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AlignFrame | 123 | 1,688 | 566 | ||
AlignFrame.AboutPanel | 2999 | 22 | 2 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.appletgui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.Canvas; | |
25 | import java.awt.CheckboxMenuItem; | |
26 | import java.awt.Color; | |
27 | import java.awt.FlowLayout; | |
28 | import java.awt.Font; | |
29 | import java.awt.FontMetrics; | |
30 | import java.awt.Frame; | |
31 | import java.awt.Graphics; | |
32 | import java.awt.Label; | |
33 | import java.awt.Menu; | |
34 | import java.awt.MenuBar; | |
35 | import java.awt.MenuItem; | |
36 | import java.awt.Panel; | |
37 | import java.awt.Rectangle; | |
38 | import java.awt.event.ActionEvent; | |
39 | import java.awt.event.ActionListener; | |
40 | import java.awt.event.FocusEvent; | |
41 | import java.awt.event.FocusListener; | |
42 | import java.awt.event.ItemEvent; | |
43 | import java.awt.event.ItemListener; | |
44 | import java.awt.event.KeyEvent; | |
45 | import java.awt.event.KeyListener; | |
46 | import java.awt.event.WindowAdapter; | |
47 | import java.awt.event.WindowEvent; | |
48 | import java.io.IOException; | |
49 | import java.io.UnsupportedEncodingException; | |
50 | import java.net.URL; | |
51 | import java.net.URLEncoder; | |
52 | import java.util.Arrays; | |
53 | import java.util.Deque; | |
54 | import java.util.HashMap; | |
55 | import java.util.List; | |
56 | import java.util.Map; | |
57 | import java.util.StringTokenizer; | |
58 | import java.util.Vector; | |
59 | ||
60 | import org.jmol.viewer.Viewer; | |
61 | ||
62 | import jalview.analysis.AlignmentSorter; | |
63 | import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; | |
64 | import jalview.analysis.TreeBuilder; | |
65 | import jalview.analysis.scoremodels.PIDModel; | |
66 | import jalview.analysis.scoremodels.ScoreModels; | |
67 | import jalview.api.AlignViewControllerGuiI; | |
68 | import jalview.api.AlignViewControllerI; | |
69 | import jalview.api.AlignViewportI; | |
70 | import jalview.api.FeatureColourI; | |
71 | import jalview.api.FeatureRenderer; | |
72 | import jalview.api.FeatureSettingsControllerI; | |
73 | import jalview.api.SequenceStructureBinding; | |
74 | import jalview.bin.JalviewLite; | |
75 | import jalview.commands.CommandI; | |
76 | import jalview.commands.EditCommand; | |
77 | import jalview.commands.EditCommand.Action; | |
78 | import jalview.commands.OrderCommand; | |
79 | import jalview.commands.RemoveGapColCommand; | |
80 | import jalview.commands.RemoveGapsCommand; | |
81 | import jalview.commands.SlideSequencesCommand; | |
82 | import jalview.commands.TrimRegionCommand; | |
83 | import jalview.datamodel.Alignment; | |
84 | import jalview.datamodel.AlignmentAnnotation; | |
85 | import jalview.datamodel.AlignmentI; | |
86 | import jalview.datamodel.AlignmentOrder; | |
87 | import jalview.datamodel.ColumnSelection; | |
88 | import jalview.datamodel.HiddenColumns; | |
89 | import jalview.datamodel.PDBEntry; | |
90 | import jalview.datamodel.Sequence; | |
91 | import jalview.datamodel.SequenceGroup; | |
92 | import jalview.datamodel.SequenceI; | |
93 | import jalview.io.AnnotationFile; | |
94 | import jalview.io.AppletFormatAdapter; | |
95 | import jalview.io.DataSourceType; | |
96 | import jalview.io.FeaturesFile; | |
97 | import jalview.io.FileFormat; | |
98 | import jalview.io.FileFormatI; | |
99 | import jalview.io.FileFormats; | |
100 | import jalview.io.TCoffeeScoreFile; | |
101 | import jalview.schemes.Blosum62ColourScheme; | |
102 | import jalview.schemes.BuriedColourScheme; | |
103 | import jalview.schemes.ClustalxColourScheme; | |
104 | import jalview.schemes.ColourSchemeI; | |
105 | import jalview.schemes.HelixColourScheme; | |
106 | import jalview.schemes.HydrophobicColourScheme; | |
107 | import jalview.schemes.NucleotideColourScheme; | |
108 | import jalview.schemes.PIDColourScheme; | |
109 | import jalview.schemes.PurinePyrimidineColourScheme; | |
110 | import jalview.schemes.RNAHelicesColour; | |
111 | import jalview.schemes.StrandColourScheme; | |
112 | import jalview.schemes.TCoffeeColourScheme; | |
113 | import jalview.schemes.TaylorColourScheme; | |
114 | import jalview.schemes.TurnColourScheme; | |
115 | import jalview.schemes.ZappoColourScheme; | |
116 | import jalview.structure.StructureSelectionManager; | |
117 | import jalview.structures.models.AAStructureBindingModel; | |
118 | import jalview.util.MappingUtils; | |
119 | import jalview.util.MessageManager; | |
120 | import jalview.viewmodel.AlignmentViewport; | |
121 | import jalview.viewmodel.ViewportRanges; | |
122 | ||
123 | public class AlignFrame extends EmbmenuFrame implements ActionListener, | |
124 | ItemListener, KeyListener, AlignViewControllerGuiI | |
125 | { | |
126 | public AlignViewControllerI avc; | |
127 | ||
128 | public AlignmentPanel alignPanel; | |
129 | ||
130 | public AlignViewport viewport; | |
131 | ||
132 | // width and height may be overridden by applet parameters | |
133 | int frameWidth = 700; | |
134 | ||
135 | int frameHeight = 500; | |
136 | ||
137 | String jalviewServletURL; | |
138 | ||
139 | /* | |
140 | * Flag for showing autocalculated consensus above or below other consensus | |
141 | * rows | |
142 | */ | |
143 | private boolean showAutoCalculatedAbove; | |
144 | ||
145 | private SequenceAnnotationOrder annotationSortOrder; | |
146 | ||
147 | /** | |
148 | * Constructor that creates the frame and adds it to the display. | |
149 | * | |
150 | * @param al | |
151 | * @param applet | |
152 | * @param title | |
153 | * @param embedded | |
154 | */ | |
155 | 0 | public AlignFrame(AlignmentI al, JalviewLite applet, String title, |
156 | boolean embedded) | |
157 | { | |
158 | 0 | this(al, applet, title, embedded, true); |
159 | } | |
160 | ||
161 | /** | |
162 | * Constructor that optionally allows the frame to be displayed or only | |
163 | * created. | |
164 | * | |
165 | * @param al | |
166 | * @param applet | |
167 | * @param title | |
168 | * @param embedded | |
169 | * @param addToDisplay | |
170 | */ | |
171 | 0 | public AlignFrame(AlignmentI al, JalviewLite applet, String title, |
172 | boolean embedded, boolean addToDisplay) | |
173 | { | |
174 | 0 | this(al, null, null, applet, title, embedded, addToDisplay); |
175 | } | |
176 | ||
177 | 0 | public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, |
178 | HiddenColumns hidden, JalviewLite applet, String title, | |
179 | boolean embedded) | |
180 | { | |
181 | 0 | this(al, hiddenSeqs, hidden, applet, title, embedded, true); |
182 | } | |
183 | ||
184 | 0 | public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, |
185 | HiddenColumns hidden, JalviewLite applet, String title, | |
186 | boolean embedded, boolean addToDisplay) | |
187 | { | |
188 | 0 | if (applet != null) |
189 | { | |
