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1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.gui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.Component; | |
25 | import java.awt.Dimension; | |
26 | import java.awt.event.ActionEvent; | |
27 | import java.awt.event.ActionListener; | |
28 | import java.awt.event.KeyAdapter; | |
29 | import java.awt.event.KeyEvent; | |
30 | import java.awt.event.KeyListener; | |
31 | import java.beans.PropertyVetoException; | |
32 | import java.util.Arrays; | |
33 | import java.util.List; | |
34 | import java.util.Map.Entry; | |
35 | ||
36 | import javax.swing.AbstractAction; | |
37 | import javax.swing.InputMap; | |
38 | import javax.swing.JButton; | |
39 | import javax.swing.JComponent; | |
40 | import javax.swing.JDesktopPane; | |
41 | import javax.swing.JInternalFrame; | |
42 | import javax.swing.JLayeredPane; | |
43 | import javax.swing.JMenuItem; | |
44 | import javax.swing.JPanel; | |
45 | import javax.swing.JTabbedPane; | |
46 | import javax.swing.KeyStroke; | |
47 | import javax.swing.event.ChangeEvent; | |
48 | import javax.swing.event.ChangeListener; | |
49 | import javax.swing.event.InternalFrameAdapter; | |
50 | import javax.swing.event.InternalFrameEvent; | |
51 | ||
52 | import jalview.api.AlignViewControllerGuiI; | |
53 | import jalview.api.FeatureSettingsControllerI; | |
54 | import jalview.api.SplitContainerI; | |
55 | import jalview.controller.FeatureSettingsControllerGuiI; | |
56 | import jalview.datamodel.AlignmentI; | |
57 | import jalview.jbgui.GAlignFrame; | |
58 | import jalview.jbgui.GSplitFrame; | |
59 | import jalview.structure.StructureSelectionManager; | |
60 | import jalview.util.MessageManager; | |
61 | import jalview.util.Platform; | |
62 | import jalview.viewmodel.AlignmentViewport; | |
63 | ||
64 | /** | |
65 | * An internal frame on the desktop that hosts a horizontally split view of | |
66 | * linked DNA and Protein alignments. Additional views can be created in linked | |
67 | * pairs, expanded to separate split frames, or regathered into a single frame. | |
68 | * <p> | |
69 | * (Some) operations on each alignment are automatically mirrored on the other. | |
70 | * These include mouseover (highlighting), sequence and column selection, | |
71 | * sequence ordering and sorting, and grouping, colouring and sorting by tree. | |
72 | * | |
73 | * @author gmcarstairs | |
74 | * | |
75 | */ | |
76 | public class SplitFrame extends GSplitFrame implements SplitContainerI | |
77 | { | |
78 | private static final int WINDOWS_INSETS_WIDTH = 28; // tbc | |
79 | ||
80 | private static final int MAC_INSETS_WIDTH = 28; | |
81 | ||
82 | private static final int WINDOWS_INSETS_HEIGHT = 50; // tbc | |
83 | ||
84 | private static final int MAC_INSETS_HEIGHT = 50; | |
85 | ||
86 | private static final int DESKTOP_DECORATORS_HEIGHT = 65; | |
87 | ||
88 | private static final long serialVersionUID = 1L; | |
89 | ||
90 | /** | |
91 | * geometry for Feature Settings Holder | |
92 | */ | |
93 | private static final int FS_MIN_WIDTH = 400; | |
94 | ||
95 | private static final int FS_MIN_HEIGHT = 400; | |
96 | ||
97 | 3 | public SplitFrame(GAlignFrame top, GAlignFrame bottom) |
98 | { | |
99 | 3 | super(top, bottom); |
100 | 3 | init(); |
101 | } | |
102 | ||
103 | /** | |
104 | * Initialise this frame. | |
105 | */ | |
106 | 3 | protected void init() |
107 | { | |
108 | 3 | setFrameIcon(null); |
109 | 3 | getTopFrame().setSplitFrame(this); |
110 | 3 | getBottomFrame().setSplitFrame(this); |
111 | 3 | getTopFrame().setVisible(true); |
112 | 3 | getBottomFrame().setVisible(true); |
113 | ||
114 | 3 | ((AlignFrame) getTopFrame()).getViewport().setCodingComplement( |
115 | ((AlignFrame) getBottomFrame()).getViewport()); | |
116 | ||
117 | /* | |
118 | * estimate width and height of SplitFrame; this.getInsets() doesn't seem to | |
119 | * give the full additional size (a few pixels short) | |
120 | */ | |
121 | 3 | int widthFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_WIDTH |
122 | : WINDOWS_INSETS_WIDTH; | |
123 | 3 | int heightFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT |
124 | : WINDOWS_INSETS_HEIGHT; | |
125 | 3 | int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge; |
126 | 3 | int height = ((AlignFrame) getTopFrame()).getHeight() |
127 | + ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE | |
128 | + heightFudge; | |
129 | 3 | height = fitHeightToDesktop(height); |
130 | 3 | setSize(width, height); |
131 | ||
132 | 3 | adjustLayout(); |
133 | ||
134 | 3 | addCloseFrameListener(); |
135 | ||
136 | 3 | addKeyListener(); |
137 | ||
138 | 3 | addKeyBindings(); |
139 | ||
140 | 3 | addCommandListeners(); |
141 | } | |
142 | ||
143 | /** | |
144 | * Reduce the height if too large to fit in the Desktop. Also adjust the | |
145 | * divider location in proportion. | |
146 | * | |
