerformed(e); |
953 | } | |
954 | ||
955 | }); | |
956 | 452 | applyAutoAnnotationSettings |
957 | .setText(MessageManager.getString("label.apply_all_groups")); | |
958 | 452 | applyAutoAnnotationSettings.setState(false); |
959 | 452 | applyAutoAnnotationSettings.setVisible(true); |
960 | 452 | applyAutoAnnotationSettings.addActionListener(new ActionListener() |
961 | { | |
962 | 0 | @Override |
963 | public void actionPerformed(ActionEvent e) | |
964 | { | |
965 | 0 | applyAutoAnnotationSettings_actionPerformed(e); |
966 | } | |
967 | }); | |
968 | ||
969 | 452 | ButtonGroup buttonGroup = new ButtonGroup(); |
970 | 452 | final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem( |
971 | MessageManager.getString("label.show_first")); | |
972 | 452 | final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem( |
973 | MessageManager.getString("label.show_last")); | |
974 | 452 | buttonGroup.add(showAutoFirst); |
975 | 452 | buttonGroup.add(showAutoLast); |
976 | 452 | final boolean autoFirst = Cache |
977 | .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); | |
978 | 452 | showAutoFirst.setSelected(autoFirst); |
979 | 452 | setShowAutoCalculatedAbove(autoFirst); |
980 | 452 | showAutoFirst.addActionListener(new ActionListener() |
981 | { | |
982 | 0 | @Override |
983 | public void actionPerformed(ActionEvent e) | |
984 | { | |
985 | 0 | setShowAutoCalculatedAbove(showAutoFirst.isSelected()); |
986 | 0 | sortAnnotations_actionPerformed(); |
987 | } | |
988 | }); | |
989 | 452 | showAutoLast.setSelected(!showAutoFirst.isSelected()); |
990 | 452 | showAutoLast.addActionListener(new ActionListener() |
991 | { | |
992 | 0 | @Override |
993 | public void actionPerformed(ActionEvent e) | |
994 | { | |
995 | 0 | setShowAutoCalculatedAbove(!showAutoLast.isSelected()); |
996 | 0 | sortAnnotations_actionPerformed(); |
997 | } | |
998 | }); | |
999 | ||
1000 | 452 | JMenuItem deleteGroups = new JMenuItem( |
1001 | MessageManager.getString("action.undefine_groups")); | |
1002 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, |
1003 | jalview.util.ShortcutKeyMaskExWrapper | |
1004 | .getMenuShortcutKeyMaskEx(), | |
1005 | false); | |
1006 | 452 | al = new ActionListener() |
1007 | { | |
1008 | 0 | @Override |
1009 | public void actionPerformed(ActionEvent e) | |
1010 | { | |
1011 | 0 | deleteGroups_actionPerformed(e); |
1012 | } | |
1013 | }; | |
1014 | 452 | addMenuActionAndAccelerator(keyStroke, deleteGroups, al); |
1015 | ||
1016 | 452 | JMenuItem annotationColumn = new JMenuItem( |
1017 | MessageManager.getString("action.select_by_annotation")); | |
1018 | 452 | annotationColumn.addActionListener(new ActionListener() |
1019 | { | |
1020 | 0 | @Override |
1021 | public void actionPerformed(ActionEvent e) | |
1022 | { | |
1023 | 0 | annotationColumn_actionPerformed(e); |
1024 | } | |
1025 | }); | |
1026 | ||
1027 | 452 | JMenuItem createGroup = new JMenuItem( |
1028 | MessageManager.getString("action.create_group")); | |
1029 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, |
1030 | jalview.util.ShortcutKeyMaskExWrapper | |
1031 | .getMenuShortcutKeyMaskEx(), | |
1032 | false); | |
1033 | 452 | al = new ActionListener() |
1034 | { | |
1035 | 0 | @Override |
1036 | public void actionPerformed(ActionEvent e) | |
1037 | { | |
1038 | 0 | createGroup_actionPerformed(e); |
1039 | } | |
1040 | }; | |
1041 | 452 | addMenuActionAndAccelerator(keyStroke, createGroup, al); |
1042 | ||
1043 | 452 | JMenuItem unGroup = new JMenuItem( |
1044 | MessageManager.getString("action.remove_group")); | |
1045 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, |
1046 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1047 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
1048 | false); | |
1049 | 452 | al = new ActionListener() |
1050 | { | |
1051 | 0 | @Override |
1052 | public void actionPerformed(ActionEvent e) | |
1053 | { | |
1054 | 0 | unGroup_actionPerformed(e); |
1055 | } | |
1056 | }; | |
1057 | 452 | addMenuActionAndAccelerator(keyStroke, unGroup, al); |
1058 | ||
1059 | 452 | copy.setText(MessageManager.getString("action.copy")); |
1060 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, |
1061 | jalview.util.ShortcutKeyMaskExWrapper | |
1062 | .getMenuShortcutKeyMaskEx(), | |
1063 | false); | |
1064 | ||
1065 | 452 | al = new ActionListener() |
1066 | { | |
1067 | 0 | @Override |
1068 | public void actionPerformed(ActionEvent e) | |
1069 | { | |
1070 | 0 | copy_actionPerformed(); |
1071 | } | |
1072 | }; | |
1073 | 452 | addMenuActionAndAccelerator(keyStroke, copy, al); |
1074 | ||
1075 | 452 | cut.setText(MessageManager.getString("action.cut")); |
1076 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, |
1077 | jalview.util.ShortcutKeyMaskExWrapper | |
1078 | .getMenuShortcutKeyMaskEx(), | |
1079 | false); | |
1080 | 452 | al = new ActionListener() |
1081 | { | |
1082 | 0 | @Override |
1083 | public void actionPerformed(ActionEvent e) | |
1084 | { | |
1085 | 0 | cut_actionPerformed(); |
1086 | } | |
1087 | }; | |
1088 | 452 | addMenuActionAndAccelerator(keyStroke, cut, al); |
1089 | ||
1090 | 452 | JMenuItem delete = new JMenuItem( |
1091 | MessageManager.getString("action.delete")); | |
1092 | 452 | delete.addActionListener(new ActionListener() |
1093 | { | |
1094 | 0 | @Override |
1095 | public void actionPerformed(ActionEvent e) | |
1096 | { | |
1097 | 0 | delete_actionPerformed(); |
1098 | } | |
1099 | }); | |
1100 | ||
1101 | 452 | pasteMenu.setText(MessageManager.getString("action.paste")); |
1102 | 452 | JMenuItem pasteNew = new JMenuItem( |
1103 | MessageManager.getString("label.to_new_alignment")); | |
1104 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, |
1105 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1106 | | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
1107 | false); | |
1108 | 452 | al = new ActionListener() |
1109 | { | |
1110 | 0 | @Override |
1111 | public void actionPerformed(ActionEvent e) | |
1112 | { | |
1113 | 0 | pasteNew_actionPerformed(e); |
1114 | } | |
1115 | }; | |
1116 | 452 | addMenuActionAndAccelerator(keyStroke, pasteNew, al); |
1117 | ||
1118 | 452 | JMenuItem pasteThis = new JMenuItem( |
1119 | MessageManager.getString("label.to_this_alignment")); | |
1120 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, |
1121 | jalview.util.ShortcutKeyMaskExWrapper | |
1122 | .getMenuShortcutKeyMaskEx(), | |
1123 | false); | |
1124 | 452 | al = new ActionListener() |
1125 | { | |
1126 | 0 | @Override |
1127 | public void actionPerformed(ActionEvent e) | |
1128 | { | |
1129 | 0 | pasteThis_actionPerformed(e); |
1130 | } | |
1131 | }; | |
1132 | 452 | addMenuActionAndAccelerator(keyStroke, pasteThis, al); |
1133 | ||
1134 | 452 | JMenuItem createPNG = new JMenuItem("PNG"); |
1135 | 452 | createPNG.addActionListener(new ActionListener() |
1136 | { | |
1137 | 0 | @Override |
1138 | public void actionPerformed(ActionEvent e) | |
1139 | { | |
1140 | 0 | createPNG_actionPerformed(e); |
1141 | } | |
1142 | }); | |
1143 | 452 | createPNG.setActionCommand( |
1144 | MessageManager.getString("label.save_png_image")); | |
1145 | ||
1146 | 452 | JMenuItem font = new JMenuItem(MessageManager.getString("action.font")); |
1147 | 452 | font.addActionListener(new ActionListener() |
1148 | { | |
1149 | 0 | @Override |
1150 | public void actionPerformed(ActionEvent e) | |
1151 | { | |
1152 | 0 | font_actionPerformed(e); |
1153 | } | |
1154 | }); | |
1155 | 452 | seqLimits.setText( |
1156 | MessageManager.getString("label.show_sequence_limits")); | |
1157 | 452 | seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true)); |
1158 | 452 | seqLimits.addActionListener(new ActionListener() |
1159 | { | |
1160 | 0 | @Override |
1161 | public void actionPerformed(ActionEvent e) | |
1162 | { | |
1163 | 0 | seqLimit_actionPerformed(e); |
1164 | } | |
1165 | }); | |
1166 | 452 | JMenuItem epsFile = new JMenuItem("EPS"); |
1167 | 452 | epsFile.addActionListener(new ActionListener() |
1168 | { | |
1169 | 0 | @Override |
1170 | public void actionPerformed(ActionEvent e) | |
1171 | { | |
1172 | 0 | createEPS_actionPerformed(e); |
1173 | } | |
1174 | }); | |
1175 | ||
1176 | 452 | JMenuItem createSVG = new JMenuItem("SVG"); |
1177 | 452 | createSVG.addActionListener(new ActionListener() |
1178 | { | |
1179 | 0 | @Override |
1180 | public void actionPerformed(ActionEvent e) | |
1181 | { | |
1182 | 0 | createSVG_actionPerformed(e); |
1183 | } | |
1184 | }); | |
1185 | ||
1186 | 452 | JMenuItem loadTreeMenuItem = new JMenuItem( |
1187 | MessageManager.getString("label.load_associated_tree")); | |