190 | 0 | jalviewServletURL = applet.getParameter("APPLICATION_URL"); |
191 | } | |
192 | ||
193 | 0 | try |
194 | { | |
195 | 0 | jbInit(); |
196 | } catch (Exception ex) | |
197 | { | |
198 | 0 | ex.printStackTrace(); |
199 | } | |
200 | // need to get window geometry before we calculate alignment layout | |
201 | 0 | if (applet != null) |
202 | { | |
203 | 0 | String param; |
204 | 0 | try |
205 | { | |
206 | 0 | param = applet.getParameter("windowWidth"); |
207 | 0 | if (param != null) |
208 | { | |
209 | 0 | int width = Integer.parseInt(param); |
210 | 0 | frameWidth = width; |
211 | } | |
212 | 0 | param = applet.getParameter("windowHeight"); |
213 | 0 | if (param != null) |
214 | { | |
215 | 0 | int height = Integer.parseInt(param); |
216 | 0 | frameHeight = height; |
217 | } | |
218 | } catch (Exception ex) | |
219 | { | |
220 | } | |
221 | } | |
222 | 0 | viewport = new AlignViewport(al, applet); |
223 | ||
224 | 0 | if (hiddenSeqs != null && hiddenSeqs.length > 0) |
225 | { | |
226 | 0 | viewport.hideSequence(hiddenSeqs); |
227 | } | |
228 | 0 | if (hidden != null) |
229 | { | |
230 | 0 | viewport.getAlignment().setHiddenColumns(hidden); |
231 | } | |
232 | 0 | viewport.setScaleAboveWrapped(scaleAbove.getState()); |
233 | ||
234 | 0 | alignPanel = new AlignmentPanel(this, viewport); |
235 | 0 | avc = new jalview.controller.AlignViewController(this, viewport, |
236 | alignPanel); | |
237 | 0 | viewport.updateConservation(alignPanel); |
238 | 0 | viewport.updateConsensus(alignPanel); |
239 | ||
240 | 0 | displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); |
241 | 0 | followMouseOverFlag.setState(viewport.isFollowHighlight()); |
242 | 0 | showGroupConsensus.setState(viewport.isShowGroupConsensus()); |
243 | 0 | showGroupConservation.setState(viewport.isShowGroupConservation()); |
244 | 0 | showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); |
245 | 0 | showSequenceLogo.setState(viewport.isShowSequenceLogo()); |
246 | 0 | normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); |
247 | 0 | applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); |
248 | 0 | annotationPanelMenuItem.setState(viewport.isShowAnnotation()); |
249 | 0 | showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
250 | 0 | showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
251 | 0 | showAlignmentAnnotations.setState(true); |
252 | 0 | showSequenceAnnotations.setState(false); |
253 | ||
254 | 0 | seqLimits.setState(viewport.getShowJVSuffix()); |
255 | ||
256 | 0 | if (applet != null) |
257 | { | |
258 | 0 | String param = applet.getParameter("sortBy"); |
259 | 0 | if (param != null) |
260 | { | |
261 | 0 | if (param.equalsIgnoreCase("Id")) |
262 | { | |
263 | 0 | sortIDMenuItem_actionPerformed(); |
264 | } | |
265 | 0 | else if (param.equalsIgnoreCase("Pairwise Identity")) |
266 | { | |
267 | 0 | sortPairwiseMenuItem_actionPerformed(); |
268 | } | |
269 | 0 | else if (param.equalsIgnoreCase("Length")) |
270 | { | |
271 | 0 | sortLengthMenuItem_actionPerformed(); |
272 | } | |
273 | } | |
274 | ||
275 | 0 | param = applet.getParameter("wrap"); |
276 | 0 | if (param != null) |
277 | { | |
278 | 0 | if (param.equalsIgnoreCase("true")) |
279 | { | |
280 | 0 | wrapMenuItem.setState(true); |
281 | 0 | wrapMenuItem_actionPerformed(); |
282 | } | |
283 | } | |
284 | 0 | param = applet.getParameter("centrecolumnlabels"); |
285 | 0 | if (param != null) |
286 | { | |
287 | 0 | centreColumnLabelFlag.setState(true); |
288 | 0 | centreColumnLabelFlag_stateChanged(); |
289 | } | |
290 | ||
291 | } | |
292 | 0 | if (viewport.getAlignment().isNucleotide()) |
293 | { | |
294 | 0 | conservationMenuItem.setEnabled(false); |
295 | 0 | clustalColour.setEnabled(false); |
296 | 0 | BLOSUM62Colour.setEnabled(false); |
297 | 0 | zappoColour.setEnabled(false); |
298 | 0 | taylorColour.setEnabled(false); |
299 | 0 | hydrophobicityColour.setEnabled(false); |
300 | 0 | helixColour.setEnabled(false); |
301 | 0 | strandColour.setEnabled(false); |
302 | 0 | turnColour.setEnabled(false); |
303 | 0 | buriedColour.setEnabled(false); |
304 | 0 | viewport.updateStrucConsensus(alignPanel); |
305 | 0 | if (viewport.getAlignment().hasRNAStructure()) |
306 | { | |
307 | 0 | RNAHelixColour.setEnabled(true); |
308 | } | |
309 | else | |
310 | { | |
311 | 0 | RNAHelixColour.setEnabled(false); |
312 | } | |
313 | } | |
314 | else | |
315 | { | |
316 | 0 | RNAHelixColour.setEnabled(false); |
317 | 0 | purinePyrimidineColour.setEnabled(false); |
318 | 0 | nucleotideColour.setEnabled(false); |
319 | } | |
320 | // Some JVMS send keyevents to Top frame or lowest panel, | |
321 | // Havent worked out why yet. So add to both this frame and seqCanvas for | |
322 | // now | |
323 | 0 | this.addKeyListener(this); |
324 | 0 | alignPanel.seqPanel.seqCanvas.addKeyListener(this); |
325 | 0 | alignPanel.idPanel.idCanvas.addKeyListener(this); |
326 | 0 | alignPanel.scalePanel.addKeyListener(this); |
327 | 0 | alignPanel.annotationPanel.addKeyListener(this); |
328 | 0 | alignPanel.annotationPanelHolder.addKeyListener(this); |
329 | 0 | alignPanel.annotationSpaceFillerHolder.addKeyListener(this); |
330 | 0 | alignPanel.alabels.addKeyListener(this); |
331 | ||
332 | 0 | setAnnotationsVisibility(); |
333 | ||
334 | 0 | if (addToDisplay) |
335 | { | |
336 | 0 | addToDisplay(embedded); |
337 | } | |
338 | } | |
339 | ||
340 | /** | |
341 | * @param embedded | |
342 | */ | |
343 | 0 | public void addToDisplay(boolean embedded) |
344 | { | |
345 | 0 | createAlignFrameWindow(embedded); |
346 | 0 | validate(); |
347 | 0 | alignPanel.adjustAnnotationHeight(); |
348 | 0 | alignPanel.paintAlignment(true, true); |
349 | } | |
350 | ||
351 | 0 | public AlignViewport getAlignViewport() |
352 | { | |
353 | 0 | return viewport; |
354 | } | |
355 | ||
356 | 0 | public SeqCanvas getSeqcanvas() |
357 | { | |
358 | 0 | return alignPanel.seqPanel.seqCanvas; |
359 | } | |
360 | ||
361 | /** | |
362 | * Load a features file onto the alignment | |
363 | * | |
364 | * @param file | |
365 | * file URL, content, or other resolvable path | |
366 | * @param type | |
367 | * is protocol for accessing data referred to by file | |
368 | */ | |
369 | ||
370 | 0 | public boolean parseFeaturesFile(String file, DataSourceType type) |
371 | { | |
372 | 0 | return parseFeaturesFile(file, type, true); |
373 | } | |
374 | ||
375 | /** | |
376 | * Load a features file onto the alignment | |
377 | * | |
378 | * @param file | |
379 | * file URL, content, or other resolvable path | |
380 | * @param sourceType | |
381 | * is protocol for accessing data referred to by file | |
382 | * @param autoenabledisplay | |
383 | * when true, display features flag will be automatically enabled if | |
384 | * features are loaded | |
385 | * @return true if data parsed as a features file | |
386 | */ | |