147 | * @param height | |
148 | * in pixels | |
149 | * @return original or reduced height | |
150 | */ | |
151 | 3 | public int fitHeightToDesktop(int height) |
152 | { | |
153 | // allow about 65 pixels for Desktop decorators on Windows | |
154 | ||
155 | 3 | int newHeight = Math.min(height, |
156 | Desktop.instance.getHeight() - DESKTOP_DECORATORS_HEIGHT); | |
157 | 3 | if (newHeight != height) |
158 | { | |
159 | 3 | int oldDividerLocation = getDividerLocation(); |
160 | 3 | setDividerLocation(oldDividerLocation * newHeight / height); |
161 | } | |
162 | 3 | return newHeight; |
163 | } | |
164 | ||
165 | /** | |
166 | * Set the top and bottom frames to listen to each others Commands (e.g. Edit, | |
167 | * Order). | |
168 | */ | |
169 | 3 | protected void addCommandListeners() |
170 | { | |
171 | // TODO if CommandListener is only ever 1:1 for complementary views, | |
172 | // may change broadcast pattern to direct messaging (more efficient) | |
173 | 3 | final StructureSelectionManager ssm = StructureSelectionManager |
174 | .getStructureSelectionManager(Desktop.instance); | |
175 | 3 | ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport()); |
176 | 3 | ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport()); |
177 | } | |
178 | ||
179 | /** | |
180 | * Do any tweaking and twerking of the layout wanted. | |
181 | */ | |
182 | 3 | public void adjustLayout() |
183 | { | |
184 | 3 | final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport; |
185 | 3 | final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport; |
186 | ||
187 | /* | |
188 | * Ensure sequence ids are the same width so sequences line up | |
189 | */ | |
190 | 3 | int w1 = topViewport.getIdWidth(); |
191 | 3 | int w2 = bottomViewport.getIdWidth(); |
192 | 3 | int w3 = Math.max(w1, w2); |
193 | 3 | topViewport.setIdWidth(w3); |
194 | 3 | bottomViewport.setIdWidth(w3); |
195 | ||
196 | /* | |
197 | * Scale protein to either 1 or 3 times character width of dna | |
198 | */ | |
199 | 3 | final AlignmentI topAlignment = topViewport.getAlignment(); |
200 | 3 | final AlignmentI bottomAlignment = bottomViewport.getAlignment(); |
201 | 3 | AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport |
202 | 0 | : (bottomAlignment.isNucleotide() ? bottomViewport : null); |
203 | 3 | AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport |
204 | 3 | : (!bottomAlignment.isNucleotide() ? bottomViewport : null); |
205 | 3 | if (protein != null && cdna != null) |
206 | { | |
207 | 3 | int scale = protein.isScaleProteinAsCdna() ? 3 : 1; |
208 | 3 | protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth()); |
209 | } | |
210 | } | |
211 | ||
212 | /** | |
213 | * Adjusts the divider for a sensible split of the real estate (for example, | |
214 | * when many transcripts are shown with a single protein). This should only be | |
215 | * called after the split pane has been laid out (made visible) so it has a | |
216 | * height. The aim is to avoid unnecessary vertical scroll bars, while | |
217 | * ensuring that at least 2 sequences are visible in each panel. | |
218 | * <p> | |
219 | * Once laid out, the user may choose to customise as they wish, so this | |
220 | * method is not called again after the initial layout. | |
221 | */ | |
222 | 2 | protected void adjustInitialLayout() |
223 | { | |
224 | 2 | AlignFrame topFrame = (AlignFrame) getTopFrame(); |
225 | 2 | AlignFrame bottomFrame = (AlignFrame) getBottomFrame(); |
226 | ||
227 | /* | |
228 | * recompute layout of top and bottom panels to reflect their | |
229 | * actual (rather than requested) height | |
230 | */ | |
231 | 2 | topFrame.alignPanel.adjustAnnotationHeight(); |
232 | 2 | bottomFrame.alignPanel.adjustAnnotationHeight(); |
233 | ||
234 | 2 | final AlignViewport topViewport = topFrame.viewport; |
235 | 2 | final AlignViewport bottomViewport = bottomFrame.viewport; |
236 | 2 | final AlignmentI topAlignment = topViewport.getAlignment(); |
237 | 2 | final AlignmentI bottomAlignment = bottomViewport.getAlignment(); |
238 | 2 | boolean topAnnotations = topViewport.isShowAnnotation(); |
239 | 2 | boolean bottomAnnotations = bottomViewport.isShowAnnotation(); |
240 | // TODO need number of visible sequences here, not #sequences - how? | |
241 | 2 | int topCount = topAlignment.getHeight(); |
242 | 2 | int bottomCount = bottomAlignment.getHeight(); |
243 | 2 | int topCharHeight = topViewport.getViewStyle().getCharHeight(); |
244 | 2 | int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight(); |
245 | ||
246 | /* | |
247 | * calculate the minimum ratio that leaves at least the height | |
248 | * of two sequences (after rounding) visible in the top panel | |
249 | */ | |
250 | 2 | int topPanelHeight = topFrame.getHeight(); |
251 | 2 | int bottomPanelHeight = bottomFrame.getHeight(); |
252 | 2 | int topSequencesHeight = topFrame.alignPanel.getSeqPanel().seqCanvas |