1188 | 452 | loadTreeMenuItem.setActionCommand( |
1189 | MessageManager.getString("label.load_tree_for_sequence_set")); | |
1190 | 452 | loadTreeMenuItem.addActionListener(new ActionListener() |
1191 | { | |
1192 | 0 | @Override |
1193 | public void actionPerformed(ActionEvent e) | |
1194 | { | |
1195 | 0 | loadTreeMenuItem_actionPerformed(e); |
1196 | } | |
1197 | }); | |
1198 | ||
1199 | 452 | scaleAbove.setVisible(false); |
1200 | 452 | scaleAbove.setText(MessageManager.getString("action.scale_above")); |
1201 | 452 | scaleAbove.addActionListener(new ActionListener() |
1202 | { | |
1203 | 0 | @Override |
1204 | public void actionPerformed(ActionEvent e) | |
1205 | { | |
1206 | 0 | scaleAbove_actionPerformed(e); |
1207 | } | |
1208 | }); | |
1209 | 452 | scaleLeft.setVisible(false); |
1210 | 452 | scaleLeft.setSelected(true); |
1211 | 452 | scaleLeft.setText(MessageManager.getString("action.scale_left")); |
1212 | 452 | scaleLeft.addActionListener(new ActionListener() |
1213 | { | |
1214 | 0 | @Override |
1215 | public void actionPerformed(ActionEvent e) | |
1216 | { | |
1217 | 0 | scaleLeft_actionPerformed(e); |
1218 | } | |
1219 | }); | |
1220 | 452 | scaleRight.setVisible(false); |
1221 | 452 | scaleRight.setSelected(true); |
1222 | 452 | scaleRight.setText(MessageManager.getString("action.scale_right")); |
1223 | 452 | scaleRight.addActionListener(new ActionListener() |
1224 | { | |
1225 | 0 | @Override |
1226 | public void actionPerformed(ActionEvent e) | |
1227 | { | |
1228 | 0 | scaleRight_actionPerformed(e); |
1229 | } | |
1230 | }); | |
1231 | 452 | centreColumnLabelsMenuItem.setVisible(true); |
1232 | 452 | centreColumnLabelsMenuItem.setState(false); |
1233 | 452 | centreColumnLabelsMenuItem.setText( |
1234 | MessageManager.getString("label.centre_column_labels")); | |
1235 | 452 | centreColumnLabelsMenuItem.addActionListener(new ActionListener() |
1236 | { | |
1237 | 0 | @Override |
1238 | public void actionPerformed(ActionEvent e) | |
1239 | { | |
1240 | 0 | centreColumnLabels_actionPerformed(e); |
1241 | } | |
1242 | }); | |
1243 | 452 | followHighlightMenuItem.setVisible(true); |
1244 | 452 | followHighlightMenuItem.setState(true); |
1245 | 452 | followHighlightMenuItem |
1246 | .setText(MessageManager.getString("label.automatic_scrolling")); | |
1247 | 452 | followHighlightMenuItem.addActionListener(new ActionListener() |
1248 | { | |
1249 | ||
1250 | 0 | @Override |
1251 | public void actionPerformed(ActionEvent e) | |
1252 | { | |
1253 | 0 | followHighlight_actionPerformed(); |
1254 | } | |
1255 | ||
1256 | }); | |
1257 | ||
1258 | 452 | sortByTreeMenu |
1259 | .setText(MessageManager.getString("action.by_tree_order")); | |
1260 | 452 | sort.setText(MessageManager.getString("action.sort")); |
1261 | 452 | sort.addMenuListener(new MenuListener() |
1262 | { | |
1263 | 0 | @Override |
1264 | public void menuSelected(MenuEvent e) | |
1265 | { | |
1266 | 0 | buildTreeSortMenu(); |
1267 | } | |
1268 | ||
1269 | 0 | @Override |
1270 | public void menuDeselected(MenuEvent e) | |
1271 | { | |
1272 | } | |
1273 | ||
1274 | 0 | @Override |
1275 | public void menuCanceled(MenuEvent e) | |
1276 | { | |
1277 | } | |
1278 | }); | |
1279 | 452 | sortByAnnotScore |
1280 | .setText(MessageManager.getString("label.sort_by_score")); | |
1281 | 452 | sort.add(sortByAnnotScore); |
1282 | 452 | sort.addMenuListener(new javax.swing.event.MenuListener() |
1283 | { | |
1284 | ||
1285 | 0 | @Override |
1286 | public void menuCanceled(MenuEvent e) | |
1287 | { | |
1288 | } | |
1289 | ||
1290 | 0 | @Override |
1291 | public void menuDeselected(MenuEvent e) | |
1292 | { | |
1293 | } | |
1294 | ||
1295 | 0 | @Override |
1296 | public void menuSelected(MenuEvent e) | |
1297 | { | |
1298 | 0 | buildSortByAnnotationScoresMenu(); |
1299 | } | |
1300 | }); | |
1301 | 452 | sortByAnnotScore.setVisible(false); |
1302 | ||
1303 | 452 | calculateTree |
1304 | .setText(MessageManager.getString("action.calculate_tree_pca")); | |
1305 | ||
1306 | 452 | padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); |
1307 | 452 | padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false)); |
1308 | 452 | padGapsMenuitem.addActionListener(new ActionListener() |
1309 | { | |
1310 | 0 | @Override |
1311 | public void actionPerformed(ActionEvent e) | |
1312 | { | |
1313 | 0 | padGapsMenuitem_actionPerformed(e); |
1314 | } | |
1315 | }); | |
1316 | 452 | JMenuItem vamsasStore = new JMenuItem( |
1317 | MessageManager.getString("label.vamsas_store")); | |
1318 | 452 | vamsasStore.setVisible(false); |
1319 | 452 | vamsasStore.addActionListener(new ActionListener() |
1320 | { | |
1321 | 0 | @Override |
1322 | public void actionPerformed(ActionEvent e) | |
1323 | { | |
1324 | 0 | vamsasStore_actionPerformed(e); |
1325 | } | |
1326 | }); | |
1327 | ||
1328 | /* | |
1329 | * Translate as cDNA with sub-menu of translation tables | |
1330 | */ | |
1331 | 452 | showTranslation |
1332 | .setText(MessageManager.getString("label.translate_cDNA")); | |
1333 | 452 | boolean first = true; |
1334 | 452 | for (final GeneticCodeI table : GeneticCodes.getInstance() |
1335 | .getCodeTables()) | |
1336 | { | |
1337 | 11300 | JMenuItem item = new JMenuItem(table.getId() + " " + table.getName()); |
1338 | 11300 | showTranslation.add(item); |
1339 | 11300 | item.addActionListener(new ActionListener() |
1340 | { | |
1341 | 0 | @Override |
1342 | public void actionPerformed(ActionEvent e) | |
1343 | { | |
1344 | 0 | showTranslation_actionPerformed(table); |
1345 | } | |
1346 | }); | |
1347 | 11300 | if (first) |
1348 | { | |
1349 | 452 | showTranslation.addSeparator(); |
1350 | } | |
1351 | 11300 | first = false; |
1352 | } | |
1353 | ||
1354 | 452 | showReverse.setText(MessageManager.getString("label.reverse")); |
1355 | 452 | showReverse.addActionListener(new ActionListener() |
1356 | { | |
1357 | 0 | @Override |
1358 | public void actionPerformed(ActionEvent e) | |
1359 | { | |
1360 | 0 | showReverse_actionPerformed(false); |
1361 | } | |
1362 | }); | |
1363 | 452 | showReverseComplement |
1364 | .setText(MessageManager.getString("label.reverse_complement")); | |
1365 | 452 | showReverseComplement.addActionListener(new ActionListener() |
1366 | { | |
1367 | 0 | @Override |
1368 | public void actionPerformed(ActionEvent e) | |
1369 | { | |
1370 | 0 | showReverse_actionPerformed(true); |
1371 | } | |
1372 | }); | |
1373 | ||
1374 | 452 | JMenuItem extractScores = new JMenuItem( |
1375 | MessageManager.getString("label.extract_scores")); | |
1376 | 452 | extractScores.addActionListener(new ActionListener() |
1377 | { | |
1378 | 0 | @Override |
1379 | public void actionPerformed(ActionEvent e) | |
1380 | { | |
1381 | 0 | extractScores_actionPerformed(e); |
1382 | } | |
1383 | }); | |
1384 | 452 | extractScores.setVisible(true); |
1385 | // JBPNote: TODO: make gui for regex based score extraction | |
1386 | ||
1387 | // for show products actions see AlignFrame.canShowProducts | |
1388 | 452 | showProducts.setText(MessageManager.getString("label.get_cross_refs")); |
1389 | ||
1390 | 452 | runGroovy.setText(MessageManager.getString("label.run_groovy")); |
1391 | 452 | runGroovy.setToolTipText( |
1392 | MessageManager.getString("label.run_groovy_tip")); | |
1393 | 452 | runGroovy.addActionListener(new ActionListener() |
1394 | { | |
1395 | 0 | @Override |
1396 | public void actionPerformed(ActionEvent e) | |
1397 | { | |
1398 | 0 | runGroovy_actionPerformed(); |
1399 | } | |
1400 | }); | |
1401 | ||
1402 | 452 | openFeatureSettings = new JMenuItem( |
1403 | MessageManager.getString("action.feature_settings")); | |
1404 | 452 | openFeatureSettings.addActionListener(new ActionListener() |
1405 | { | |
1406 | 0 | @Override |
1407 | public void actionPerformed(ActionEvent e) | |
1408 | { | |
1409 | 0 | featureSettings_actionPerformed(e); |
1410 | } | |
1411 | }); | |
1412 | ||
1413 | /* | |
1414 | * add sub-menu of database we can fetch from | |
1415 | */ | |
1416 | 452 | JMenuItem fetchSequence = new JMenuItem( |
1417 | MessageManager.getString("label.fetch_sequences")); | |
1418 | 452 | fetchSequence.addActionListener(new ActionListener() |
1419 | { | |
1420 | 0 | @Override |
1421 | public void actionPerformed(ActionEvent e) | |
1422 | { | |
1423 | 0 | fetchSequence_actionPerformed(); |
1424 | } | |
1425 | }); | |
1426 | ||
1427 | 452 | JMenuItem associatedData = new JMenuItem( |
1428 | MessageManager.getString("label.load_features_annotations")); | |
1429 | 452 | associatedData.addActionListener(new ActionListener() |
1430 | { | |
1431 | 0 | @Override |
1432 | public void actionPerformed(ActionEvent e) | |