387 | 0 | public boolean parseFeaturesFile(String file, DataSourceType sourceType, |
388 | boolean autoenabledisplay) | |
389 | { | |
390 | 0 | boolean featuresFile = false; |
391 | 0 | try |
392 | { | |
393 | 0 | Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas |
394 | .getFeatureRenderer().getFeatureColours(); | |
395 | 0 | boolean relaxedIdMatching = viewport.applet |
396 | .getDefaultParameter("relaxedidmatch", false); | |
397 | 0 | featuresFile = new FeaturesFile(file, sourceType).parse( |
398 | viewport.getAlignment(), colours, true, relaxedIdMatching); | |
399 | } catch (Exception ex) | |
400 | { | |
401 | 0 | ex.printStackTrace(); |
402 | } | |
403 | ||
404 | 0 | if (featuresFile) |
405 | { | |
406 | 0 | if (autoenabledisplay) |
407 | { | |
408 | 0 | viewport.setShowSequenceFeatures(true); |
409 | 0 | sequenceFeatures.setState(true); |
410 | } | |
411 | 0 | if (alignPanel.seqPanel.seqCanvas.fr != null) |
412 | { | |
413 | // update the min/max ranges where necessary | |
414 | 0 | alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); |
415 | } | |
416 | 0 | if (viewport.featureSettings != null) |
417 | { | |
418 | 0 | viewport.featureSettings.refreshTable(); |
419 | } | |
420 | 0 | alignPanel.paintAlignment(true, true); |
421 | 0 | setStatus(MessageManager |
422 | .getString("label.successfully_added_features_alignment")); | |
423 | } | |
424 | 0 | return featuresFile; |
425 | } | |
426 | ||
427 | 0 | @Override |
428 | public void keyPressed(KeyEvent evt) | |
429 | { | |
430 | 0 | ViewportRanges ranges = viewport.getRanges(); |
431 | ||
432 | 0 | if (viewport.cursorMode |
433 | && ((evt.getKeyCode() >= KeyEvent.VK_0 | |
434 | && evt.getKeyCode() <= KeyEvent.VK_9) | |
435 | || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 | |
436 | && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)) | |
437 | && Character.isDigit(evt.getKeyChar())) | |
438 | { | |
439 | 0 | alignPanel.seqPanel.numberPressed(evt.getKeyChar()); |
440 | } | |
441 | ||
442 | 0 | switch (evt.getKeyCode()) |
443 | { | |
444 | 0 | case 27: // escape key |
445 | 0 | deselectAllSequenceMenuItem_actionPerformed(); |
446 | ||
447 | 0 | alignPanel.alabels.cancelDrag(); |
448 | 0 | break; |
449 | 0 | case KeyEvent.VK_X: |
450 | 0 | if (evt.isControlDown() || evt.isMetaDown()) |
451 | { | |
452 | 0 | cut_actionPerformed(); |
453 | } | |
454 | 0 | break; |
455 | 0 | case KeyEvent.VK_C: |
456 | 0 | if (viewport.cursorMode && !evt.isControlDown()) |
457 | { | |
458 | 0 | alignPanel.seqPanel.setCursorColumn(); |
459 | } | |
460 | 0 | if (evt.isControlDown() || evt.isMetaDown()) |
461 | { | |
462 | 0 | copy_actionPerformed(); |
463 | } | |
464 | 0 | break; |
465 | 0 | case KeyEvent.VK_V: |
466 | 0 | if (evt.isControlDown()) |
467 | { | |
468 | 0 | paste(evt.isShiftDown()); |
469 | } | |
470 | 0 | break; |
471 | 0 | case KeyEvent.VK_A: |
472 | 0 | if (evt.isControlDown() || evt.isMetaDown()) |
473 | { | |
474 | 0 | selectAllSequenceMenuItem_actionPerformed(); |
475 | } | |
476 | 0 | break; |
477 | 0 | case KeyEvent.VK_DOWN: |
478 | 0 | if (viewport.cursorMode) |
479 | { | |
480 | 0 | alignPanel.seqPanel.moveCursor(0, 1); |
481 | } | |
482 | else | |
483 | { | |
484 | 0 | moveSelectedSequences(false); |
485 | } | |
486 | 0 | break; |
487 | ||
488 | 0 | case KeyEvent.VK_UP: |
489 | 0 | if (viewport.cursorMode) |
490 | { | |
491 | 0 | alignPanel.seqPanel.moveCursor(0, -1); |
492 | } | |
493 | else | |
494 | { | |
495 | 0 | moveSelectedSequences(true); |
496 | } | |
497 | 0 | break; |
498 | ||
499 | 0 | case KeyEvent.VK_LEFT: |
500 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
501 | { | |
502 | 0 | slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); |
503 | } | |
504 | else | |
505 | { | |
506 | 0 | alignPanel.seqPanel.moveCursor(-1, 0); |
507 | } | |
508 | 0 | break; |
509 | ||
510 | 0 | case KeyEvent.VK_RIGHT: |
511 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
512 | { | |
513 | 0 | slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); |
514 | } | |
515 | else | |
516 | { | |
517 | 0 | alignPanel.seqPanel.moveCursor(1, 0); |
518 | } | |
519 | 0 | break; |
520 | ||
521 | 0 | case KeyEvent.VK_SPACE: |
522 | 0 | if (viewport.cursorMode) |
523 | { | |
524 | 0 | alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() |
525 | || evt.isShiftDown() || evt.isAltDown()); | |
526 | } | |
527 | 0 | break; |
528 | ||
529 | 0 | case KeyEvent.VK_DELETE: |
530 | 0 | case KeyEvent.VK_BACK_SPACE: |
531 | 0 | if (viewport.cursorMode) |
532 | { | |
533 | 0 | alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() |
534 | || evt.isShiftDown() || evt.isAltDown()); | |
535 | } | |
536 | else | |
537 | { | |
538 | 0 | cut_actionPerformed(); |
539 | 0 | alignPanel.seqPanel.seqCanvas.repaint(); |
540 | } | |
541 | 0 | break; |
542 | ||
543 | 0 | case KeyEvent.VK_S: |
544 | 0 | if (viewport.cursorMode) |
545 | { | |
546 | 0 | alignPanel.seqPanel.setCursorRow(); |
547 | } | |
548 | 0 | break; |
549 | 0 | case KeyEvent.VK_P: |
550 | 0 | if (viewport.cursorMode) |
551 | { | |
552 | 0 | alignPanel.seqPanel.setCursorPosition(); |
553 | } | |
554 | 0 | break; |
555 | ||
556 | 0 | case KeyEvent.VK_ENTER: |
557 | 0 | case KeyEvent.VK_COMMA: |
558 | 0 | if (viewport.cursorMode) |
559 | { | |
560 | 0 | alignPanel.seqPanel.setCursorRowAndColumn(); |
561 | } | |
562 | 0 | break; |
563 | ||
564 | 0 | case KeyEvent.VK_Q: |
565 | 0 | if (viewport.cursorMode) |
566 | { | |
567 | 0 | alignPanel.seqPanel.setSelectionAreaAtCursor(true); |
568 | } | |
569 | 0 | break; |
570 | 0 | case KeyEvent.VK_M: |
571 | 0 | if (viewport.cursorMode) |
572 | { | |
573 | 0 | alignPanel.seqPanel.setSelectionAreaAtCursor(false); |
574 | } | |
575 | 0 | break; |
576 | ||
577 | 0 | case KeyEvent.VK_F2: |
578 | 0 | viewport.cursorMode = !viewport.cursorMode; |
579 | 0 | setStatus(MessageManager.formatMessage("label.keyboard_editing_mode", |
580 | new String[] | |
581 | 0 | { (viewport.cursorMode ? "on" : "off") })); |
582 | 0 | if (viewport.cursorMode) |
583 | { | |
584 | 0 | alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes(); |
585 | 0 | alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq(); |
586 | } | |
587 | 0 | break; |
588 | ||
589 | 0 | case KeyEvent.VK_F: |
590 | 0 | if (evt.isControlDown()) |
591 | { | |
592 | 0 | findMenuItem_actionPerformed(); |
593 | } | |
594 | 0 | break; |
595 | ||
596 | 0 | case KeyEvent.VK_H: |
597 | { | |
598 | 0 | boolean toggleSeqs = !evt.isControlDown(); |
599 | 0 | boolean toggleCols = !evt.isShiftDown(); |
600 | 0 | toggleHiddenRegions(toggleSeqs, toggleCols); |
601 | 0 | break; |
602 | } | |
603 | ||
604 | 0 | case KeyEvent.VK_PAGE_UP: |
605 | 0 | ranges.pageUp(); |
606 | 0 | break; |
607 | ||
608 | 0 | case KeyEvent.VK_PAGE_DOWN: |
609 | 0 | ranges.pageDown(); |
610 | 0 | break; |
611 | ||
612 | 0 | case KeyEvent.VK_Z: |