253 | .getHeight(); | |
254 | 2 | int topPanelMinHeight = topPanelHeight |
255 | - Math.max(0, topSequencesHeight - 3 * topCharHeight); | |
256 | 2 | double totalHeight = (double) topPanelHeight + bottomPanelHeight; |
257 | 2 | double minRatio = topPanelMinHeight / totalHeight; |
258 | ||
259 | /* | |
260 | * calculate the maximum ratio that leaves at least the height | |
261 | * of two sequences (after rounding) visible in the bottom panel | |
262 | */ | |
263 | 2 | int bottomSequencesHeight = bottomFrame.alignPanel |
264 | .getSeqPanel().seqCanvas.getHeight(); | |
265 | 2 | int bottomPanelMinHeight = bottomPanelHeight |
266 | - Math.max(0, bottomSequencesHeight - 3 * bottomCharHeight); | |
267 | 2 | double maxRatio = (totalHeight - bottomPanelMinHeight) / totalHeight; |
268 | ||
269 | /* | |
270 | * estimate ratio of (topFrameContent / bottomFrameContent) | |
271 | */ | |
272 | 2 | int insets = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT |
273 | : WINDOWS_INSETS_HEIGHT; | |
274 | // allow 3 'rows' for scale, scrollbar, status bar | |
275 | 2 | int topHeight = insets + (3 + topCount) * topCharHeight |
276 | 2 | + (topAnnotations ? topViewport.calcPanelHeight() : 0); |
277 | 2 | int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight |
278 | 2 | + (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0); |
279 | 2 | double ratio = ((double) topHeight) |
280 | / (double) (topHeight + bottomHeight); | |
281 | ||
282 | /* | |
283 | * limit ratio to avoid concealing all sequences | |
284 | */ | |
285 | 2 | ratio = Math.min(ratio, maxRatio); |
286 | 2 | ratio = Math.max(ratio, minRatio); |
287 | 2 | setRelativeDividerLocation(ratio); |
288 | } | |
289 | ||
290 | /** | |
291 | * Add a listener to tidy up when the frame is closed. | |
292 | */ | |
293 | 3 | protected void addCloseFrameListener() |
294 | { | |
295 | 3 | addInternalFrameListener(new InternalFrameAdapter() |
296 | { | |
297 | 3 | @Override |
298 | public void internalFrameClosed(InternalFrameEvent evt) | |
299 | { | |
300 | 3 | close(); |
301 | }; | |
302 | }); | |
303 | } | |
304 | ||
305 | /** | |
306 | * Add a key listener that delegates to whichever split component the mouse is | |
307 | * in (or does nothing if neither). | |
308 | */ | |
309 | 3 | protected void addKeyListener() |
310 | { | |
311 | 3 | addKeyListener(new KeyAdapter() |
312 | { | |
313 | ||
314 | 0 | @Override |
315 | public void keyPressed(KeyEvent e) | |
316 | { | |
317 | 0 | AlignFrame af = (AlignFrame) getFrameAtMouse(); |
318 | ||
319 | /* | |
320 | * Intercept and override any keys here if wanted. | |
321 | */ | |
322 | 0 | if (!overrideKey(e, af)) |
323 | { | |
324 | 0 | if (af != null) |
325 | { | |
326 | 0 | for (KeyListener kl : af.getKeyListeners()) |
327 | { | |
328 | 0 | kl.keyPressed(e); |
329 | } | |
330 | } | |
331 | } | |
332 | } | |
333 | ||
334 | 0 | @Override |
335 | public void keyReleased(KeyEvent e) | |
336 | { | |
337 | 0 | Component c = getFrameAtMouse(); |
338 | 0 | if (c != null) |
339 | { | |
340 | 0 | for (KeyListener kl : c.getKeyListeners()) |
341 | { | |
342 | 0 | kl.keyReleased(e); |
343 | } | |
344 | } | |
345 | } | |
346 | ||
347 | }); | |
348 | } | |
349 | ||
350 | /** | |
351 | * Returns true if the key event is overriden and actioned (or ignored) here, | |
352 | * else returns false, indicating it should be delegated to the AlignFrame's | |
353 | * usual handler. | |
354 | * <p> | |
355 | * We can't handle Cmd-Key combinations here, instead this is done by | |
356 | * overriding key bindings. | |
357 | * | |
358 | * @see addKeyOverrides | |
359 | * @param e | |
360 | * @param af | |
361 | * @return | |
362 | */ | |
363 | 0 | protected boolean overrideKey(KeyEvent e, AlignFrame af) |
364 | { | |
365 | 0 | boolean actioned = false; |
366 | 0 | int keyCode = e.getKeyCode(); |
367 | 0 | switch (keyCode) |
368 | { | |
369 | 0 | case KeyEvent.VK_DOWN: |
370 | 0 | if (e.isAltDown() || !af.viewport.cursorMode) |
371 | { | |
372 | /* | |
373 | * Key down (or Alt-key-down in cursor mode) - move selected sequences | |
374 | */ | |
375 | 0 | ((AlignFrame) getTopFrame()).moveSelectedSequences(false); |
376 | 0 | ((AlignFrame) getBottomFrame()).moveSelectedSequences(false); |
377 | 0 | actioned = true; |
378 | 0 | e.consume(); |
379 | } | |
380 | 0 | break; |
381 | 0 | case KeyEvent.VK_UP: |
382 | 0 | if (e.isAltDown() || !af.viewport.cursorMode) |
383 | { | |
384 | /* | |
385 | * Key up (or Alt-key-up in cursor mode) - move selected sequences | |
386 | */ | |
387 | 0 | ((AlignFrame) getTopFrame()).moveSelectedSequences(true); |
388 | 0 | ((AlignFrame) getBottomFrame()).moveSelectedSequences(true); |
389 | 0 | actioned = true; |
390 | 0 | e.consume(); |
391 | } | |
392 | 0 | break; |
393 | 0 | default: |
394 | } | |
395 | 0 | return actioned; |
396 | } | |
397 | ||
398 | /** | |