1433 | { | |
1434 | 0 | associatedData_actionPerformed(e); |
1435 | } | |
1436 | }); | |
1437 | 452 | loadVcf = new JMenuItem( |
1438 | MessageManager.getString("label.load_vcf_file")); | |
1439 | 452 | loadVcf.setToolTipText(MessageManager.getString("label.load_vcf")); |
1440 | 452 | loadVcf.addActionListener(new ActionListener() |
1441 | { | |
1442 | 0 | @Override |
1443 | public void actionPerformed(ActionEvent e) | |
1444 | { | |
1445 | 0 | loadVcf_actionPerformed(); |
1446 | } | |
1447 | }); | |
1448 | 452 | autoCalculate.setText( |
1449 | MessageManager.getString("label.autocalculate_consensus")); | |
1450 | 452 | autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true)); |
1451 | 452 | autoCalculate.addActionListener(new ActionListener() |
1452 | { | |
1453 | 0 | @Override |
1454 | public void actionPerformed(ActionEvent e) | |
1455 | { | |
1456 | 0 | autoCalculate_actionPerformed(e); |
1457 | } | |
1458 | }); | |
1459 | 452 | sortByTree.setText( |
1460 | MessageManager.getString("label.sort_alignment_new_tree")); | |
1461 | 452 | sortByTree.setToolTipText("<html>" + MessageManager.getString( |
1462 | "label.enable_automatically_sort_alignment_when_open_new_tree")); | |
1463 | 452 | sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false)); |
1464 | 452 | sortByTree.addActionListener(new ActionListener() |
1465 | { | |
1466 | 0 | @Override |
1467 | public void actionPerformed(ActionEvent e) | |
1468 | { | |
1469 | 0 | sortByTreeOption_actionPerformed(e); |
1470 | } | |
1471 | }); | |
1472 | ||
1473 | 452 | listenToViewSelections.setText( |
1474 | MessageManager.getString("label.listen_for_selections")); | |
1475 | 452 | listenToViewSelections |
1476 | .setToolTipText("<html>" + MessageManager.getString( | |
1477 | "label.selections_mirror_selections_made_same_sequences_other_views")); | |
1478 | 452 | listenToViewSelections.setState(false); |
1479 | 452 | listenToViewSelections.addActionListener(new ActionListener() |
1480 | { | |
1481 | 0 | @Override |
1482 | public void actionPerformed(ActionEvent e) | |
1483 | { | |
1484 | 0 | listenToViewSelections_actionPerformed(e); |
1485 | } | |
1486 | }); | |
1487 | ||
1488 | 452 | JMenu addSequenceMenu = new JMenu( |
1489 | MessageManager.getString("label.add_sequences")); | |
1490 | 452 | JMenuItem addFromFile = new JMenuItem( |
1491 | MessageManager.getString("label.from_file")); | |
1492 | 452 | addFromFile.addActionListener(new ActionListener() |
1493 | { | |
1494 | 0 | @Override |
1495 | public void actionPerformed(ActionEvent e) | |
1496 | { | |
1497 | 0 | addFromFile_actionPerformed(e); |
1498 | } | |
1499 | }); | |
1500 | 452 | JMenuItem addFromText = new JMenuItem( |
1501 | MessageManager.getString("label.from_textbox")); | |
1502 | 452 | addFromText.addActionListener(new ActionListener() |
1503 | { | |
1504 | 0 | @Override |
1505 | public void actionPerformed(ActionEvent e) | |
1506 | { | |
1507 | 0 | addFromText_actionPerformed(e); |
1508 | } | |
1509 | }); | |
1510 | 452 | JMenuItem addFromURL = new JMenuItem( |
1511 | MessageManager.getString("label.from_url")); | |
1512 | 452 | addFromURL.addActionListener(new ActionListener() |
1513 | { | |
1514 | 0 | @Override |
1515 | public void actionPerformed(ActionEvent e) | |
1516 | { | |
1517 | 0 | addFromURL_actionPerformed(e); |
1518 | } | |
1519 | }); | |
1520 | 452 | JMenuItem exportFeatures = new JMenuItem( |
1521 | MessageManager.getString("label.export_features")); | |
1522 | 452 | exportFeatures.addActionListener(new ActionListener() |
1523 | { | |
1524 | 0 | @Override |
1525 | public void actionPerformed(ActionEvent e) | |
1526 | { | |
1527 | 0 | exportFeatures_actionPerformed(e); |
1528 | } | |
1529 | }); | |
1530 | 452 | JMenuItem exportAnnotations = new JMenuItem( |
1531 | MessageManager.getString("label.export_annotations")); | |
1532 | 452 | exportAnnotations.addActionListener(new ActionListener() |
1533 | { | |
1534 | 0 | @Override |
1535 | public void actionPerformed(ActionEvent e) | |
1536 | { | |
1537 | 0 | exportAnnotations_actionPerformed(e); |
1538 | } | |
1539 | }); | |
1540 | 452 | statusPanel.setLayout(new GridLayout()); |
1541 | 452 | JMenuItem showAllSeqs = new JMenuItem( |
1542 | MessageManager.getString("label.all_sequences")); | |
1543 | 452 | showAllSeqs.setToolTipText( |
1544 | MessageManager.getString("label.toggle_sequence_visibility")); | |
1545 | 452 | showAllSeqs.addActionListener(new ActionListener() |
1546 | { | |
1547 | 0 | @Override |
1548 | public void actionPerformed(ActionEvent e) | |
1549 | { | |
1550 | 0 | showAllSeqs_actionPerformed(e); |
1551 | } | |
1552 | }); | |
1553 | 452 | JMenuItem showAllColumns = new JMenuItem( |
1554 | MessageManager.getString("label.all_columns")); | |
1555 | 452 | showAllColumns.setToolTipText( |
1556 | MessageManager.getString("label.toggle_columns_visibility")); | |
1557 | 452 | showAllColumns.addActionListener(new ActionListener() |
1558 | { | |
1559 | 0 | @Override |
1560 | public void actionPerformed(ActionEvent e) | |
1561 | { | |
1562 | 0 | showAllColumns_actionPerformed(e); |
1563 | } | |
1564 | }); | |
1565 | 452 | JMenu hideMenu = new JMenu(MessageManager.getString("action.hide")); |
1566 | 452 | JMenuItem hideSelSequences = new JMenuItem( |
1567 | MessageManager.getString("label.selected_sequences")); | |
1568 | 452 | hideSelSequences.setToolTipText( |
1569 | MessageManager.getString("label.toggle_sequence_visibility")); | |
1570 | 452 | hideSelSequences.addActionListener(new ActionListener() |
1571 | { | |
1572 | 0 | @Override |
1573 | public void actionPerformed(ActionEvent e) | |
1574 | { | |
1575 | 0 | hideSelSequences_actionPerformed(e); |
1576 | } | |
1577 | }); | |
1578 | 452 | JMenuItem hideSelColumns = new JMenuItem( |
1579 | MessageManager.getString("label.selected_columns")); | |
1580 | 452 | hideSelColumns.setToolTipText( |
1581 | MessageManager.getString("label.toggle_columns_visibility")); | |
1582 | 452 | hideSelColumns.addActionListener(new ActionListener() |
1583 | { | |
1584 | 0 | @Override |
1585 | public void actionPerformed(ActionEvent e) | |
1586 | { | |
1587 | 0 | hideSelColumns_actionPerformed(e); |
1588 | } | |
1589 | }); | |
1590 | 452 | JMenuItem hideAllSelection = new JMenuItem( |
1591 | MessageManager.getString("label.selected_region")); | |
1592 | 452 | hideAllSelection.addActionListener(new ActionListener() |
1593 | { | |
1594 | 0 | @Override |
1595 | public void actionPerformed(ActionEvent e) | |
1596 | { | |
1597 | 0 | hideAllSelection_actionPerformed(e); |
1598 | } | |
1599 | }); | |
1600 | // TODO: should be hidden if no selection exists. | |
1601 | 452 | JMenuItem hideAllButSelection = new JMenuItem( |
1602 | MessageManager.getString("label.all_but_selected_region")); | |
1603 | 452 | hideAllButSelection.addActionListener(new ActionListener() |
1604 | { | |
1605 | 0 | @Override |
1606 | public void actionPerformed(ActionEvent e) | |
1607 | { | |
1608 | 0 | hideAllButSelection_actionPerformed(e); |
1609 | } | |
1610 | }); | |
1611 | 452 | JMenuItem showAllhidden = new JMenuItem( |
1612 | MessageManager.getString("label.all_sequences_columns")); | |
1613 | 452 | showAllhidden.setToolTipText(MessageManager |
1614 | .getString("label.toggles_visibility_hidden_selected_regions")); | |
1615 | 452 | showAllhidden.addActionListener(new ActionListener() |
1616 | { | |
1617 | 0 | @Override |
1618 | public void actionPerformed(ActionEvent e) | |
1619 | { | |
1620 | 0 | showAllhidden_actionPerformed(e); |
1621 | } | |
1622 | }); | |
1623 | 452 | hiddenMarkers.setText( |
1624 | MessageManager.getString("action.show_hidden_markers")); | |
1625 | 452 | hiddenMarkers.addActionListener(new ActionListener() |
1626 | { | |
1627 | 0 | @Override |
1628 | public void actionPerformed(ActionEvent e) | |
1629 | { | |
1630 | 0 | hiddenMarkers_actionPerformed(e); |
1631 | } | |
1632 | }); | |
1633 | ||
1634 | 452 | JMenuItem invertColSel = new JMenuItem( |
1635 | MessageManager.getString("action.invert_column_selection")); | |
1636 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, |
1637 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1638 | | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK, | |
1639 | false); | |
1640 | 452 | al = new ActionListener() |
1641 | { | |
1642 | 0 | @Override |
1643 | public void actionPerformed(ActionEvent e) | |
1644 | { | |
1645 | 0 | invertColSel_actionPerformed(e); |
1646 | } | |
1647 | }; | |
1648 | 452 | addMenuActionAndAccelerator(keyStroke, invertColSel, al); |
1649 | ||
1650 | 452 | showComplementMenuItem.setVisible(false); |
1651 | 452 | showComplementMenuItem.addActionListener(new ActionListener() |