613 | 0 | if (evt.isControlDown()) |
614 | { | |
615 | 0 | undoMenuItem_actionPerformed(); |
616 | } | |
617 | 0 | break; |
618 | ||
619 | 0 | case KeyEvent.VK_Y: |
620 | 0 | if (evt.isControlDown()) |
621 | { | |
622 | 0 | redoMenuItem_actionPerformed(); |
623 | } | |
624 | 0 | break; |
625 | ||
626 | 0 | case KeyEvent.VK_L: |
627 | 0 | if (evt.isControlDown()) |
628 | { | |
629 | 0 | trimAlignment(true); |
630 | } | |
631 | 0 | break; |
632 | ||
633 | 0 | case KeyEvent.VK_R: |
634 | 0 | if (evt.isControlDown()) |
635 | { | |
636 | 0 | trimAlignment(false); |
637 | } | |
638 | 0 | break; |
639 | ||
640 | 0 | case KeyEvent.VK_E: |
641 | 0 | if (evt.isControlDown()) |
642 | { | |
643 | 0 | if (evt.isShiftDown()) |
644 | { | |
645 | 0 | this.removeAllGapsMenuItem_actionPerformed(); |
646 | } | |
647 | else | |
648 | { | |
649 | 0 | removeGappedColumnMenuItem_actionPerformed(); |
650 | } | |
651 | } | |
652 | 0 | break; |
653 | 0 | case KeyEvent.VK_I: |
654 | 0 | if (evt.isControlDown()) |
655 | { | |
656 | 0 | if (evt.isAltDown()) |
657 | { | |
658 | 0 | invertColSel_actionPerformed(); |
659 | } | |
660 | else | |
661 | { | |
662 | 0 | invertSequenceMenuItem_actionPerformed(); |
663 | } | |
664 | } | |
665 | 0 | break; |
666 | ||
667 | 0 | case KeyEvent.VK_G: |
668 | 0 | if (evt.isControlDown()) |
669 | { | |
670 | 0 | if (evt.isShiftDown()) |
671 | { | |
672 | 0 | this.unGroup_actionPerformed(); |
673 | } | |
674 | else | |
675 | { | |
676 | 0 | this.createGroup_actionPerformed(); |
677 | } | |
678 | } | |
679 | 0 | break; |
680 | ||
681 | 0 | case KeyEvent.VK_U: |
682 | 0 | if (evt.isControlDown()) |
683 | { | |
684 | 0 | this.deleteGroups_actionPerformed(); |
685 | } | |
686 | 0 | break; |
687 | ||
688 | 0 | case KeyEvent.VK_T: |
689 | 0 | if (evt.isControlDown()) |
690 | { | |
691 | 0 | newView(null); |
692 | } | |
693 | 0 | break; |
694 | ||
695 | } | |
696 | // TODO: repaint flags set only if the keystroke warrants it | |
697 | 0 | alignPanel.paintAlignment(true, true); |
698 | } | |
699 | ||
700 | /** | |
701 | * called by key handler and the hide all/show all menu items | |
702 | * | |
703 | * @param toggleSeqs | |
704 | * @param toggleCols | |
705 | */ | |
706 | 0 | private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) |
707 | { | |
708 | 0 | boolean hide = false; |
709 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
710 | 0 | if (!toggleSeqs && !toggleCols) |
711 | { | |
712 | // Hide everything by the current selection - this is a hack - we do the | |
713 | // invert and then hide | |
714 | // first check that there will be visible columns after the invert. | |
715 | 0 | if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 |
716 | && sg.getStartRes() <= sg.getEndRes())) | |
717 | { | |
718 | // now invert the sequence set, if required - empty selection implies | |
719 | // that no hiding is required. | |
720 | 0 | if (sg != null) |
721 | { | |
722 | 0 | invertSequenceMenuItem_actionPerformed(); |
723 | 0 | sg = viewport.getSelectionGroup(); |
724 | 0 | toggleSeqs = true; |
725 | ||
726 | } | |
727 | 0 | viewport.expandColSelection(sg, true); |
728 | // finally invert the column selection and get the new sequence | |
729 | // selection and indicate it should be hidden. | |
730 | 0 | invertColSel_actionPerformed(); |
731 | 0 | toggleCols = true; |
732 | } | |
733 | } | |
734 | ||
735 | 0 | if (toggleSeqs) |
736 | { | |
737 | 0 | if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) |
738 | { | |
739 | 0 | hide = true; |
740 | 0 | viewport.hideAllSelectedSeqs(); |
741 | } | |
742 | 0 | else if (!(toggleCols && viewport.hasSelectedColumns())) |
743 | { | |
744 | 0 | viewport.showAllHiddenSeqs(); |
745 | } | |
746 | } | |
747 | ||
748 | 0 | if (toggleCols) |
749 | { | |
750 | 0 | if (viewport.hasSelectedColumns()) |
751 | { | |
752 | 0 | viewport.hideSelectedColumns(); |
753 | 0 | if (!toggleSeqs) |
754 | { | |
755 | 0 | viewport.setSelectionGroup(sg); |
756 | } | |
757 | } | |
758 | 0 | else if (!hide) |
759 | { | |
760 | 0 | viewport.showAllHiddenColumns(); |
761 | } | |
762 | 0 | viewport.sendSelection(); |
763 | } | |
764 | } | |
765 | ||
766 | 0 | @Override |
767 | public void keyReleased(KeyEvent evt) | |
768 | { | |
769 | } | |
770 | ||
771 | 0 | @Override |
772 | public void keyTyped(KeyEvent evt) | |
773 | { | |
774 | } | |
775 | ||
776 | 0 | @Override |
777 | public void itemStateChanged(ItemEvent evt) | |
778 | { | |
779 | 0 | final Object source = evt.getSource(); |
780 | 0 | if (source == displayNonconservedMenuItem) |
781 | { | |
782 | 0 | displayNonconservedMenuItem_actionPerformed(); |
783 | } | |
784 | 0 | else if (source == colourTextMenuItem) |
785 | { | |
786 | 0 | colourTextMenuItem_actionPerformed(); |
787 | } | |
788 | 0 | else if (source == wrapMenuItem) |
789 | { | |
790 | 0 | wrapMenuItem_actionPerformed(); |
791 | } | |
792 | 0 | else if (source == scaleAbove) |
793 | { | |
794 | 0 | viewport.setScaleAboveWrapped(scaleAbove.getState()); |
795 | } | |
796 | 0 | else if (source == scaleLeft) |
797 | { | |
798 | 0 | viewport.setScaleLeftWrapped(scaleLeft.getState()); |
799 | } | |
800 | 0 | else if (source == scaleRight) |
801 | { | |
802 | 0 | viewport.setScaleRightWrapped(scaleRight.getState()); |
803 | } | |
804 | 0 | else if (source == seqLimits) |
805 | { | |
806 | 0 | seqLimits_itemStateChanged(); |
807 | } | |
808 | 0 | else if (source == viewBoxesMenuItem) |
809 | { | |
810 | 0 | viewport.setShowBoxes(viewBoxesMenuItem.getState()); |
811 | } | |
812 | 0 | else if (source == viewTextMenuItem) |
813 | { | |
814 | 0 | viewport.setShowText(viewTextMenuItem.getState()); |
815 | } | |
816 | 0 | else if (source == renderGapsMenuItem) |
817 | { | |
818 | 0 | viewport.setRenderGaps(renderGapsMenuItem.getState()); |
819 | } | |
820 | 0 | else if (source == annotationPanelMenuItem) |
821 | { | |
822 | 0 | boolean showAnnotations = annotationPanelMenuItem.getState(); |
823 | 0 | showAlignmentAnnotations.setEnabled(showAnnotations); |
824 | 0 | showSequenceAnnotations.setEnabled(showAnnotations); |
825 | 0 | viewport.setShowAnnotation(showAnnotations); |
826 | 0 | alignPanel.setAnnotationVisible(showAnnotations); |
827 | } | |
828 | 0 | else if (source == sequenceFeatures) |
829 | { | |
830 | 0 | viewport.setShowSequenceFeatures(sequenceFeatures.getState()); |
831 | 0 | alignPanel.seqPanel.seqCanvas.repaint(); |
832 | } | |
833 | 0 | else if (source == showAlignmentAnnotations) |
834 | { | |
835 | 0 | setAnnotationsVisibility(); |
836 | } | |
837 | 0 | else if (source == showSequenceAnnotations) |
838 | { | |
839 | 0 | setAnnotationsVisibility(); |
840 | } | |
841 | 0 | else if (source == sortAnnBySequence) |
842 | { | |
843 | 0 | boolean newState = sortAnnBySequence.getState(); |
844 | 0 | sortAnnByLabel.setState(false); |