399 | * Set key bindings (recommended for Swing over key accelerators). | |
400 | */ | |
401 | 3 | private void addKeyBindings() |
402 | { | |
403 | 3 | overrideDelegatedKeyBindings(); |
404 | ||
405 | 3 | overrideImplementedKeyBindings(); |
406 | } | |
407 | ||
408 | /** | |
409 | * Override key bindings with alternative action methods implemented in this | |
410 | * class. | |
411 | */ | |
412 | 3 | protected void overrideImplementedKeyBindings() |
413 | { | |
414 | 3 | overrideFind(); |
415 | 3 | overrideNewView(); |
416 | 3 | overrideCloseView(); |
417 | 3 | overrideExpandViews(); |
418 | 3 | overrideGatherViews(); |
419 | } | |
420 | ||
421 | /** | |
422 | * Replace Cmd-W close view action with our version. | |
423 | */ | |
424 | 3 | protected void overrideCloseView() |
425 | { | |
426 | 3 | AbstractAction action; |
427 | /* | |
428 | * Ctrl-W / Cmd-W - close view or window | |
429 | */ | |
430 | 3 | KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
431 | jalview.util.ShortcutKeyMaskExWrapper | |
432 | .getMenuShortcutKeyMaskEx(), | |
433 | false); | |
434 | 3 | action = new AbstractAction() |
435 | { | |
436 | 0 | @Override |
437 | public void actionPerformed(ActionEvent e) | |
438 | { | |
439 | 0 | closeView_actionPerformed(); |
440 | } | |
441 | }; | |
442 | 3 | overrideKeyBinding(key_cmdW, action); |
443 | } | |
444 | ||
445 | /** | |
446 | * Replace Cmd-T new view action with our version. | |
447 | */ | |
448 | 3 | protected void overrideNewView() |
449 | { | |
450 | /* | |
451 | * Ctrl-T / Cmd-T open new view | |
452 | */ | |
453 | 3 | KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T, |
454 | jalview.util.ShortcutKeyMaskExWrapper | |
455 | .getMenuShortcutKeyMaskEx(), | |
456 | false); | |
457 | 3 | AbstractAction action = new AbstractAction() |
458 | { | |
459 | 0 | @Override |
460 | public void actionPerformed(ActionEvent e) | |
461 | { | |
462 | 0 | newView_actionPerformed(); |
463 | } | |
464 | }; | |
465 | 3 | overrideKeyBinding(key_cmdT, action); |
466 | } | |
467 | ||
468 | /** | |
469 | * For now, delegates key events to the corresponding key accelerator for the | |
470 | * AlignFrame that the mouse is in. Hopefully can be simplified in future if | |
471 | * AlignFrame is changed to use key bindings rather than accelerators. | |
472 | */ | |
473 | 3 | protected void overrideDelegatedKeyBindings() |
474 | { | |
475 | 3 | if (getTopFrame() instanceof AlignFrame) |
476 | { | |
477 | /* | |
478 | * Get all accelerator keys in the top frame (the bottom should be | |
479 | * identical) and override each one. | |
480 | */ | |
481 | 3 | for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame()) |
482 | .getAccelerators().entrySet()) | |
483 | { | |
484 | 81 | overrideKeyBinding(acc); |
485 | } | |
486 | } | |
487 | } | |
488 | ||
489 | /** | |
490 | * Overrides an AlignFrame key accelerator with our version which delegates to | |
491 | * the action listener in whichever frame has the mouse (and does nothing if | |
492 | * neither has). | |
493 | * | |
494 | * @param acc | |
495 | */ | |
496 | 81 | private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc) |
497 | { | |
498 | 81 | final KeyStroke ks = acc.getKey(); |
499 | 81 | InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED); |
500 | 81 | inputMap.put(ks, ks); |
501 | 81 | this.getActionMap().put(ks, new AbstractAction() |
502 | { | |
503 | 0 | @Override |
504 | public void actionPerformed(ActionEvent e) | |
505 | { | |
506 | 0 | Component c = getFrameAtMouse(); |
507 | 0 | if (c != null && c instanceof AlignFrame) |
508 | { | |
509 | 0 | for (ActionListener a : ((AlignFrame) c).getAccelerators().get(ks) |
510 | .getActionListeners()) | |
511 | { | |
512 | 0 | a.actionPerformed(null); |
513 | } | |
514 | } | |
515 | } | |
516 | }); | |
517 | } | |
518 | ||
519 | /** | |
520 | * Replace an accelerator key's action with the specified action. | |
521 | * | |
522 | * @param ks | |
523 | */ | |
524 | 9 | protected void overrideKeyBinding(KeyStroke ks, AbstractAction action) |
525 | { | |
526 | 9 | this.getActionMap().put(ks, action); |
527 | 9 | overrideMenuItem(ks, action); |
528 | } | |
529 | ||
530 | /** | |
531 | * Create and link new views (with matching names) in both panes. | |
532 | * <p> | |
533 | * Note this is _not_ multiple tabs, each hosting a split pane view, rather it | |
534 | * is a single split pane with each split holding multiple tabs which are | |
535 | * linked in pairs. | |
536 | * <p> | |
537 | * TODO implement instead with a tabbed holder in the SplitView, each tab | |
538 | * holding a single JSplitPane. Would avoid a duplicated tab, at the cost of | |
539 | * some additional coding. | |
540 | */ | |
541 | 0 | protected void newView_actionPerformed() |
542 | { | |
543 | 0 | AlignFrame topFrame = (AlignFrame) getTopFrame(); |
544 | 0 | AlignFrame bottomFrame = (AlignFrame) getBottomFrame(); |