1652 | { | |
1653 | 0 | @Override |
1654 | public void actionPerformed(ActionEvent e) | |
1655 | { | |
1656 | 0 | showComplement_actionPerformed(showComplementMenuItem.getState()); |
1657 | } | |
1658 | }); | |
1659 | ||
1660 | 452 | tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() |
1661 | { | |
1662 | 157 | @Override |
1663 | public void stateChanged(ChangeEvent evt) | |
1664 | { | |
1665 | 157 | JTabbedPane pane = (JTabbedPane) evt.getSource(); |
1666 | 157 | int sel = pane.getSelectedIndex(); |
1667 | 157 | tabSelectionChanged(sel); |
1668 | } | |
1669 | }); | |
1670 | 452 | tabbedPane.addMouseListener(new MouseAdapter() |
1671 | { | |
1672 | 0 | @Override |
1673 | public void mousePressed(MouseEvent e) | |
1674 | { | |
1675 | 0 | if (e.isPopupTrigger()) // Mac |
1676 | { | |
1677 | 0 | tabbedPane_mousePressed(e); |
1678 | } | |
1679 | } | |
1680 | ||
1681 | 0 | @Override |
1682 | public void mouseReleased(MouseEvent e) | |
1683 | { | |
1684 | 0 | if (e.isPopupTrigger()) // Windows |
1685 | { | |
1686 | 0 | tabbedPane_mousePressed(e); |
1687 | } | |
1688 | } | |
1689 | }); | |
1690 | 452 | tabbedPane.addFocusListener(new FocusAdapter() |
1691 | { | |
1692 | 62 | @Override |
1693 | public void focusGained(FocusEvent e) | |
1694 | { | |
1695 | 62 | tabbedPane_focusGained(e); |
1696 | } | |
1697 | }); | |
1698 | ||
1699 | 452 | JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); |
1700 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, |
1701 | jalview.util.ShortcutKeyMaskExWrapper | |
1702 | .getMenuShortcutKeyMaskEx(), | |
1703 | false); | |
1704 | 452 | al = new ActionListener() |
1705 | { | |
1706 | 0 | @Override |
1707 | public void actionPerformed(ActionEvent e) | |
1708 | { | |
1709 | 0 | save_actionPerformed(e); |
1710 | } | |
1711 | }; | |
1712 | 452 | addMenuActionAndAccelerator(keyStroke, save, al); |
1713 | ||
1714 | 452 | reload.setEnabled(false); |
1715 | 452 | reload.setText(MessageManager.getString("action.reload")); |
1716 | 452 | reload.addActionListener(new ActionListener() |
1717 | { | |
1718 | 0 | @Override |
1719 | public void actionPerformed(ActionEvent e) | |
1720 | { | |
1721 | 0 | reload_actionPerformed(e); |
1722 | } | |
1723 | }); | |
1724 | ||
1725 | 452 | JMenuItem newView = new JMenuItem( |
1726 | MessageManager.getString("action.new_view")); | |
1727 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, |
1728 | jalview.util.ShortcutKeyMaskExWrapper | |
1729 | .getMenuShortcutKeyMaskEx(), | |
1730 | false); | |
1731 | 452 | al = new ActionListener() |
1732 | { | |
1733 | 0 | @Override |
1734 | public void actionPerformed(ActionEvent e) | |
1735 | { | |
1736 | 0 | newView_actionPerformed(e); |
1737 | } | |
1738 | }; | |
1739 | 452 | addMenuActionAndAccelerator(keyStroke, newView, al); |
1740 | ||
1741 | 452 | tabbedPane.setToolTipText("<html><i>" |
1742 | + MessageManager.getString("label.rename_tab_eXpand_reGroup") | |
1743 | + "</i></html>"); | |
1744 | ||
1745 | 452 | formatMenu.setText(MessageManager.getString("action.format")); |
1746 | 452 | JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); |
1747 | ||
1748 | 452 | idRightAlign.setText( |
1749 | MessageManager.getString("label.right_align_sequence_id")); | |
1750 | 452 | idRightAlign.addActionListener(new ActionListener() |
1751 | { | |
1752 | 0 | @Override |
1753 | public void actionPerformed(ActionEvent e) | |
1754 | { | |
1755 | 0 | idRightAlign_actionPerformed(e); |
1756 | } | |
1757 | }); | |
1758 | ||
1759 | 452 | gatherViews.setEnabled(false); |
1760 | 452 | gatherViews.setText(MessageManager.getString("action.gather_views")); |
1761 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); |
1762 | 452 | al = new ActionListener() |
1763 | { | |
1764 | 0 | @Override |
1765 | public void actionPerformed(ActionEvent e) | |
1766 | { | |
1767 | 0 | gatherViews_actionPerformed(e); |
1768 | } | |
1769 | }; | |
1770 | 452 | addMenuActionAndAccelerator(keyStroke, gatherViews, al); |
1771 | ||
1772 | 452 | expandViews.setEnabled(false); |
1773 | 452 | expandViews.setText(MessageManager.getString("action.expand_views")); |
1774 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); |
1775 | 452 | al = new ActionListener() |
1776 | { | |
1777 | 0 | @Override |
1778 | public void actionPerformed(ActionEvent e) | |
1779 | { | |
1780 | 0 | expandViews_actionPerformed(e); |
1781 | } | |
1782 | }; | |
1783 | 452 | addMenuActionAndAccelerator(keyStroke, expandViews, al); |
1784 | ||
1785 | 452 | JMenuItem pageSetup = new JMenuItem( |
1786 | MessageManager.getString("action.page_setup")); | |
1787 | 452 | pageSetup.addActionListener(new ActionListener() |
1788 | { | |
1789 | 0 | @Override |
1790 | public void actionPerformed(ActionEvent e) | |
1791 | { | |
1792 | 0 | pageSetup_actionPerformed(e); |
1793 | } | |
1794 | }); | |
1795 | 452 | JMenuItem alignmentProperties = new JMenuItem( |
1796 | MessageManager.getString("label.alignment_props")); | |
1797 | 452 | alignmentProperties.addActionListener(new ActionListener() |
1798 | { | |
1799 | 0 | @Override |
1800 | public void actionPerformed(ActionEvent actionEvent) | |
1801 | { | |
1802 | 0 | alignmentProperties(); |
1803 | } | |
1804 | }); | |
1805 | 452 | JMenuItem selectHighlighted = new JMenuItem( |
1806 | MessageManager.getString("action.select_highlighted_columns")); | |
1807 | 452 | selectHighlighted.setToolTipText( |
1808 | MessageManager.getString("tooltip.select_highlighted_columns")); | |
1809 | 452 | al = new ActionListener() |
1810 | { | |
1811 | 0 | @Override |
1812 | public void actionPerformed(ActionEvent actionEvent) | |
1813 | { | |
1814 | 0 | selectHighlightedColumns_actionPerformed(actionEvent); |
1815 | } | |
1816 | }; | |
1817 | 452 | selectHighlighted.addActionListener(al); |
1818 | ||
1819 | 452 | copyHighlighted = new JMenuItem( |
1820 | MessageManager.getString("action.copy_highlighted_regions")); | |
1821 | 452 | keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, |
1822 | jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() | |
1823 | + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, | |
1824 | false); | |
1825 | 452 | copyHighlighted.setToolTipText( |
1826 | MessageManager.getString("tooltip.copy_highlighted_regions")); | |
1827 | 452 | al = new ActionListener() |
1828 | { | |
1829 | 0 | @Override |
1830 | public void actionPerformed(ActionEvent actionEvent) | |
1831 | { | |
1832 | 0 | copyHighlightedColumns_actionPerformed(actionEvent); |
1833 | } | |
1834 | }; | |
1835 | 452 | addMenuActionAndAccelerator(keyStroke, copyHighlighted, al); |
1836 | 452 | copyHighlighted.addActionListener(al); |
1837 | ||
1838 | 452 | ButtonGroup ssButtonGroup = new ButtonGroup(); |
1839 | ||
1840 | 452 | JMenu tooltipSettingsMenu = new JMenu( |
1841 | MessageManager.getString("label.sequence_id_tooltip")); | |
1842 | 452 | JMenu autoAnnMenu = new JMenu( |
1843 | MessageManager.getString("label.autocalculated_annotation")); | |
1844 | ||
1845 | 452 | JMenu showSS = new JMenu( |
1846 | MessageManager.getString("label.show_secondary_structure")); | |
1847 | ||
1848 | 452 | JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem( |
1849 | MessageManager.getString("option.ss_providers_all")); | |
1850 | 452 | radioButtonAllSS.addActionListener(new ActionListener() |
1851 | { | |
1852 | 0 | @Override |
1853 | public void actionPerformed(ActionEvent e) | |
1854 | { | |
1855 | 0 | showOrHideSecondaryStructureForSource( |
1856 | MessageManager.getString("option.ss_providers_all"), true); | |
1857 | // Select all checkboxes if "All" is selected | |
1858 | 0 | Component[] components = showSS.getMenuComponents(); |
1859 | 0 | for (Component component : components) |
1860 | { | |
1861 | 0 | if (component instanceof JCheckBoxMenuItem) |
1862 | { | |
1863 | 0 | ((JCheckBoxMenuItem) component).setSelected(true); |
1864 | } | |
1865 | } | |
1866 | } | |
1867 | }); | |
1868 | 452 | ssButtonGroup.add(radioButtonAllSS); |
1869 | 452 | showSS.add(radioButtonAllSS); |
1870 | ||
1871 | 452 | JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem( |
1872 | MessageManager.getString("option.ss_providers_none")); | |
1873 | 452 | radioButtonNoneSS.addActionListener(new ActionListener() |
1874 | { | |
1875 | 0 | @Override |
1876 | public void actionPerformed(ActionEvent e) | |
1877 | { | |
1878 | 0 | showOrHideSecondaryStructureForSource( |
1879 | MessageManager.getString("option.ss_providers_none"), | |
1880 | false); | |
1881 | // Remove selection of all checkboxes if "None" is selected | |
1882 | 0 | Component[] components = showSS.getMenuComponents(); |