845 | 0 | setAnnotationSortOrder( |
846 | 0 | newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL |
847 | : SequenceAnnotationOrder.NONE); | |
848 | 0 | setViewportAnnotationOrder(); |
849 | } | |
850 | 0 | else if (source == sortAnnByLabel) |
851 | { | |
852 | 0 | boolean newState = sortAnnByLabel.getState(); |
853 | 0 | sortAnnBySequence.setState(false); |
854 | 0 | setAnnotationSortOrder( |
855 | 0 | newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE |
856 | : SequenceAnnotationOrder.NONE); | |
857 | 0 | setViewportAnnotationOrder(); |
858 | } | |
859 | 0 | else if (source == showAutoFirst) |
860 | { | |
861 | 0 | showAutoLast.setState(!showAutoFirst.getState()); |
862 | 0 | setShowAutoCalculatedAbove(showAutoFirst.getState()); |
863 | 0 | setViewportAnnotationOrder(); |
864 | } | |
865 | 0 | else if (source == showAutoLast) |
866 | { | |
867 | 0 | showAutoFirst.setState(!showAutoLast.getState()); |
868 | 0 | setShowAutoCalculatedAbove(showAutoFirst.getState()); |
869 | 0 | setViewportAnnotationOrder(); |
870 | } | |
871 | 0 | else if (source == conservationMenuItem) |
872 | { | |
873 | 0 | conservationMenuItem_actionPerformed(); |
874 | } | |
875 | 0 | else if (source == abovePIDThreshold) |
876 | { | |
877 | 0 | abovePIDThreshold_actionPerformed(); |
878 | } | |
879 | 0 | else if (source == applyToAllGroups) |
880 | { | |
881 | 0 | viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); |
882 | } | |
883 | 0 | else if (source == autoCalculate) |
884 | { | |
885 | 0 | viewport.autoCalculateConsensus = autoCalculate.getState(); |
886 | } | |
887 | 0 | else if (source == sortByTree) |
888 | { | |
889 | 0 | viewport.sortByTree = sortByTree.getState(); |
890 | } | |
891 | 0 | else if (source == this.centreColumnLabelFlag) |
892 | { | |
893 | 0 | centreColumnLabelFlag_stateChanged(); |
894 | } | |
895 | 0 | else if (source == this.followMouseOverFlag) |
896 | { | |
897 | 0 | mouseOverFlag_stateChanged(); |
898 | } | |
899 | 0 | else if (source == showGroupConsensus) |
900 | { | |
901 | 0 | showGroupConsensus_actionPerformed(); |
902 | } | |
903 | 0 | else if (source == showGroupConservation) |
904 | { | |
905 | 0 | showGroupConservation_actionPerformed(); |
906 | } | |
907 | 0 | else if (source == showSequenceLogo) |
908 | { | |
909 | 0 | showSequenceLogo_actionPerformed(); |
910 | } | |
911 | 0 | else if (source == normSequenceLogo) |
912 | { | |
913 | 0 | normSequenceLogo_actionPerformed(); |
914 | } | |
915 | 0 | else if (source == showConsensusHistogram) |
916 | { | |
917 | 0 | showConsensusHistogram_actionPerformed(); |
918 | } | |
919 | 0 | else if (source == applyAutoAnnotationSettings) |
920 | { | |
921 | 0 | applyAutoAnnotationSettings_actionPerformed(); |
922 | } | |
923 | // TODO: repaint flags set only if warranted | |
924 | 0 | alignPanel.paintAlignment(true, true); |
925 | } | |
926 | ||
927 | /** | |
928 | * Set the visibility state of sequence-related and/or alignment-related | |
929 | * annotations depending on checkbox selections, and repaint. | |
930 | * | |
931 | * @param visible | |
932 | */ | |
933 | 0 | private void setAnnotationsVisibility() |
934 | { | |
935 | 0 | boolean showForAlignment = showAlignmentAnnotations.getState(); |
936 | 0 | boolean showForSequences = showSequenceAnnotations.getState(); |
937 | 0 | if (alignPanel.getAlignment().getAlignmentAnnotation() != null) |
938 | { | |
939 | 0 | for (AlignmentAnnotation aa : alignPanel.getAlignment() |
940 | .getAlignmentAnnotation()) | |
941 | { | |
942 | 0 | boolean visible = (aa.sequenceRef == null ? showForAlignment |
943 | : showForSequences); | |
944 | 0 | aa.visible = visible; |
945 | } | |
946 | } | |
947 | 0 | alignPanel.validateAnnotationDimensions(true); |
948 | 0 | validate(); |
949 | 0 | repaint(); |
950 | } | |
951 | ||
952 | 0 | private void setAnnotationSortOrder(SequenceAnnotationOrder order) |
953 | { | |
954 | 0 | this.annotationSortOrder = order; |
955 | } | |
956 | ||
957 | /** | |
958 | * Set flags on the viewport that control annotation ordering | |
959 | */ | |
960 | 0 | private void setViewportAnnotationOrder() |
961 | { | |
962 | 0 | this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder); |
963 | 0 | this.alignPanel.av |
964 | .setShowAutocalculatedAbove(this.showAutoCalculatedAbove); | |
965 | } | |
966 | ||
967 | 0 | private void setShowAutoCalculatedAbove(boolean showAbove) |
968 | { | |
969 | 0 | this.showAutoCalculatedAbove = showAbove; |
970 | } | |
971 | ||
972 | 0 | private void mouseOverFlag_stateChanged() |
973 | { | |
974 | 0 | viewport.setFollowHighlight(followMouseOverFlag.getState()); |
975 | // TODO: could kick the scrollTo mechanism to reset view for current | |
976 | // searchresults. | |
977 | } | |
978 | ||
979 | 0 | private void centreColumnLabelFlag_stateChanged() |
980 | { | |
981 | 0 | viewport.centreColumnLabels = centreColumnLabelFlag.getState(); |
982 | 0 | this.alignPanel.annotationPanel.repaint(); |
983 | } | |
984 | ||
985 | 0 | @Override |
986 | public void actionPerformed(ActionEvent evt) | |
987 | { | |
988 | 0 | viewport.applet.currentAlignFrame = this; |
989 | ||
990 | 0 | Object source = evt.getSource(); |
991 | ||
992 | 0 | if (source == inputText) |
993 | { | |
994 | 0 | inputText_actionPerformed(); |
995 | } | |
996 | 0 | else if (source == loadTree) |
997 | { | |
998 | 0 | loadTree_actionPerformed(); |
999 | } | |
1000 | 0 | else if (source == loadApplication) |
1001 | { | |
1002 | 0 | launchFullApplication(); |
1003 | } | |
1004 | 0 | else if (source == loadAnnotations) |
1005 | { | |
1006 | 0 | loadAnnotations(); |
1007 | } | |
1008 | 0 | else if (source == outputAnnotations) |
1009 | { | |
1010 | 0 | outputAnnotations(true); |
1011 | } | |
1012 | 0 | else if (source == outputFeatures) |
1013 | { | |
1014 | 0 | outputFeatures(true, "Jalview"); |
1015 | } | |
1016 | 0 | else if (source == closeMenuItem) |
1017 | { | |
1018 | 0 | closeMenuItem_actionPerformed(); |
1019 | } | |
1020 | 0 | else if (source == copy) |
1021 | { | |
1022 | 0 | copy_actionPerformed(); |
1023 | } | |
1024 | 0 | else if (source == undoMenuItem) |
1025 | { | |
1026 | 0 | undoMenuItem_actionPerformed(); |
1027 | } | |
1028 | 0 | else if (source == redoMenuItem) |
1029 | { | |
1030 | 0 | redoMenuItem_actionPerformed(); |
1031 | } | |
1032 | 0 | else if (source == inputText) |
1033 | { | |
1034 | 0 | inputText_actionPerformed(); |
1035 | } | |
1036 | 0 | else if (source == closeMenuItem) |
1037 | { | |
1038 | 0 | closeMenuItem_actionPerformed(); |
1039 | } | |
1040 | 0 | else if (source == undoMenuItem) |
1041 | { | |
1042 | 0 | undoMenuItem_actionPerformed(); |
1043 | } | |
1044 | 0 | else if (source == redoMenuItem) |
1045 | { | |
1046 | 0 | redoMenuItem_actionPerformed(); |
1047 | } | |
1048 | 0 | else if (source == copy) |
1049 | { | |
1050 | 0 | copy_actionPerformed(); |
1051 | } | |