545 | 0 | final boolean scaleProteinAsCdna = topFrame.viewport |
546 | .isScaleProteinAsCdna(); | |
547 | ||
548 | 0 | AlignmentPanel newTopPanel = topFrame.newView(null, true); |
549 | 0 | AlignmentPanel newBottomPanel = bottomFrame.newView(null, true); |
550 | ||
551 | /* | |
552 | * This currently (for the first new view only) leaves the top pane on tab 0 | |
553 | * but the bottom on tab 1. This results from 'setInitialTabVisible' echoing | |
554 | * from the bottom back to the first frame. Next line is a fudge to work | |
555 | * around this. TODO find a better way. | |
556 | */ | |
557 | 0 | if (topFrame.getTabIndex() != bottomFrame.getTabIndex()) |
558 | { | |
559 | 0 | topFrame.setDisplayedView(newTopPanel); |
560 | } | |
561 | ||
562 | 0 | newBottomPanel.av.setViewName(newTopPanel.av.getViewName()); |
563 | 0 | newTopPanel.av.setCodingComplement(newBottomPanel.av); |
564 | ||
565 | /* | |
566 | * These lines can be removed once scaleProteinAsCdna is added to element | |
567 | * Viewport in jalview.xsd, as Jalview2XML.copyAlignPanel will then take | |
568 | * care of it | |
569 | */ | |
570 | 0 | newTopPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna); |
571 | 0 | newBottomPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna); |
572 | ||
573 | /* | |
574 | * Line up id labels etc | |
575 | */ | |
576 | 0 | adjustLayout(); |
577 | ||
578 | 0 | final StructureSelectionManager ssm = StructureSelectionManager |
579 | .getStructureSelectionManager(Desktop.instance); | |
580 | 0 | ssm.addCommandListener(newTopPanel.av); |
581 | 0 | ssm.addCommandListener(newBottomPanel.av); |
582 | } | |
583 | ||
584 | /** | |
585 | * Close the currently selected view in both panes. If there is only one view, | |
586 | * close this split frame. | |
587 | */ | |
588 | 0 | protected void closeView_actionPerformed() |
589 | { | |
590 | 0 | int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size(); |
591 | 0 | if (viewCount < 2) |
592 | { | |
593 | 0 | close(); |
594 | 0 | return; |
595 | } | |
596 | ||
597 | 0 | AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel; |
598 | 0 | AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel; |
599 | ||
600 | 0 | ((AlignFrame) getTopFrame()).closeView(topPanel); |
601 | 0 | ((AlignFrame) getBottomFrame()).closeView(bottomPanel); |
602 | ||
603 | } | |
604 | ||
605 | /** | |
606 | * Close child frames and this split frame. | |
607 | */ | |
608 | 3 | public void close() |
609 | { | |
610 | 3 | ((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true); |
611 | 3 | ((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true); |
612 | 3 | try |
613 | { | |
614 | 3 | this.setClosed(true); |
615 | } catch (PropertyVetoException e) | |
616 | { | |
617 | // ignore | |
618 | } | |
619 | } | |
620 | ||
621 | /** | |
622 | * Replace AlignFrame 'expand views' action with SplitFrame version. | |
623 | */ | |
624 | 3 | protected void overrideExpandViews() |
625 | { | |
626 | 3 | KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); |
627 | 3 | AbstractAction action = new AbstractAction() |
628 | { | |
629 | 0 | @Override |
630 | public void actionPerformed(ActionEvent e) | |
631 | { | |
632 | 0 | expandViews_actionPerformed(); |
633 | } | |
634 | }; | |
635 | 3 | overrideMenuItem(key_X, action); |
636 | } | |
637 | ||
638 | /** | |
639 | * Replace AlignFrame 'gather views' action with SplitFrame version. | |
640 | */ | |
641 | 3 | protected void overrideGatherViews() |
642 | { | |
643 | 3 | KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); |
644 | 3 | AbstractAction action = new AbstractAction() |
645 | { | |
646 | 0 | @Override |
647 | public void actionPerformed(ActionEvent e) | |
648 | { | |
649 | 0 | gatherViews_actionPerformed(); |
650 | } | |
651 | }; | |
652 | 3 | overrideMenuItem(key_G, action); |
653 | } | |
654 | ||
655 | /** | |
656 | * Override the menu action associated with the keystroke in the child frames, | |
657 | * replacing it with the given action. | |
658 | * | |
659 | * @param ks | |
660 | * @param action | |
661 | */ | |
662 | 15 | private void overrideMenuItem(KeyStroke ks, AbstractAction action) |
663 | { | |
664 | 15 | overrideMenuItem(ks, action, getTopFrame()); |
665 | 15 | overrideMenuItem(ks, action, getBottomFrame()); |
666 | } | |
667 | ||
668 | /** | |
669 | * Override the menu action associated with the keystroke in one child frame, | |
670 | * replacing it with the given action. Mwahahahaha. | |
671 | * | |
672 | * @param key | |
673 | * @param action | |
674 | * @param comp | |
675 | */ | |
676 | 30 | private void overrideMenuItem(KeyStroke key, final AbstractAction action, |
677 | JComponent comp) | |
678 | { | |
679 | 30 | if (comp instanceof AlignFrame) |
680 | { | |
681 | 30 | JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key); |
682 | 30 | if (mi != null) |
683 | { | |