1883 | 0 | for (Component component : components) |
1884 | { | |
1885 | 0 | if (component instanceof JCheckBoxMenuItem) |
1886 | { | |
1887 | 0 | ((JCheckBoxMenuItem) component).setSelected(false); |
1888 | } | |
1889 | } | |
1890 | } | |
1891 | }); | |
1892 | 452 | ssButtonGroup.add(radioButtonNoneSS); |
1893 | 452 | showSS.add(radioButtonNoneSS); |
1894 | 452 | showSS.addSeparator(); |
1895 | ||
1896 | 452 | annotationsMenu.addMouseListener(new MouseAdapter() |
1897 | { | |
1898 | ||
1899 | 0 | @Override |
1900 | public void mouseEntered(MouseEvent e) | |
1901 | { | |
1902 | ||
1903 | 0 | updateShowSecondaryStructureMenu(showSS, ssButtonGroup); // Update radio |
1904 | // buttons | |
1905 | // every time | |
1906 | // the menu is | |
1907 | // clicked | |
1908 | ||
1909 | } | |
1910 | }); | |
1911 | ||
1912 | 452 | JMenu exportImageMenu = new JMenu( |
1913 | MessageManager.getString("label.export_image")); | |
1914 | 452 | JMenu fileMenu = new JMenu(MessageManager.getString("action.file")); |
1915 | 452 | alignFrameMenuBar.add(fileMenu); |
1916 | 452 | alignFrameMenuBar.add(editMenu); |
1917 | 452 | alignFrameMenuBar.add(selectMenu); |
1918 | 452 | alignFrameMenuBar.add(viewMenu); |
1919 | 452 | alignFrameMenuBar.add(annotationsMenu); |
1920 | 452 | alignFrameMenuBar.add(formatMenu); |
1921 | 452 | alignFrameMenuBar.add(colourMenu); |
1922 | 452 | alignFrameMenuBar.add(calculateMenu); |
1923 | 452 | if (!Platform.isJS()) |
1924 | { | |
1925 | 452 | alignFrameMenuBar.add(webService); |
1926 | } | |
1927 | ||
1928 | 452 | fileMenu.add(fetchSequence); |
1929 | 452 | fileMenu.add(addSequenceMenu); |
1930 | 452 | fileMenu.add(reload); |
1931 | 452 | fileMenu.addSeparator(); |
1932 | 452 | fileMenu.add(vamsasStore); |
1933 | 452 | fileMenu.add(save); |
1934 | 452 | fileMenu.add(saveAs); |
1935 | 452 | fileMenu.add(outputTextboxMenu); |
1936 | 452 | fileMenu.add(pageSetup); |
1937 | 452 | fileMenu.add(printMenuItem); |
1938 | 452 | fileMenu.addSeparator(); |
1939 | 452 | fileMenu.add(exportImageMenu); |
1940 | 452 | fileMenu.add(exportFeatures); |
1941 | 452 | fileMenu.add(exportAnnotations); |
1942 | 452 | fileMenu.add(loadTreeMenuItem); |
1943 | 452 | fileMenu.add(associatedData); |
1944 | 452 | if (!Platform.isJS()) |
1945 | { | |
1946 | 452 | fileMenu.add(loadVcf); |
1947 | } | |
1948 | 452 | fileMenu.addSeparator(); |
1949 | 452 | fileMenu.add(closeMenuItem); |
1950 | ||
1951 | 452 | pasteMenu.add(pasteNew); |
1952 | 452 | pasteMenu.add(pasteThis); |
1953 | 452 | editMenu.add(undoMenuItem); |
1954 | 452 | editMenu.add(redoMenuItem); |
1955 | 452 | editMenu.add(cut); |
1956 | 452 | editMenu.add(copy); |
1957 | 452 | editMenu.add(copyHighlighted); |
1958 | 452 | editMenu.add(pasteMenu); |
1959 | 452 | editMenu.add(delete); |
1960 | 452 | editMenu.addSeparator(); |
1961 | 452 | editMenu.add(remove2LeftMenuItem); |
1962 | 452 | editMenu.add(remove2RightMenuItem); |
1963 | 452 | editMenu.add(removeGappedColumnMenuItem); |
1964 | 452 | editMenu.add(removeAllGapsMenuItem); |
1965 | 452 | editMenu.add(removeRedundancyMenuItem); |
1966 | 452 | editMenu.addSeparator(); |
1967 | ||
1968 | 452 | editMenu.add(justifyLeftMenuItem); |
1969 | 452 | editMenu.add(justifyRightMenuItem); |
1970 | ||
1971 | 452 | editMenu.addSeparator(); |
1972 | 452 | editMenu.add(padGapsMenuitem); |
1973 | ||
1974 | 452 | showMenu.add(showAllColumns); |
1975 | 452 | showMenu.add(showAllSeqs); |
1976 | 452 | showMenu.add(showAllhidden); |
1977 | 452 | hideMenu.add(hideSelColumns); |
1978 | 452 | hideMenu.add(hideSelSequences); |
1979 | 452 | hideMenu.add(hideAllSelection); |
1980 | 452 | hideMenu.add(hideAllButSelection); |
1981 | 452 | viewMenu.add(newView); |
1982 | 452 | viewMenu.add(expandViews); |
1983 | 452 | viewMenu.add(gatherViews); |
1984 | 452 | viewMenu.addSeparator(); |
1985 | 452 | viewMenu.add(showMenu); |
1986 | 452 | viewMenu.add(hideMenu); |
1987 | 452 | viewMenu.add(showComplementMenuItem); |
1988 | 452 | viewMenu.addSeparator(); |
1989 | 452 | viewMenu.add(followHighlightMenuItem); |
1990 | 452 | viewMenu.addSeparator(); |
1991 | 452 | viewMenu.add(showSeqFeatures); |
1992 | // viewMenu.add(showSeqFeaturesHeight); | |
1993 | 452 | viewMenu.add(openFeatureSettings); |
1994 | 452 | tooltipSettingsMenu.add(showDbRefsMenuitem); |
1995 | 452 | tooltipSettingsMenu.add(showNpFeatsMenuitem); |
1996 | 452 | viewMenu.add(tooltipSettingsMenu); |
1997 | 452 | viewMenu.addSeparator(); |
1998 | 452 | viewMenu.add(alignmentProperties); |
1999 | 452 | viewMenu.addSeparator(); |
2000 | 452 | viewMenu.add(overviewMenuItem); |
2001 | ||
2002 | 452 | annotationsMenu.add(annotationPanelMenuItem); |
2003 | 452 | annotationsMenu.addSeparator(); |
2004 | 452 | annotationsMenu.add(showAllAlAnnotations); |
2005 | 452 | annotationsMenu.add(hideAllAlAnnotations); |
2006 | 452 | annotationsMenu.addSeparator(); |
2007 | 452 | annotationsMenu.add(showAllSeqAnnotations); |
2008 | 452 | annotationsMenu.add(hideAllSeqAnnotations); |
2009 | 452 | annotationsMenu.add(sortAnnBySequence); |
2010 | 452 | annotationsMenu.add(sortAnnByLabel); |
2011 | 452 | annotationsMenu.addSeparator(); |
2012 | 452 | annotationsMenu.add(showSS); |
2013 | 452 | annotationsMenu.add(showStrucProvider); |
2014 | 452 | annotationsMenu.addSeparator(); |
2015 | 452 | autoAnnMenu.add(showAutoFirst); |
2016 | 452 | autoAnnMenu.add(showAutoLast); |
2017 | 452 | autoAnnMenu.addSeparator(); |
2018 | 452 | autoAnnMenu.add(applyAutoAnnotationSettings); |
2019 | 452 | autoAnnMenu.add(showConsensusHistogram); |
2020 | 452 | autoAnnMenu.add(showSequenceLogo); |
2021 | 452 | autoAnnMenu.add(normaliseSequenceLogo); |
2022 | // autoAnnMenu.add(showSSConsensus); | |
2023 | 452 | autoAnnMenu.addSeparator(); |
2024 | 452 | autoAnnMenu.add(showGroupConservation); |
2025 | 452 | autoAnnMenu.add(showGroupConsensus); |
2026 | 452 | autoAnnMenu.add(showGroupSSConsensus); |
2027 | 452 | annotationsMenu.add(autoAnnMenu); |
2028 | ||
2029 | 452 | sort.add(sortIDMenuItem); |
2030 | 452 | sort.add(sortLengthMenuItem); |
2031 | 452 | sort.add(sortGroupMenuItem); |
2032 | 452 | sort.add(sortPairwiseMenuItem); |
2033 | 452 | sort.add(sortByTreeMenu); |
2034 | 452 | calculateMenu.add(sort); |
2035 | 452 | calculateMenu.add(calculateTree); |
2036 | 452 | calculateMenu.addSeparator(); |
2037 | 452 | calculateMenu.add(pairwiseAlignmentMenuItem); |
2038 | 452 | calculateMenu.addSeparator(); |
2039 | 452 | calculateMenu.add(showTranslation); |
2040 | 452 | calculateMenu.add(showReverse); |
2041 | 452 | calculateMenu.add(showReverseComplement); |
2042 | 452 | calculateMenu.add(showProducts); |
2043 | 452 | calculateMenu.add(autoCalculate); |
2044 | 452 | calculateMenu.add(sortByTree); |
2045 | 452 | calculateMenu.addSeparator(); |
2046 | 452 | calculateMenu.add(expandAlignment); |
2047 | 452 | calculateMenu.add(extractScores); |
2048 | 452 | if (!Platform.isJS()) |
2049 | { | |
2050 | 452 | calculateMenu.addSeparator(); |
2051 | 452 | calculateMenu.add(runGroovy); |
2052 | } | |
2053 | ||
2054 | 452 | webServiceNoServices = new JMenuItem( |
2055 | MessageManager.getString("label.no_services")); | |
2056 | 452 | webService.add(webServiceNoServices); |
2057 | 452 | if (!Platform.isJS()) |
2058 | { | |
2059 | 452 | exportImageMenu.add(htmlMenuItem); |
2060 | } | |
2061 | 452 | exportImageMenu.add(epsFile); |
2062 | 452 | exportImageMenu.add(createPNG); |
2063 | 452 | if (!Platform.isJS()) |
2064 | { | |
2065 | 452 | exportImageMenu.add(createBioJS); |
2066 | 452 | exportImageMenu.add(createSVG); |
2067 | } | |
2068 | 452 | addSequenceMenu.add(addFromFile); |
2069 | 452 | addSequenceMenu.add(addFromText); |
2070 | 452 | addSequenceMenu.add(addFromURL); |
2071 | 452 | this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); |
2072 | 452 | statusPanel.add(statusBar, null); |
2073 | 452 | this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); |
2074 | ||
2075 | 452 | formatMenu.add(font); |
2076 | 452 | formatMenu.addSeparator(); |
2077 | 452 | formatMenu.add(wrapMenuItem); |
2078 | 452 | formatMenu.add(scaleAbove); |
2079 | 452 | formatMenu.add(scaleLeft); |
2080 | 452 | formatMenu.add(scaleRight); |
2081 | 452 | formatMenu.add(seqLimits); |
2082 | 452 | formatMenu.add(idRightAlign); |
2083 | 452 | formatMenu.add(hiddenMarkers); |
2084 | 452 | formatMenu.add(viewBoxesMenuItem); |
2085 | 452 | formatMenu.add(viewTextMenuItem); |
2086 | 452 | formatMenu.add(colourTextMenuItem); |
2087 | 452 | formatMenu.add(renderGapsMenuItem); |
2088 | 452 | formatMenu.add(centreColumnLabelsMenuItem); |
2089 | 452 | formatMenu.add(showNonconservedMenuItem); |