1052 | 0 | else if (source == pasteNew) |
1053 | { | |
1054 | 0 | pasteNew_actionPerformed(); |
1055 | } | |
1056 | 0 | else if (source == pasteThis) |
1057 | { | |
1058 | 0 | pasteThis_actionPerformed(); |
1059 | } | |
1060 | 0 | else if (source == cut) |
1061 | { | |
1062 | 0 | cut_actionPerformed(); |
1063 | } | |
1064 | 0 | else if (source == delete) |
1065 | { | |
1066 | 0 | delete_actionPerformed(); |
1067 | } | |
1068 | 0 | else if (source == createGroup) |
1069 | { | |
1070 | 0 | createGroup_actionPerformed(); |
1071 | } | |
1072 | 0 | else if (source == unGroup) |
1073 | { | |
1074 | 0 | unGroup_actionPerformed(); |
1075 | } | |
1076 | 0 | else if (source == grpsFromSelection) |
1077 | { | |
1078 | 0 | makeGrpsFromSelection_actionPerformed(); |
1079 | } | |
1080 | 0 | else if (source == deleteGroups) |
1081 | { | |
1082 | 0 | deleteGroups_actionPerformed(); |
1083 | } | |
1084 | 0 | else if (source == selectAllSequenceMenuItem) |
1085 | { | |
1086 | 0 | selectAllSequenceMenuItem_actionPerformed(); |
1087 | } | |
1088 | 0 | else if (source == deselectAllSequenceMenuItem) |
1089 | { | |
1090 | 0 | deselectAllSequenceMenuItem_actionPerformed(); |
1091 | } | |
1092 | 0 | else if (source == invertSequenceMenuItem) |
1093 | { | |
1094 | 0 | invertSequenceMenuItem_actionPerformed(); |
1095 | // uncomment to slave sequence selections in split frame | |
1096 | // viewport.sendSelection(); | |
1097 | } | |
1098 | 0 | else if (source == invertColSel) |
1099 | { | |
1100 | 0 | viewport.invertColumnSelection(); |
1101 | 0 | alignPanel.paintAlignment(false, false); |
1102 | 0 | viewport.sendSelection(); |
1103 | } | |
1104 | 0 | else if (source == remove2LeftMenuItem) |
1105 | { | |
1106 | 0 | trimAlignment(true); |
1107 | } | |
1108 | 0 | else if (source == remove2RightMenuItem) |
1109 | { | |
1110 | 0 | trimAlignment(false); |
1111 | } | |
1112 | 0 | else if (source == removeGappedColumnMenuItem) |
1113 | { | |
1114 | 0 | removeGappedColumnMenuItem_actionPerformed(); |
1115 | } | |
1116 | 0 | else if (source == removeAllGapsMenuItem) |
1117 | { | |
1118 | 0 | removeAllGapsMenuItem_actionPerformed(); |
1119 | } | |
1120 | 0 | else if (source == findMenuItem) |
1121 | { | |
1122 | 0 | findMenuItem_actionPerformed(); |
1123 | } | |
1124 | 0 | else if (source == font) |
1125 | { | |
1126 | 0 | new FontChooser(alignPanel); |
1127 | } | |
1128 | 0 | else if (source == newView) |
1129 | { | |
1130 | 0 | newView(null); |
1131 | } | |
1132 | 0 | else if (source == showColumns) |
1133 | { | |
1134 | 0 | viewport.showAllHiddenColumns(); |
1135 | 0 | alignPanel.paintAlignment(true, true); |
1136 | 0 | viewport.sendSelection(); |
1137 | } | |
1138 | 0 | else if (source == showSeqs) |
1139 | { | |
1140 | 0 | viewport.showAllHiddenSeqs(); |
1141 | 0 | alignPanel.paintAlignment(true, true); |
1142 | // uncomment if we want to slave sequence selections in split frame | |
1143 | // viewport.sendSelection(); | |
1144 | } | |
1145 | 0 | else if (source == hideColumns) |
1146 | { | |
1147 | 0 | viewport.hideSelectedColumns(); |
1148 | 0 | alignPanel.paintAlignment(true, true); |
1149 | 0 | viewport.sendSelection(); |
1150 | } | |
1151 | 0 | else if (source == hideSequences |
1152 | && viewport.getSelectionGroup() != null) | |
1153 | { | |
1154 | 0 | viewport.hideAllSelectedSeqs(); |
1155 | 0 | alignPanel.paintAlignment(true, true); |
1156 | // uncomment if we want to slave sequence selections in split frame | |
1157 | // viewport.sendSelection(); | |
1158 | } | |
1159 | 0 | else if (source == hideAllButSelection) |
1160 | { | |
1161 | 0 | toggleHiddenRegions(false, false); |
1162 | 0 | alignPanel.paintAlignment(true, true); |
1163 | 0 | viewport.sendSelection(); |
1164 | } | |
1165 | 0 | else if (source == hideAllSelection) |
1166 | { | |
1167 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
1168 | 0 | viewport.expandColSelection(sg, false); |
1169 | 0 | viewport.hideAllSelectedSeqs(); |
1170 | 0 | viewport.hideSelectedColumns(); |
1171 | 0 | alignPanel.paintAlignment(true, true); |
1172 | 0 | viewport.sendSelection(); |
1173 | } | |
1174 | 0 | else if (source == showAllHidden) |
1175 | { | |
1176 | 0 | viewport.showAllHiddenColumns(); |
1177 | 0 | viewport.showAllHiddenSeqs(); |
1178 | 0 | alignPanel.paintAlignment(true, true); |
1179 | 0 | viewport.sendSelection(); |
1180 | } | |
1181 | 0 | else if (source == showGroupConsensus) |
1182 | { | |
1183 | 0 | showGroupConsensus_actionPerformed(); |
1184 | } | |
1185 | 0 | else if (source == showGroupConservation) |
1186 | { | |
1187 | 0 | showGroupConservation_actionPerformed(); |
1188 | } | |
1189 | 0 | else if (source == showSequenceLogo) |
1190 | { | |
1191 | 0 | showSequenceLogo_actionPerformed(); |
1192 | } | |
1193 | 0 | else if (source == normSequenceLogo) |
1194 | { | |
1195 | 0 | normSequenceLogo_actionPerformed(); |
1196 | } | |
1197 | 0 | else if (source == showConsensusHistogram) |
1198 | { | |
1199 | 0 | showConsensusHistogram_actionPerformed(); |
1200 | } | |
1201 | 0 | else if (source == applyAutoAnnotationSettings) |
1202 | { | |
1203 | 0 | applyAutoAnnotationSettings_actionPerformed(); |
1204 | } | |
1205 | 0 | else if (source == featureSettings) |
1206 | { | |
1207 | 0 | showFeatureSettingsUI(); |
1208 | } | |
1209 | 0 | else if (source == alProperties) |
1210 | { | |
1211 | 0 | StringBuffer contents = new jalview.io.AlignmentProperties( |
1212 | viewport.getAlignment()).formatAsString(); | |
1213 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); |
1214 | 0 | cap.setText(contents.toString()); |
1215 | 0 | Frame frame = new Frame(); |
1216 | 0 | frame.add(cap); |
1217 | 0 | jalview.bin.JalviewLite.addFrame(frame, MessageManager |
1218 | .formatMessage("label.alignment_properties", new String[] | |
1219 | { getTitle() }), 400, 250); | |
1220 | } | |
1221 | 0 | else if (source == overviewMenuItem) |
1222 | { | |
1223 | 0 | overviewMenuItem_actionPerformed(); |
1224 | } | |
1225 | 0 | else if (source == noColourmenuItem) |
1226 | { | |
1227 | 0 | changeColour(null); |
1228 | } | |
1229 | 0 | else if (source == clustalColour) |
1230 | { | |
1231 | 0 | abovePIDThreshold.setState(false); |
1232 | 0 | changeColour(new ClustalxColourScheme(viewport.getAlignment(), null)); |
1233 | } | |
1234 | 0 | else if (source == zappoColour) |
1235 | { | |
1236 | 0 | changeColour(new ZappoColourScheme()); |
1237 | } | |
1238 | 0 | else if (source == taylorColour) |
1239 | { | |
1240 | 0 | changeColour(new TaylorColourScheme()); |
1241 | } | |
1242 | 0 | else if (source == hydrophobicityColour) |
1243 | { | |
1244 | 0 | changeColour(new HydrophobicColourScheme()); |
1245 | } | |
1246 | 0 | else if (source == helixColour) |
1247 | { | |
1248 | 0 | changeColour(new HelixColourScheme()); |
1249 | } | |
1250 | 0 | else if (source == strandColour) |
1251 | { | |