684 | 30 | for (ActionListener al : mi.getActionListeners()) |
685 | { | |
686 | 30 | mi.removeActionListener(al); |
687 | } | |
688 | 30 | mi.addActionListener(new ActionListener() |
689 | { | |
690 | 0 | @Override |
691 | public void actionPerformed(ActionEvent e) | |
692 | { | |
693 | 0 | action.actionPerformed(e); |
694 | } | |
695 | }); | |
696 | } | |
697 | } | |
698 | } | |
699 | ||
700 | /** | |
701 | * Expand any multiple views (which are always in pairs) into separate split | |
702 | * frames. | |
703 | */ | |
704 | 0 | protected void expandViews_actionPerformed() |
705 | { | |
706 | 0 | Desktop.instance.explodeViews(this); |
707 | } | |
708 | ||
709 | /** | |
710 | * Gather any other SplitFrame views of this alignment back in as multiple | |
711 | * (pairs of) views in this SplitFrame. | |
712 | */ | |
713 | 0 | protected void gatherViews_actionPerformed() |
714 | { | |
715 | 0 | Desktop.instance.gatherViews(this); |
716 | } | |
717 | ||
718 | /** | |
719 | * Returns the alignment in the complementary frame to the one given. | |
720 | */ | |
721 | 0 | @Override |
722 | public AlignmentI getComplement(Object alignFrame) | |
723 | { | |
724 | 0 | if (alignFrame == this.getTopFrame()) |
725 | { | |
726 | 0 | return ((AlignFrame) getBottomFrame()).viewport.getAlignment(); |
727 | } | |
728 | 0 | else if (alignFrame == this.getBottomFrame()) |
729 | { | |
730 | 0 | return ((AlignFrame) getTopFrame()).viewport.getAlignment(); |
731 | } | |
732 | 0 | return null; |
733 | } | |
734 | ||
735 | /** | |
736 | * Returns the title of the complementary frame to the one given. | |
737 | */ | |
738 | 0 | @Override |
739 | public String getComplementTitle(Object alignFrame) | |
740 | { | |
741 | 0 | if (alignFrame == this.getTopFrame()) |
742 | { | |
743 | 0 | return ((AlignFrame) getBottomFrame()).getTitle(); |
744 | } | |
745 | 0 | else if (alignFrame == this.getBottomFrame()) |
746 | { | |
747 | 0 | return ((AlignFrame) getTopFrame()).getTitle(); |
748 | } | |
749 | 0 | return null; |
750 | } | |
751 | ||
752 | /** | |
753 | * Set the 'other half' to hidden / revealed. | |
754 | */ | |
755 | 0 | @Override |
756 | public void setComplementVisible(Object alignFrame, boolean show) | |
757 | { | |
758 | /* | |
759 | * Hiding the AlignPanel suppresses unnecessary repaints | |
760 | */ | |
761 | 0 | if (alignFrame == getTopFrame()) |
762 | { | |
763 | 0 | ((AlignFrame) getBottomFrame()).alignPanel.setVisible(show); |
764 | } | |
765 | 0 | else if (alignFrame == getBottomFrame()) |
766 | { | |
767 | 0 | ((AlignFrame) getTopFrame()).alignPanel.setVisible(show); |
768 | } | |
769 | 0 | super.setComplementVisible(alignFrame, show); |
770 | } | |
771 | ||
772 | /** | |
773 | * return the AlignFrames held by this container | |
774 | * | |
775 | * @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually | |
776 | * Protein)} | |
777 | */ | |
778 | 0 | public List<AlignFrame> getAlignFrames() |
779 | { | |
780 | 0 | return Arrays |
781 | .asList(new AlignFrame[] | |
782 | { (AlignFrame) getTopFrame(), (AlignFrame) getBottomFrame() }); | |
783 | } | |
784 | ||
785 | 0 | @Override |
786 | public AlignFrame getComplementAlignFrame( | |
787 | AlignViewControllerGuiI alignFrame) | |
788 | { | |
789 | 0 | if (getTopFrame() == alignFrame) |
790 | { | |
791 | 0 | return (AlignFrame) getBottomFrame(); |
792 | } | |
793 | 0 | if (getBottomFrame() == alignFrame) |
794 | { | |
795 | 0 | return (AlignFrame) getTopFrame(); |
796 | } | |
797 | // we didn't know anything about this frame... | |
798 | 0 | return null; |
799 | } | |
800 | ||
801 | /** | |
802 | * Replace Cmd-F Find action with our version. This is necessary because the | |
803 | * 'default' Finder searches in the first AlignFrame it finds. We need it to | |
804 | * search in the half of the SplitFrame that has the mouse. | |
805 | */ | |
806 | 3 | protected void overrideFind() |
807 | { | |
808 | /* | |
809 | * Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment | |
810 | */ | |
811 | 3 | KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F, |
812 | jalview.util.ShortcutKeyMaskExWrapper | |
813 | .getMenuShortcutKeyMaskEx(), | |
814 | false); | |
815 | 3 | AbstractAction action = new AbstractAction() |
816 | { | |
817 | 0 | @Override |
818 | public void actionPerformed(ActionEvent e) | |
819 | { | |
820 | 0 | Component c = getFrameAtMouse(); |
821 | 0 | if (c != null && c instanceof AlignFrame) |
822 | { | |
823 | 0 | AlignFrame af = (AlignFrame) c; |
824 | 0 | boolean dna = af.getViewport().getAlignment().isNucleotide(); |
825 | 0 | String scope = MessageManager.getString("label.in") + " " |
826 | 0 | + (dna ? MessageManager.getString("label.nucleotide") |
827 | : MessageManager.getString("label.protein")); | |
828 | 0 | new Finder(af.alignPanel, true, scope); |
829 | } | |
830 | } | |
831 | }; | |
832 | 3 | overrideKeyBinding(key_cmdF, action); |