2090 | 452 | selectMenu.add(findMenuItem); |
2091 | 452 | selectMenu.addSeparator(); |
2092 | 452 | selectMenu.add(selectAllSequenceMenuItem); |
2093 | 452 | selectMenu.add(deselectAllSequenceMenuItem); |
2094 | 452 | selectMenu.add(invertSequenceMenuItem); |
2095 | 452 | selectMenu.add(invertColSel); |
2096 | 452 | selectMenu.add(createGroup); |
2097 | 452 | selectMenu.add(unGroup); |
2098 | 452 | selectMenu.add(grpsFromSelection); |
2099 | 452 | selectMenu.add(deleteGroups); |
2100 | 452 | selectMenu.add(annotationColumn); |
2101 | 452 | selectMenu.add(selectHighlighted); |
2102 | // TODO - determine if the listenToViewSelections button is needed : see bug | |
2103 | // JAL-574 | |
2104 | // selectMenu.addSeparator(); | |
2105 | // selectMenu.add(listenToViewSelections); | |
2106 | } | |
2107 | ||
2108 | 0 | protected void showStructureProvider_actionPerformed(ActionEvent e) |
2109 | { | |
2110 | // TODO Auto-generated method stub | |
2111 | ||
2112 | } | |
2113 | ||
2114 | 0 | protected void showSSConsensus_actionPerformed(ActionEvent e) |
2115 | { | |
2116 | // TODO Auto-generated method stub | |
2117 | ||
2118 | } | |
2119 | ||
2120 | 0 | protected void createPNG_actionPerformed(ActionEvent object) |
2121 | { | |
2122 | // TODO Auto-generated method stub | |
2123 | ||
2124 | } | |
2125 | ||
2126 | 0 | protected void createEPS_actionPerformed(ActionEvent object) |
2127 | { | |
2128 | // TODO Auto-generated method stub | |
2129 | ||
2130 | } | |
2131 | ||
2132 | 0 | protected void createSVG_actionPerformed(ActionEvent object) |
2133 | { | |
2134 | // TODO Auto-generated method stub | |
2135 | ||
2136 | } | |
2137 | ||
2138 | 0 | protected void copyHighlightedColumns_actionPerformed( |
2139 | ActionEvent actionEvent) | |
2140 | { | |
2141 | ||
2142 | } | |
2143 | ||
2144 | 0 | protected void loadVcf_actionPerformed() |
2145 | { | |
2146 | } | |
2147 | ||
2148 | /** | |
2149 | * Constructs the entries on the Colour menu (but does not add them to the | |
2150 | * menu). | |
2151 | */ | |
2152 | 452 | protected void initColourMenu() |
2153 | { | |
2154 | 452 | applyToAllGroups = new JCheckBoxMenuItem( |
2155 | MessageManager.getString("label.apply_colour_to_all_groups")); | |
2156 | 452 | applyToAllGroups.addActionListener(new ActionListener() |
2157 | { | |
2158 | 0 | @Override |
2159 | public void actionPerformed(ActionEvent e) | |
2160 | { | |
2161 | 0 | applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); |
2162 | } | |
2163 | }); | |
2164 | ||
2165 | 452 | textColour = new JMenuItem( |
2166 | MessageManager.getString("label.text_colour")); | |
2167 | 452 | textColour.addActionListener(new ActionListener() |
2168 | { | |
2169 | 0 | @Override |
2170 | public void actionPerformed(ActionEvent e) | |
2171 | { | |
2172 | 0 | textColour_actionPerformed(); |
2173 | } | |
2174 | }); | |
2175 | ||
2176 | 452 | conservationMenuItem = new JCheckBoxMenuItem( |
2177 | MessageManager.getString("action.by_conservation")); | |
2178 | 452 | conservationMenuItem.addActionListener(new ActionListener() |
2179 | { | |
2180 | 0 | @Override |
2181 | public void actionPerformed(ActionEvent e) | |
2182 | { | |
2183 | 0 | conservationMenuItem_actionPerformed( |
2184 | conservationMenuItem.isSelected()); | |
2185 | } | |
2186 | }); | |
2187 | ||
2188 | 452 | byConsensusSecondaryStructureMenuItem = new JCheckBoxMenuItem( |
2189 | MessageManager.getString( | |
2190 | "action.by_secondary_structure_conservation")); | |
2191 | 452 | byConsensusSecondaryStructureMenuItem |
2192 | .addActionListener(new ActionListener() | |
2193 | { | |
2194 | 0 | @Override |
2195 | public void actionPerformed(ActionEvent e) | |
2196 | { | |
2197 | 0 | colourByConsensusSecondaryStructureMenuItem_actionPerformed( |
2198 | byConsensusSecondaryStructureMenuItem.isSelected()); | |
2199 | } | |
2200 | }); | |
2201 | ||
2202 | 452 | abovePIDThreshold = new JCheckBoxMenuItem( |
2203 | MessageManager.getString("label.above_identity_threshold")); | |
2204 | 452 | abovePIDThreshold.addActionListener(new ActionListener() |
2205 | { | |
2206 | 0 | @Override |
2207 | public void actionPerformed(ActionEvent e) | |
2208 | { | |
2209 | 0 | abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); |
2210 | } | |
2211 | }); | |
2212 | 452 | modifyPID = new JMenuItem( |
2213 | MessageManager.getString("label.modify_identity_threshold")); | |
2214 | 452 | modifyPID.addActionListener(new ActionListener() |
2215 | { | |
2216 | 0 | @Override |
2217 | public void actionPerformed(ActionEvent e) | |
2218 | { | |
2219 | 0 | modifyPID_actionPerformed(); |
2220 | } | |
2221 | }); | |
2222 | 452 | modifyConservation = new JMenuItem(MessageManager |
2223 | .getString("label.modify_conservation_threshold")); | |
2224 | 452 | modifyConservation.addActionListener(new ActionListener() |
2225 | { | |
2226 | 0 | @Override |
2227 | public void actionPerformed(ActionEvent e) | |
2228 | { | |
2229 | 0 | modifyConservation_actionPerformed(); |
2230 | } | |
2231 | }); | |
2232 | ||
2233 | 452 | modifyConsensusSecondaryStructureThreshold = new JMenuItem( |
2234 | MessageManager.getString( | |
2235 | "label.modify_secondary_structure_conservation_threshold")); | |
2236 | 452 | modifyConsensusSecondaryStructureThreshold |
2237 | .addActionListener(new ActionListener() | |
2238 | { | |
2239 | 0 | @Override |
2240 | public void actionPerformed(ActionEvent e) | |
2241 | { | |
2242 | 0 | modifyConsensusSecondaryStructureThreshold_actionPerformed(); |
2243 | } | |
2244 | }); | |
2245 | ||
2246 | 452 | annotationColour = new JRadioButtonMenuItem( |
2247 | MessageManager.getString("action.by_annotation")); | |
2248 | 452 | annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); |
2249 | 452 | annotationColour.addActionListener(new ActionListener() |
2250 | { | |
2251 | 0 | @Override |
2252 | public void actionPerformed(ActionEvent e) | |
2253 | { | |
2254 | 0 | annotationColour_actionPerformed(); |
2255 | } | |
2256 | }); | |
2257 | } | |
2258 | ||
2259 | 0 | protected void selectHighlightedColumns_actionPerformed( |
2260 | ActionEvent actionEvent) | |
2261 | { | |
2262 | // TODO Auto-generated method stub | |
2263 | ||
2264 | } | |
2265 | ||
2266 | /** | |
2267 | * Generate the reverse sequence (or reverse complement if the flag is true) | |
2268 | * and add it to the alignment | |
2269 | * | |
2270 | * @param complement | |
2271 | */ | |
2272 | 0 | protected void showReverse_actionPerformed(boolean complement) |
2273 | { | |
2274 | } | |
2275 | ||
2276 | /** | |
2277 | * Try to run script in a Groovy console, having first ensured that this | |
2278 | * alignframe is set as currentAlignFrame in Desktop | |
2279 | */ | |
2280 | 0 | protected void runGroovy_actionPerformed() |
2281 | { | |
2282 | ||
2283 | } | |
2284 | ||
2285 | /** | |
2286 | * Adds the given action listener and key accelerator to the given menu item. | |
2287 | * Also saves in a lookup table to support lookup of action by key stroke. | |
2288 | * | |
2289 | * @param keyStroke | |
2290 | * @param menuItem | |
2291 | * @param actionListener | |
2292 | */ | |
2293 | 12204 | protected void addMenuActionAndAccelerator(KeyStroke keyStroke, |
2294 | JMenuItem menuItem, ActionListener actionListener) | |
2295 | { | |
2296 | 12204 | menuItem.setAccelerator(keyStroke); |
2297 | 12204 | accelerators.put(keyStroke, menuItem); |
2298 | 12204 | menuItem.addActionListener(actionListener); |
2299 | } | |
2300 | ||
2301 | /** | |
2302 | * Action on clicking sort annotations by type. | |
2303 | * | |
2304 | * @param sortOrder | |
2305 | */ | |
2306 | 0 | protected void sortAnnotations_actionPerformed() |
2307 | { | |
2308 | } | |
2309 | ||
2310 | /** | |
2311 | * Action on clicking Show all annotations. | |
2312 | * | |
2313 | * @param forSequences | |
2314 | * update sequence-related annotations | |
2315 | * @param forAlignment | |
2316 | * update non-sequence-related annotations | |
2317 | */ | |
2318 | 0 | protected void showAllAnnotations_actionPerformed(boolean forSequences, |
2319 | boolean forAlignment) | |
2320 | { | |
2321 | 0 | setAnnotationsVisibility(true, forSequences, forAlignment); |
2322 | } | |
2323 | ||
2324 | /** | |
2325 | * Action on clicking Hide all annotations. | |
2326 | * | |
2327 | * @param forSequences | |
2328 | * update sequence-related annotations | |
2329 | * @param forAlignment | |
2330 | * update non-sequence-related annotations | |
2331 | */ | |
2332 | 0 | protected void hideAllAnnotations_actionPerformed(boolean forSequences, |
2333 | boolean forAlignment) | |
2334 | { | |
2335 | 0 | setAnnotationsVisibility(false, forSequences, forAlignment); |