1252 | 0 | changeColour(new StrandColourScheme()); |
1253 | } | |
1254 | 0 | else if (source == turnColour) |
1255 | { | |
1256 | 0 | changeColour(new TurnColourScheme()); |
1257 | } | |
1258 | 0 | else if (source == buriedColour) |
1259 | { | |
1260 | 0 | changeColour(new BuriedColourScheme()); |
1261 | } | |
1262 | 0 | else if (source == nucleotideColour) |
1263 | { | |
1264 | 0 | changeColour(new NucleotideColourScheme()); |
1265 | } | |
1266 | 0 | else if (source == purinePyrimidineColour) |
1267 | { | |
1268 | 0 | changeColour(new PurinePyrimidineColourScheme()); |
1269 | } | |
1270 | // else if (source == RNAInteractionColour) | |
1271 | // { | |
1272 | // changeColour(new RNAInteractionColourScheme()); | |
1273 | // } | |
1274 | 0 | else if (source == RNAHelixColour) |
1275 | { | |
1276 | 0 | changeColour(new RNAHelicesColour(viewport.getAlignment())); |
1277 | // new RNAHelicesColourChooser(viewport, alignPanel); | |
1278 | } | |
1279 | 0 | else if (source == modifyPID) |
1280 | { | |
1281 | 0 | modifyPID_actionPerformed(); |
1282 | } | |
1283 | 0 | else if (source == modifyConservation) |
1284 | { | |
1285 | 0 | modifyConservation_actionPerformed(); |
1286 | } | |
1287 | 0 | else if (source == userDefinedColour) |
1288 | { | |
1289 | 0 | new UserDefinedColours(alignPanel, null); |
1290 | } | |
1291 | 0 | else if (source == PIDColour) |
1292 | { | |
1293 | 0 | changeColour(new PIDColourScheme()); |
1294 | } | |
1295 | 0 | else if (source == BLOSUM62Colour) |
1296 | { | |
1297 | 0 | changeColour(new Blosum62ColourScheme()); |
1298 | } | |
1299 | 0 | else if (source == tcoffeeColour) |
1300 | { | |
1301 | 0 | changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); |
1302 | } | |
1303 | 0 | else if (source == annotationColour) |
1304 | { | |
1305 | 0 | new AnnotationColourChooser(viewport, alignPanel); |
1306 | } | |
1307 | 0 | else if (source == annotationColumnSelection) |
1308 | { | |
1309 | 0 | new AnnotationColumnChooser(viewport, alignPanel); |
1310 | } | |
1311 | 0 | else if (source == sortPairwiseMenuItem) |
1312 | { | |
1313 | 0 | sortPairwiseMenuItem_actionPerformed(); |
1314 | } | |
1315 | 0 | else if (source == sortIDMenuItem) |
1316 | { | |
1317 | 0 | sortIDMenuItem_actionPerformed(); |
1318 | } | |
1319 | 0 | else if (source == sortLengthMenuItem) |
1320 | { | |
1321 | 0 | sortLengthMenuItem_actionPerformed(); |
1322 | } | |
1323 | 0 | else if (source == sortGroupMenuItem) |
1324 | { | |
1325 | 0 | sortGroupMenuItem_actionPerformed(); |
1326 | } | |
1327 | 0 | else if (source == removeRedundancyMenuItem) |
1328 | { | |
1329 | 0 | removeRedundancyMenuItem_actionPerformed(); |
1330 | } | |
1331 | 0 | else if (source == pairwiseAlignmentMenuItem) |
1332 | { | |
1333 | 0 | pairwiseAlignmentMenuItem_actionPerformed(); |
1334 | } | |
1335 | 0 | else if (source == PCAMenuItem) |
1336 | { | |
1337 | 0 | PCAMenuItem_actionPerformed(); |
1338 | } | |
1339 | 0 | else if (source == averageDistanceTreeMenuItem) |
1340 | { | |
1341 | 0 | averageDistanceTreeMenuItem_actionPerformed(); |
1342 | } | |
1343 | 0 | else if (source == neighbourTreeMenuItem) |
1344 | { | |
1345 | 0 | neighbourTreeMenuItem_actionPerformed(); |
1346 | } | |
1347 | 0 | else if (source == njTreeBlosumMenuItem) |
1348 | { | |
1349 | 0 | njTreeBlosumMenuItem_actionPerformed(); |
1350 | } | |
1351 | 0 | else if (source == avDistanceTreeBlosumMenuItem) |
1352 | { | |
1353 | 0 | avTreeBlosumMenuItem_actionPerformed(); |
1354 | } | |
1355 | 0 | else if (source == documentation) |
1356 | { | |
1357 | 0 | documentation_actionPerformed(); |
1358 | } | |
1359 | 0 | else if (source == about) |
1360 | { | |
1361 | 0 | about_actionPerformed(); |
1362 | } | |
1363 | ||
1364 | } | |
1365 | ||
1366 | 0 | public void inputText_actionPerformed() |
1367 | { | |
1368 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
1369 | 0 | Frame frame = new Frame(); |
1370 | 0 | frame.add(cap); |
1371 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
1372 | MessageManager.getString("label.input_cut_paste"), 500, 500); | |
1373 | } | |
1374 | ||
1375 | 0 | protected void outputText_actionPerformed(ActionEvent e) |
1376 | { | |
1377 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
1378 | 0 | Frame frame = new Frame(); |
1379 | 0 | frame.add(cap); |
1380 | 0 | JalviewLite.addFrame(frame, MessageManager |
1381 | .formatMessage("label.alignment_output_command", new Object[] | |
1382 | { e.getActionCommand() }), 600, 500); | |
1383 | ||
1384 | 0 | FileFormatI fileFormat = FileFormats.getInstance() |
1385 | .forName(e.getActionCommand()); | |
1386 | 0 | cap.setText( |
1387 | new AppletFormatAdapter(alignPanel).formatSequences(fileFormat, | |
1388 | viewport.getAlignment(), viewport.getShowJVSuffix())); | |
1389 | } | |
1390 | ||
1391 | 0 | public void loadAnnotations() |
1392 | { | |
1393 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
1394 | 0 | cap.setText(MessageManager |
1395 | .getString("label.paste_features_annotations_Tcoffee_here")); | |
1396 | 0 | cap.setAnnotationImport(); |
1397 | 0 | Frame frame = new Frame(); |
1398 | 0 | frame.add(cap); |
1399 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
1400 | MessageManager.getString("action.paste_annotations"), 400, 300); | |
1401 | ||
1402 | } | |
1403 | ||
1404 | 0 | public String outputAnnotations(boolean displayTextbox) |
1405 | { | |
1406 | 0 | String annotation = new AnnotationFile() |
1407 | .printAnnotationsForView(viewport); | |
1408 | ||
1409 | 0 | if (displayTextbox) |
1410 | { | |
1411 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); |
1412 | 0 | Frame frame = new Frame(); |
1413 | 0 | frame.add(cap); |
1414 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
1415 | MessageManager.getString("label.annotations"), 600, 500); | |
1416 | 0 | cap.setText(annotation); |
1417 | } | |
1418 | ||
1419 | 0 | return annotation; |
1420 | } | |
1421 | ||
1422 | 0 | private Map<String, FeatureColourI> getDisplayedFeatureCols() |
1423 | { | |
1424 | 0 | if (alignPanel.getFeatureRenderer() != null |
1425 | && viewport.getFeaturesDisplayed() != null) | |
1426 | { | |
1427 | 0 | return alignPanel.getFeatureRenderer().getDisplayedFeatureCols(); |
1428 | ||
1429 | } | |
1430 | 0 | return null; |
1431 | } | |
1432 | ||
1433 | 0 | private List<String> getDisplayedFeatureGroups() |
1434 | { | |
1435 | 0 | if (alignPanel.getFeatureRenderer() != null |
1436 | && viewport.getFeaturesDisplayed() != null) | |
1437 | { | |
1438 | 0 | return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups(); |
1439 | ||
1440 | } | |
1441 | 0 | return null; |
1442 | } | |
1443 | ||
1444 | 0 | public String outputFeatures(boolean displayTextbox, String format) |
1445 | { | |
1446 | 0 | String features; |
1447 | 0 | FeaturesFile formatter = new FeaturesFile(); |
1448 | 0 | if (format.equalsIgnoreCase("Jalview")) |