833 | } | |
834 | ||
835 | /** | |
836 | * Override to do nothing if triggered from one of the child frames | |
837 | */ | |
838 | 11 | @Override |
839 | public void setSelected(boolean selected) throws PropertyVetoException | |
840 | { | |
841 | 11 | JDesktopPane desktopPane = getDesktopPane(); |
842 | 11 | JInternalFrame fr = desktopPane == null ? null |
843 | : desktopPane.getSelectedFrame(); | |
844 | 11 | if (fr == getTopFrame() || fr == getBottomFrame()) |
845 | { | |
846 | /* | |
847 | * patch for JAL-3288 (deselecting top/bottom frame closes popup menu); | |
848 | * it may be possible to remove this method in future | |
849 | * if the underlying Java behaviour changes | |
850 | */ | |
851 | 0 | if (selected) |
852 | { | |
853 | 0 | moveToFront(); |
854 | } | |
855 | 0 | return; |
856 | } | |
857 | 11 | super.setSelected(selected); |
858 | } | |
859 | ||
860 | /** | |
861 | * holds the frame for feature settings, so Protein and DNA tabs can be | |
862 | * managed | |
863 | */ | |
864 | JInternalFrame featureSettingsUI; | |
865 | ||
866 | JTabbedPane featureSettingsPanels; | |
867 | ||
868 | 0 | @Override |
869 | public void addFeatureSettingsUI( | |
870 | FeatureSettingsControllerGuiI featureSettings) | |
871 | { | |
872 | 0 | boolean showInternalFrame = false; |
873 | 0 | if (featureSettingsUI == null || featureSettingsPanels == null) |
874 | { | |
875 | 0 | showInternalFrame = true; |
876 | 0 | featureSettingsPanels = new JTabbedPane(); |
877 | 0 | featureSettingsPanels.addChangeListener(new ChangeListener() |
878 | { | |
879 | ||
880 | 0 | @Override |
881 | public void stateChanged(ChangeEvent e) | |
882 | { | |
883 | 0 | if (e.getSource() != featureSettingsPanels |
884 | || featureSettingsUI == null | |
885 | || featureSettingsUI.isClosed() | |
886 | || !featureSettingsUI.isVisible()) | |
887 | { | |
888 | // not our tabbed pane | |
889 | 0 | return; |
890 | } | |
891 | 0 | int tab = featureSettingsPanels.getSelectedIndex(); |
892 | 0 | if (tab < 0 || featureSettingsPanels |
893 | .getSelectedComponent() instanceof FeatureSettingsControllerGuiI) | |
894 | { | |
895 | // no tab selected or already showing a feature settings GUI | |
896 | 0 | return; |
897 | } | |
898 | 0 | getAlignFrames().get(tab).showFeatureSettingsUI(); |
899 | } | |
900 | }); | |
901 | 0 | featureSettingsUI = new JInternalFrame(MessageManager.getString( |
902 | "label.sequence_feature_settings_for_CDS_and_Protein")); | |
903 | 0 | featureSettingsUI.setFrameIcon(null); |
904 | 0 | featureSettingsPanels.setOpaque(true); |
905 | ||
906 | 0 | JPanel dialog = new JPanel(); |
907 | 0 | dialog.setOpaque(true); |
908 | 0 | dialog.setLayout(new BorderLayout()); |
909 | 0 | dialog.add(featureSettingsPanels, BorderLayout.CENTER); |
910 | 0 | JPanel buttons = new JPanel(); |
911 | 0 | JButton ok = new JButton(MessageManager.getString("action.ok")); |
912 | 0 | ok.addActionListener(new ActionListener() |
913 | { | |
914 | ||
915 | 0 | @Override |
916 | public void actionPerformed(ActionEvent e) | |
917 | { | |
918 | 0 | try |
919 | { | |
920 | 0 | featureSettingsUI.setClosed(true); |
921 | } catch (PropertyVetoException pv) | |
922 | { | |
923 | 0 | pv.printStackTrace(); |
924 | } | |
925 | } | |
926 | }); | |
927 | 0 | JButton cancel = new JButton( |
928 | MessageManager.getString("action.cancel")); | |
929 | 0 | cancel.addActionListener(new ActionListener() |
930 | { | |
931 | ||
932 | 0 | @Override |
933 | public void actionPerformed(ActionEvent e) | |
934 | { | |
935 | 0 | try |
936 | { | |
937 | 0 | for (Component fspanel : featureSettingsPanels.getComponents()) |
938 | { | |
939 | 0 | if (fspanel instanceof FeatureSettingsControllerGuiI) |
940 | { | |
941 | 0 | ((FeatureSettingsControllerGuiI) fspanel).revert(); |
942 | } | |
943 | } | |
944 | 0 | featureSettingsUI.setClosed(true); |
945 | } catch (Exception pv) | |
946 | { | |
947 | 0 | pv.printStackTrace(); |
948 | } | |
949 | } | |
950 | }); | |
951 | 0 | buttons.add(ok); |
952 | 0 | buttons.add(cancel); |
953 | 0 | dialog.add(buttons, BorderLayout.SOUTH); |
954 | 0 | featureSettingsUI.setContentPane(dialog); |
955 | 0 | createDummyTabs(); |
956 | } | |
957 | 0 | if (featureSettingsPanels |
958 | .indexOfTabComponent((Component) featureSettings) > -1) | |
959 | { | |
960 | // just show the feature settings ! | |
961 | 0 | featureSettingsPanels |
962 | .setSelectedComponent((Component) featureSettings); | |
963 | 0 | return; |
964 | } | |
965 | // otherwise replace the dummy tab with the given feature settings | |
966 | 0 | int pos = getAlignFrames().indexOf(featureSettings.getAlignframe()); |
967 | // if pos==-1 then alignFrame isn't managed by this splitframe | |
968 | 0 | if (pos == 0) |
969 | { | |
970 | 0 | featureSettingsPanels.removeTabAt(0); |
971 | 0 | featureSettingsPanels.insertTab(tabName[0], null, |