2336 | } | |
2337 | ||
2338 | /** | |
2339 | * Set the visibility of annotations to true or false. Can act on | |
2340 | * sequence-related annotations, or alignment-related, or both. | |
2341 | * | |
2342 | * @param visible | |
2343 | * @param forSequences | |
2344 | * update sequence-related annotations | |
2345 | * @param forAlignment | |
2346 | * update non-sequence-related annotations | |
2347 | */ | |
2348 | 0 | public void setAnnotationsVisibility(boolean visible, |
2349 | boolean forSequences, boolean forAlignment) | |
2350 | { | |
2351 | ||
2352 | } | |
2353 | ||
2354 | 0 | protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) |
2355 | { | |
2356 | // TODO Auto-generated method stub | |
2357 | ||
2358 | } | |
2359 | ||
2360 | 0 | protected void listenToViewSelections_actionPerformed(ActionEvent e) |
2361 | { | |
2362 | // TODO Auto-generated method stub | |
2363 | ||
2364 | } | |
2365 | ||
2366 | 0 | protected void showAllhidden_actionPerformed(ActionEvent e) |
2367 | { | |
2368 | // TODO Auto-generated method stub | |
2369 | ||
2370 | } | |
2371 | ||
2372 | 0 | protected void hideAllButSelection_actionPerformed(ActionEvent e) |
2373 | { | |
2374 | // TODO Auto-generated method stub | |
2375 | ||
2376 | } | |
2377 | ||
2378 | 0 | protected void hideAllSelection_actionPerformed(ActionEvent e) |
2379 | { | |
2380 | // TODO Auto-generated method stub | |
2381 | ||
2382 | } | |
2383 | ||
2384 | 0 | protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) |
2385 | { | |
2386 | // TODO Auto-generated method stub | |
2387 | ||
2388 | } | |
2389 | ||
2390 | 0 | protected void showConsensusHistogram_actionPerformed(ActionEvent e) |
2391 | { | |
2392 | // TODO Auto-generated method stub | |
2393 | ||
2394 | } | |
2395 | ||
2396 | 0 | protected void showSequenceLogo_actionPerformed(ActionEvent e) |
2397 | { | |
2398 | // TODO Auto-generated method stub | |
2399 | ||
2400 | } | |
2401 | ||
2402 | 0 | protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) |
2403 | { | |
2404 | // TODO Auto-generated method stub | |
2405 | ||
2406 | } | |
2407 | ||
2408 | 0 | protected void showGroupConsensus_actionPerformed(ActionEvent e) |
2409 | { | |
2410 | // TODO Auto-generated method stub | |
2411 | ||
2412 | } | |
2413 | ||
2414 | 0 | protected void showGroupSSConsensus_actionPerformed(ActionEvent e) |
2415 | { | |
2416 | // TODO Auto-generated method stub | |
2417 | ||
2418 | } | |
2419 | ||
2420 | 0 | protected void showGroupConservation_actionPerformed(ActionEvent e) |
2421 | { | |
2422 | // TODO Auto-generated method stub | |
2423 | ||
2424 | } | |
2425 | ||
2426 | 0 | protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) |
2427 | { | |
2428 | // TODO Auto-generated method stub | |
2429 | ||
2430 | } | |
2431 | ||
2432 | 0 | protected void justifyRightMenuItem_actionPerformed(ActionEvent e) |
2433 | { | |
2434 | // TODO Auto-generated method stub | |
2435 | ||
2436 | } | |
2437 | ||
2438 | 0 | protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) |
2439 | { | |
2440 | // TODO Auto-generated method stub | |
2441 | ||
2442 | } | |
2443 | ||
2444 | 0 | protected void followHighlight_actionPerformed() |
2445 | { | |
2446 | // TODO Auto-generated method stub | |
2447 | ||
2448 | } | |
2449 | ||
2450 | 0 | protected void showNpFeats_actionPerformed(ActionEvent e) |
2451 | { | |
2452 | // TODO Auto-generated method stub | |
2453 | ||
2454 | } | |
2455 | ||
2456 | 0 | protected void showDbRefs_actionPerformed(ActionEvent e) |
2457 | { | |
2458 | // TODO Auto-generated method stub | |
2459 | ||
2460 | } | |
2461 | ||
2462 | 0 | protected void centreColumnLabels_actionPerformed(ActionEvent e) |
2463 | { | |
2464 | } | |
2465 | ||
2466 | 0 | protected void buildSortByAnnotationScoresMenu() |
2467 | { | |
2468 | } | |
2469 | ||
2470 | 0 | protected void extractScores_actionPerformed(ActionEvent e) |
2471 | { | |
2472 | } | |
2473 | ||
2474 | 0 | protected void outputText_actionPerformed(String formatName) |
2475 | { | |
2476 | } | |
2477 | ||
2478 | 0 | public void addFromFile_actionPerformed(ActionEvent e) |
2479 | { | |
2480 | ||
2481 | } | |
2482 | ||
2483 | 0 | public void addFromText_actionPerformed(ActionEvent e) |
2484 | { | |
2485 | ||
2486 | } | |
2487 | ||
2488 | 0 | public void addFromURL_actionPerformed(ActionEvent e) |
2489 | { | |
2490 | ||
2491 | } | |
2492 | ||
2493 | 0 | public void exportFeatures_actionPerformed(ActionEvent e) |
2494 | { | |
2495 | ||
2496 | } | |
2497 | ||
2498 | 0 | public void exportAnnotations_actionPerformed(ActionEvent e) |
2499 | { | |
2500 | ||
2501 | } | |
2502 | ||
2503 | 0 | protected void htmlMenuItem_actionPerformed(ActionEvent e) |
2504 | { | |
2505 | } | |
2506 | ||
2507 | 0 | protected void bioJSMenuItem_actionPerformed(ActionEvent e) |
2508 | { | |
2509 | ||
2510 | } | |
2511 | ||
2512 | 0 | protected void closeMenuItem_actionPerformed(boolean b) |
2513 | { | |
2514 | } | |
2515 | ||
2516 | 0 | protected void redoMenuItem_actionPerformed(ActionEvent e) |
2517 | { | |
2518 | } | |
2519 | ||
2520 | 0 | protected void undoMenuItem_actionPerformed(ActionEvent e) |
2521 | { | |
2522 | } | |
2523 | ||
2524 | 0 | protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) |
2525 | { | |
2526 | } | |
2527 | ||
2528 | 0 | protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) |
2529 | { | |
2530 | } | |
2531 | ||
2532 | 0 | protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) |
2533 | { | |
2534 | } | |
2535 | ||
2536 | 0 | protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) |
2537 | { | |
2538 | } | |
2539 | ||
2540 | 0 | protected void remove2RightMenuItem_actionPerformed(ActionEvent e) |
2541 | { | |
2542 | } | |
2543 | ||
2544 | 0 | protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) |
2545 | { | |
2546 | } | |
2547 | ||
2548 | 0 | protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) |
2549 | { | |
2550 | } | |
2551 | ||
2552 | 0 | protected void wrapMenuItem_actionPerformed(ActionEvent e) |
2553 | { | |
2554 | } | |
2555 | ||
2556 | 0 | protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) |
2557 | { | |
2558 | } | |
2559 | ||
2560 | 0 | protected void viewTextMenuItem_actionPerformed(ActionEvent e) |
2561 | { | |
2562 | } | |
2563 | ||
2564 | 0 | protected void colourTextMenuItem_actionPerformed(ActionEvent e) |
2565 | { | |
2566 | } | |
2567 | ||
2568 | 0 | protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) |
2569 | { | |
2570 | } | |
2571 | ||
2572 | 0 | protected void overviewMenuItem_actionPerformed(ActionEvent e) |
2573 | { | |
2574 | } | |
2575 | ||
2576 | 0 | protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) |
2577 | { | |
2578 | } | |
2579 | ||
2580 | 0 | protected void sortIDMenuItem_actionPerformed(ActionEvent e) |
2581 | { | |
2582 | } | |
2583 | ||
2584 | 0 | protected void sortLengthMenuItem_actionPerformed(ActionEvent e) |
2585 | { | |
2586 | } | |
2587 | ||
2588 | 0 | protected void sortGroupMenuItem_actionPerformed(ActionEvent e) |
2589 | { | |
2590 | } | |
2591 | ||
2592 | 0 | protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) |
2593 | { | |
2594 | } | |
2595 | ||
2596 | 0 | protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) |
2597 | { | |
2598 | } | |
2599 | ||
2600 | 0 | protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) |
2601 | { | |
2602 | } | |
2603 | ||
2604 | 0 | protected void conservationMenuItem_actionPerformed(boolean selected) |
2605 | { | |
2606 | } | |
2607 | ||
2608 | 0 | public void colourByConsensusSecondaryStructureMenuItem_actionPerformed( |
2609 | boolean selected) | |
2610 | { | |
2611 | } | |
2612 | ||
2613 | 0 | protected void printMenuItem_actionPerformed(ActionEvent e) |
2614 | { | |
2615 | } | |
2616 | ||
2617 | 0 | protected void renderGapsMenuItem_actionPerformed(ActionEvent e) |
2618 | { | |
2619 | } | |
2620 | ||
2621 | 0 | protected void findMenuItem_actionPerformed(ActionEvent e) |
2622 | { | |
2623 | } | |
2624 | ||
2625 | 0 | protected void abovePIDThreshold_actionPerformed(boolean selected) |
2626 | { | |
2627 | } | |
2628 | ||
2629 | 0 | public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) |
2630 | { | |
2631 | } | |
2632 | ||
2633 | 0 | protected void deleteGroups_actionPerformed(ActionEvent e) |
2634 | { | |
2635 | } | |
2636 | ||
2637 | 0 | protected void createGroup_actionPerformed(ActionEvent e) |
2638 | { | |
2639 | } | |
2640 | ||
2641 | 0 | protected void unGroup_actionPerformed(ActionEvent e) |
2642 | { | |
2643 | } | |
2644 | ||
2645 | 0 | protected void copy_actionPerformed() |
2646 | { | |
2647 | } | |
2648 | ||
2649 | 0 | protected void cut_actionPerformed() |
2650 | { | |
2651 | } | |
2652 | ||
2653 | 0 | protected void delete_actionPerformed() |
2654 | { | |
2655 | } | |
2656 | ||
2657 | 0 | protected void pasteNew_actionPerformed(ActionEvent e) |
2658 | { | |
2659 | } | |
2660 | ||
2661 | 0 | protected void pasteThis_actionPerformed(ActionEvent e) |
2662 | { | |
2663 | } | |
2664 | ||
2665 | 0 | protected void applyToAllGroups_actionPerformed(boolean selected) |
2666 | { | |
2667 | } | |
2668 | ||
2669 | 0 | protected void font_actionPerformed(ActionEvent e) |
2670 | { | |
2671 | } | |
2672 | ||
2673 | 0 | protected void seqLimit_actionPerformed(ActionEvent e) |
2674 | { | |
2675 | } | |
2676 | ||
2677 | 0 | public void seqDBRef_actionPerformed(ActionEvent e) |
2678 | { | |
2679 | ||
2680 | } | |
2681 | ||
2682 | 0 | protected void loadTreeMenuItem_actionPerformed(ActionEvent e) |
2683 | { | |
2684 | ||
2685 | } | |
2686 | ||
2687 | /** | |
2688 | * Template method to handle the 'load T-Coffee scores' menu event. | |
2689 | * <p> | |
2690 | * Subclasses override this method to provide a custom action. | |
2691 | * | |
2692 | * @param event | |
2693 | * The raised event | |
2694 | */ | |
2695 | 0 | protected void loadScores_actionPerformed(ActionEvent event) |
2696 | { | |
2697 | ||
2698 | } | |
2699 | ||
2700 | 0 | protected void scaleAbove_actionPerformed(ActionEvent e) |
2701 | { | |
2702 | } | |
2703 | ||
2704 | 0 | protected void scaleLeft_actionPerformed(ActionEvent e) |
2705 | { | |
2706 | } | |
2707 | ||
2708 | 0 | protected void scaleRight_actionPerformed(ActionEvent e) |
2709 | { | |
2710 | } | |
2711 | ||
2712 | 0 | protected void modifyPID_actionPerformed() |
2713 | { | |
2714 | } | |
2715 | ||
2716 | 0 | protected void modifyConservation_actionPerformed() |
2717 | { | |
2718 | } | |
2719 | ||
2720 | 0 | protected void modifyConsensusSecondaryStructureThreshold_actionPerformed() |
2721 | { | |
2722 | } | |
2723 | ||
2724 | 0 | protected void saveAs_actionPerformed() |
2725 | { | |
2726 | } | |
2727 | ||
2728 | 0 | protected void padGapsMenuitem_actionPerformed(ActionEvent e) |
2729 | { | |
2730 | } | |
2731 | ||
2732 | 0 | public void vamsasStore_actionPerformed(ActionEvent e) |
2733 | { | |
2734 | ||
2735 | } | |
2736 | ||
2737 | 0 | public void vamsasLoad_actionPerformed(ActionEvent e) |
2738 | { | |
2739 | ||
2740 | } | |
2741 | ||
2742 | 0 | public void showTranslation_actionPerformed(GeneticCodeI codeTable) |
2743 | { | |
2744 | ||
2745 | } | |
2746 | ||
2747 | 0 | public void featureSettings_actionPerformed(ActionEvent e) |
2748 | { | |
2749 | ||
2750 | } | |
2751 | ||
2752 | 0 | public void fetchSequence_actionPerformed() |
2753 | { | |
2754 | ||
2755 | } | |
2756 | ||
2757 | 0 | public void smoothFont_actionPerformed(ActionEvent e) |
2758 | { | |
2759 | ||
2760 | } | |
2761 | ||
2762 | 0 | public void annotationColour_actionPerformed() |
2763 | { | |
2764 | } | |
2765 | ||
2766 | 0 | public void annotationColumn_actionPerformed(ActionEvent e) |
2767 | { | |
2768 | } | |
2769 | ||
2770 | 0 | public void associatedData_actionPerformed(ActionEvent e) |
2771 | { | |
2772 | ||
2773 | } | |
2774 | ||
2775 | 0 | public void autoCalculate_actionPerformed(ActionEvent e) |
2776 | { | |
2777 | ||
2778 | } | |
2779 | ||
2780 | 0 | public void sortByTreeOption_actionPerformed(ActionEvent e) |
2781 | { | |
2782 | ||
2783 | } | |
2784 | ||
2785 | 0 | public void showAllSeqs_actionPerformed(ActionEvent e) |
2786 | { | |
2787 | ||
2788 | } | |
2789 | ||
2790 | 0 | public void showAllColumns_actionPerformed(ActionEvent e) |
2791 | { | |
2792 | ||
2793 | } | |
2794 | ||
2795 | 0 | public void hideSelSequences_actionPerformed(ActionEvent e) |
2796 | { | |
2797 | ||
2798 | } | |
2799 | ||
2800 | 0 | public void hideSelColumns_actionPerformed(ActionEvent e) |
2801 | { | |
2802 | ||
2803 | } | |
2804 | ||
2805 | 0 | public void hiddenMarkers_actionPerformed(ActionEvent e) |
2806 | { | |
2807 | ||
2808 | } | |
2809 | ||
2810 | 0 | public void findPdbId_actionPerformed(ActionEvent e) |
2811 | { | |
2812 | ||
2813 | } | |
2814 | ||
2815 | 0 | public void enterPdbId_actionPerformed(ActionEvent e) |
2816 | { | |
2817 | ||
2818 | } | |
2819 | ||
2820 | 0 | public void pdbFile_actionPerformed(ActionEvent e) |
2821 | { | |
2822 | ||
2823 | } | |
2824 | ||
2825 | 0 | public void invertColSel_actionPerformed(ActionEvent e) |
2826 | { | |
2827 | ||
2828 | } | |
2829 | ||
2830 | 0 | public void tabSelectionChanged(int sel) |
2831 | { | |
2832 | ||
2833 | } | |
2834 | ||
2835 | 0 | public void tabbedPane_mousePressed(MouseEvent e) |
2836 | { | |
2837 | ||
2838 | } | |
2839 | ||
2840 | 62 | public void tabbedPane_focusGained(FocusEvent e) |
2841 | { | |
2842 | 62 | requestFocus(); |
2843 | } | |
2844 | ||
2845 | 0 | public void save_actionPerformed(ActionEvent e) |
2846 | { | |
2847 | ||
2848 | } | |
2849 | ||
2850 | 0 | public void reload_actionPerformed(ActionEvent e) |
2851 | { | |
2852 | ||
2853 | } | |
2854 | ||
2855 | 0 | public void newView_actionPerformed(ActionEvent e) |
2856 | { | |
2857 | ||
2858 | } | |
2859 | ||
2860 | 0 | public void textColour_actionPerformed() |
2861 | { | |
2862 | ||
2863 | } | |
2864 | ||
2865 | 0 | public void idRightAlign_actionPerformed(ActionEvent e) |
2866 | { | |
2867 | ||
2868 | } | |
2869 | ||
2870 | 0 | public void expandViews_actionPerformed(ActionEvent e) |
2871 | { | |
2872 | ||
2873 | } | |
2874 | ||
2875 | 0 | public void gatherViews_actionPerformed(ActionEvent e) |
2876 | { | |
2877 | ||
2878 | } | |
2879 | ||
2880 | 0 | public void buildTreeSortMenu() |
2881 | { | |
2882 | ||
2883 | } | |
2884 | ||
2885 | 0 | public void pageSetup_actionPerformed(ActionEvent e) |
2886 | { | |
2887 | ||
2888 | } | |
2889 | ||
2890 | 0 | public void alignmentProperties() |
2891 | { | |
2892 | ||
2893 | } | |
2894 | ||
2895 | 0 | protected void expand_newalign(ActionEvent e) |
2896 | { | |
2897 | // TODO Auto-generated method stub | |
2898 | ||
2899 | } | |
2900 | ||
2901 | 452 | protected boolean isShowAutoCalculatedAbove() |
2902 | { | |
2903 | 452 | return showAutoCalculatedAbove; |
2904 | } | |
2905 | ||
2906 | 452 | protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove) |
2907 | { | |
2908 | 452 | this.showAutoCalculatedAbove = showAutoCalculatedAbove; |
2909 | } | |
2910 | ||
2911 | 0 | protected SequenceAnnotationOrder getAnnotationSortOrder() |
2912 | { | |
2913 | 0 | return annotationSortOrder; |
2914 | } | |
2915 | ||
2916 | 0 | protected void setAnnotationSortOrder( |
2917 | SequenceAnnotationOrder annotationSortOrder) | |
2918 | { | |
2919 | 0 | this.annotationSortOrder = annotationSortOrder; |
2920 | } | |
2921 | ||
2922 | 33 | public Map<KeyStroke, JMenuItem> getAccelerators() |
2923 | { | |
2924 | 33 | return this.accelerators; |
2925 | } | |
2926 | ||
2927 | /** | |
2928 | * Returns the selected index of the tabbed pane, or -1 if none selected | |
2929 | * (including the case where the tabbed pane has not been made visible). | |
2930 | * | |
2931 | * @return | |
2932 | */ | |
2933 | 0 | public int getTabIndex() |
2934 | { | |
2935 | 0 | return tabbedPane.getSelectedIndex(); |
2936 | } | |
2937 | ||
2938 | 0 | public JPanel getStatusPanel() |
2939 | { | |
2940 | 0 | return statusPanel; |
2941 | } | |
2942 | ||
2943 | /** | |
2944 | * Sets a reference to the containing split frame. Also makes the 'toggle | |
2945 | * split view' menu item visible and checked. | |
2946 | * | |
2947 | * @param sf | |
2948 | */ | |
2949 | 6 | public void setSplitFrame(SplitContainerI sf) |
2950 | { | |
2951 | 6 | this.splitFrame = sf; |
2952 | 6 | if (sf != null) |
2953 | { | |
2954 | 6 | this.showComplementMenuItem.setVisible(true); |
2955 | 6 | this.showComplementMenuItem.setState(true); |
2956 | } | |
2957 | } | |
2958 | ||
2959 | 3 | public SplitContainerI getSplitViewContainer() |
2960 | { | |
2961 | 3 | return this.splitFrame; |
2962 | } | |
2963 | ||
2964 | 0 | protected void showComplement_actionPerformed(boolean complement) |
2965 | { | |
2966 | } | |
2967 | ||
2968 | 0 | protected List<String> updateShowSSRadioButtons() |
2969 | { | |
2970 | // TODO Auto-generated method stub | |
2971 | 0 | return null; |
2972 | } | |
2973 | ||
2974 | 0 | protected void showOrHideSecondaryStructureForSource( |
2975 | String ssSourceSelection, boolean visible) | |
2976 | { | |
2977 | // TODO Auto-generated method stub | |
2978 | ||
2979 | } | |
2980 | ||
2981 | 0 | protected void updateShowSecondaryStructureMenu(JMenu showSS, |
2982 | ButtonGroup ssButtonGroup) | |
2983 | { | |
2984 | // TODO Auto-generated method stub | |
2985 | ||
2986 | } | |
2987 | } |