972 | (Component) featureSettings, | |
973 | MessageManager.formatMessage( | |
974 | "label.sequence_feature_settings_for", tabName[0]), | |
975 | 0); | |
976 | } | |
977 | 0 | if (pos == 1) |
978 | { | |
979 | 0 | featureSettingsPanels.removeTabAt(1); |
980 | 0 | featureSettingsPanels.insertTab(tabName[1], null, |
981 | (Component) featureSettings, | |
982 | MessageManager.formatMessage( | |
983 | "label.sequence_feature_settings_for", tabName[1]), | |
984 | 1); | |
985 | } | |
986 | 0 | featureSettingsPanels.setSelectedComponent((Component) featureSettings); |
987 | ||
988 | // TODO: JAL-3535 - construct a feature settings title including names of | |
989 | // currently selected CDS and Protein names | |
990 | ||
991 | 0 | if (showInternalFrame) |
992 | { | |
993 | 0 | if (Platform.isAMacAndNotJS()) |
994 | { | |
995 | 0 | Desktop.addInternalFrame(featureSettingsUI, |
996 | MessageManager.getString( | |
997 | "label.sequence_feature_settings_for_CDS_and_Protein"), | |
998 | 600, 480); | |
999 | } | |
1000 | else | |
1001 | { | |
1002 | 0 | Desktop.addInternalFrame(featureSettingsUI, |
1003 | MessageManager.getString( | |
1004 | "label.sequence_feature_settings_for_CDS_and_Protein"), | |
1005 | 600, 450); | |
1006 | } | |
1007 | 0 | featureSettingsUI |
1008 | .setMinimumSize(new Dimension(FS_MIN_WIDTH, FS_MIN_HEIGHT)); | |
1009 | ||
1010 | 0 | featureSettingsUI.addInternalFrameListener( |
1011 | new javax.swing.event.InternalFrameAdapter() | |
1012 | { | |
1013 | 0 | @Override |
1014 | public void internalFrameClosed( | |
1015 | javax.swing.event.InternalFrameEvent evt) | |
1016 | { | |
1017 | 0 | for (int tab = 0; tab < featureSettingsPanels |
1018 | .getTabCount();) | |
1019 | { | |
1020 | 0 | FeatureSettingsControllerGuiI fsettings = (FeatureSettingsControllerGuiI) featureSettingsPanels |
1021 | .getTabComponentAt(tab); | |
1022 | 0 | if (fsettings != null) |
1023 | { | |
1024 | 0 | featureSettingsPanels.removeTabAt(tab); |
1025 | 0 | fsettings.featureSettings_isClosed(); |
1026 | } | |
1027 | else | |
1028 | { | |
1029 | 0 | tab++; |
1030 | } | |
1031 | } | |
1032 | 0 | featureSettingsPanels = null; |
1033 | 0 | featureSettingsUI = null; |
1034 | }; | |
1035 | }); | |
1036 | 0 | featureSettingsUI.setLayer(JLayeredPane.PALETTE_LAYER); |
1037 | } | |
1038 | } | |
1039 | ||
1040 | /** | |
1041 | * tab names for feature settings | |
1042 | */ | |
1043 | private String[] tabName = new String[] { | |
1044 | MessageManager.getString("label.CDS"), | |
1045 | MessageManager.getString("label.protein") }; | |
1046 | ||
1047 | /** | |
1048 | * create placeholder tabs which materialise the feature settings for a given | |
1049 | * view. Also reinitialises any tabs containing stale feature settings | |
1050 | */ | |
1051 | 0 | private void createDummyTabs() |
1052 | { | |
1053 | 0 | for (int tabIndex = 0; tabIndex < 2; tabIndex++) |
1054 | { | |
1055 | 0 | JPanel dummyTab = new JPanel(); |
1056 | 0 | featureSettingsPanels.addTab(tabName[tabIndex], dummyTab); |
1057 | } | |
1058 | } | |
1059 | ||
1060 | 0 | private void replaceWithDummyTab(FeatureSettingsControllerI toClose) |
1061 | { | |
1062 | 0 | Component dummyTab = null; |
1063 | 0 | for (int tabIndex = 0; tabIndex < 2; tabIndex++) |
1064 | { | |
1065 | 0 | if (featureSettingsPanels.getTabCount() > tabIndex) |
1066 | { | |
1067 | 0 | dummyTab = featureSettingsPanels.getTabComponentAt(tabIndex); |
1068 | 0 | if (dummyTab instanceof FeatureSettingsControllerGuiI |
1069 | && !dummyTab.isVisible()) | |
1070 | { | |
1071 | 0 | featureSettingsPanels.removeTabAt(tabIndex); |
1072 | // close the feature Settings tab | |
1073 | 0 | ((FeatureSettingsControllerGuiI) dummyTab) |
1074 | .featureSettings_isClosed(); | |
1075 | // create a dummy tab in its place | |
1076 | 0 | dummyTab = new JPanel(); |
1077 | 0 | featureSettingsPanels.insertTab(tabName[tabIndex], null, dummyTab, |
1078 | MessageManager.formatMessage( | |
1079 | "label.sequence_feature_settings_for", | |
1080 | tabName[tabIndex]), | |
1081 | tabIndex); | |
1082 | } | |
1083 | } | |
1084 | } | |
1085 | } | |
1086 | ||
1087 | 0 | @Override |
1088 | public void closeFeatureSettings( | |
1089 | FeatureSettingsControllerI featureSettings, | |
1090 | boolean closeContainingFrame) | |
1091 | { | |
1092 | 0 | if (featureSettingsUI != null) |
1093 | { | |
1094 | 0 | if (closeContainingFrame) |
1095 | { | |
1096 | 0 | try |
1097 | { | |
1098 | 0 | featureSettingsUI.setClosed(true); |
1099 | } catch (Exception x) | |
1100 | { | |
1101 | } | |
1102 | 0 | featureSettingsUI = null; |
1103 | } | |
1104 | else | |
1105 | { | |
1106 | 0 | replaceWithDummyTab(featureSettings); |
1107 | } | |
1108 | } | |
1109 | } | |
1110 | ||
1111 | 0 | @Override |
1112 | public boolean isFeatureSettingsOpen() | |
1113 | { | |
1114 | 0 | return featureSettingsUI != null && !featureSettingsUI.isClosed(); |
1115 | } | |
1116 | } |