1449 | { | |
1450 | 0 | features = formatter.printJalviewFormat( |
1451 | viewport.getAlignment().getSequencesArray(), | |
1452 | alignPanel.getFeatureRenderer(), true, false); | |
1453 | } | |
1454 | else | |
1455 | { | |
1456 | 0 | features = formatter.printGffFormat( |
1457 | viewport.getAlignment().getSequencesArray(), | |
1458 | alignPanel.getFeatureRenderer(), true, false); | |
1459 | } | |
1460 | ||
1461 | 0 | if (displayTextbox) |
1462 | { | |
1463 | 0 | boolean frimport = false; |
1464 | 0 | if (features == null || features.equals("No Features Visible")) |
1465 | { | |
1466 | 0 | features = "# No features visible - paste some and import them here."; |
1467 | 0 | frimport = true; |
1468 | } | |
1469 | ||
1470 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this); |
1471 | 0 | if (frimport) |
1472 | { | |
1473 | 0 | cap.setAnnotationImport(); |
1474 | } | |
1475 | 0 | Frame frame = new Frame(); |
1476 | 0 | frame.add(cap); |
1477 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
1478 | MessageManager.getString("label.features"), 600, 500); | |
1479 | 0 | cap.setText(features); |
1480 | } | |
1481 | else | |
1482 | { | |
1483 | 0 | if (features == null) |
1484 | { | |
1485 | 0 | features = ""; |
1486 | } | |
1487 | } | |
1488 | ||
1489 | 0 | return features; |
1490 | } | |
1491 | ||
1492 | 0 | void launchFullApplication() |
1493 | { | |
1494 | 0 | StringBuffer url = new StringBuffer(jalviewServletURL); |
1495 | ||
1496 | // allow servlet parameters to be passed in applet parameter | |
1497 | 0 | String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&" |
1498 | : "?"; | |
1499 | 0 | url.append(firstSep); |
1500 | ||
1501 | 0 | url.append( |
1502 | "open=" + appendProtocol(viewport.applet.getParameter("file"))); | |
1503 | ||
1504 | 0 | if (viewport.applet.getParameter("features") != null) |
1505 | { | |
1506 | 0 | url.append("&features="); |
1507 | 0 | url.append(appendProtocol(viewport.applet.getParameter("features"))); |
1508 | } | |
1509 | ||
1510 | 0 | if (viewport.applet.getParameter("annotations") != null) |
1511 | { | |
1512 | 0 | url.append("&annotations="); |
1513 | 0 | url.append( |
1514 | appendProtocol(viewport.applet.getParameter("annotations"))); | |
1515 | } | |
1516 | ||
1517 | 0 | if (viewport.applet.getParameter("jnetfile") != null |
1518 | || viewport.applet.getParameter("jpredfile") != null) | |
1519 | { | |
1520 | 0 | url.append("&annotations="); |
1521 | 0 | url.append(appendProtocol( |
1522 | 0 | viewport.applet.getParameter("jnetfile") != null |
1523 | ? viewport.applet.getParameter("jnetfile") | |
1524 | : viewport.applet.getParameter("jpredfile"))); | |
1525 | } | |
1526 | ||
1527 | 0 | if (viewport.applet.getParameter("defaultColour") != null) |
1528 | { | |
1529 | 0 | url.append("&colour=" + removeWhiteSpace( |
1530 | viewport.applet.getParameter("defaultColour"))); | |
1531 | } | |
1532 | ||
1533 | 0 | if (viewport.applet.getParameter("userDefinedColour") != null) |
1534 | { | |
1535 | 0 | url.append("&colour=" + removeWhiteSpace( |
1536 | viewport.applet.getParameter("userDefinedColour"))); | |
1537 | } | |
1538 | 0 | if (viewport.applet.getParameter("tree") != null) |
1539 | { | |
1540 | 0 | url.append("&tree=" |
1541 | + appendProtocol(viewport.applet.getParameter("tree"))); | |
1542 | } | |
1543 | 0 | if (viewport.applet.getParameter("treeFile") != null) |
1544 | { | |
1545 | 0 | url.append("&tree=" |
1546 | + appendProtocol(viewport.applet.getParameter("treeFile"))); | |
1547 | } | |
1548 | ||
1549 | 0 | showURL(url.toString(), "FULL_APP"); |
1550 | } | |
1551 | ||
1552 | 0 | String removeWhiteSpace(String colour) |
1553 | { | |
1554 | 0 | StringBuffer sb = new StringBuffer(); |
1555 | 0 | for (int i = 0; i < colour.length(); i++) |
1556 | { | |
1557 | 0 | if (Character.isWhitespace(colour.charAt(i))) |
1558 | { | |
1559 | 0 | sb.append("%20"); |
1560 | } | |
1561 | else | |
1562 | { | |
1563 | 0 | sb.append(colour.charAt(i)); |
1564 | } | |
1565 | } | |
1566 | ||
1567 | 0 | return sb.toString(); |
1568 | } | |
1569 | ||
1570 | 0 | String appendProtocol(String url) |
1571 | { | |
1572 | 0 | try |
1573 | { | |
1574 | 0 | new URL(url); |
1575 | 0 | url = URLEncoder.encode(url, "UTF-8"); |
1576 | } | |
1577 | /* | |
1578 | * When we finally deprecate 1.1 compatibility, we can start to use | |
1579 | * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch | |
1580 | * (UnsupportedEncodingException ex) { jalview.bin.Console.errPrintln("WARNING - | |
1581 | * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url); | |
1582 | * ex.printStackTrace(); } | |
1583 | */ | |
1584 | catch (java.net.MalformedURLException ex) | |
1585 | { | |
1586 | 0 | url = viewport.applet.getCodeBase() + url; |
1587 | } catch (UnsupportedEncodingException ex) | |
1588 | { | |
1589 | 0 | jalview.bin.Console.errPrintln( |
1590 | "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR " | |
1591 | + url); | |
1592 | 0 | ex.printStackTrace(); |
1593 | } | |
1594 | 0 | return url; |
1595 | } | |
1596 | ||
1597 | 0 | public void closeMenuItem_actionPerformed() |
1598 | { | |
1599 | 0 | PaintRefresher.RemoveComponent(alignPanel); |
1600 | 0 | if (alignPanel.seqPanel != null |
1601 | && alignPanel.seqPanel.seqCanvas != null) | |
1602 | { | |
1603 | 0 | PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); |
1604 | } | |
1605 | 0 | if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null) |
1606 | { | |
1607 | 0 | PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); |
1608 | } | |
1609 | ||
1610 | 0 | if (PaintRefresher.components.size() == 0 && viewport.applet == null) |
1611 | { | |
1612 | 0 | System.exit(0); |
1613 | } | |
1614 | ||
1615 | 0 | viewport = null; |
1616 | 0 | if (alignPanel != null && alignPanel.overviewPanel != null) |
1617 | { | |
1618 | 0 | alignPanel.overviewPanel.dispose(); |
1619 | } | |
1620 | 0 | alignPanel = null; |
1621 | 0 | this.dispose(); |
1622 | } | |
1623 | ||
1624 | /** | |
1625 | * TODO: JAL-1104 | |
1626 | */ | |
1627 | 0 | void updateEditMenuBar() |
1628 | { | |
1629 | ||
1630 | 0 | if (viewport.getHistoryList().size() > 0) |
1631 | { | |
1632 | 0 | undoMenuItem.setEnabled(true); |
1633 | 0 | CommandI command = viewport.getHistoryList().peek(); |
1634 | 0 | undoMenuItem.setLabel(MessageManager |
1635 | .formatMessage("label.undo_command", new Object[] | |
1636 | { command.getDescription() })); | |
1637 | } | |
1638 | else | |
1639 | { | |
1640 | 0 | undoMenuItem.setEnabled(false); |
1641 | 0 | undoMenuItem.setLabel(MessageManager.getString("action.undo")); |
1642 | } | |
1643 | ||
1644 | 0 | if (viewport.getRedoList().size() > 0) |
1645 | { | |
1646 | 0 | redoMenuItem.setEnabled(true); |
1647 | ||
1648 | 0 | CommandI command = viewport.getRedoList().peek(); |
1649 | 0 | redoMenuItem.setLabel(MessageManager |
1650 | .formatMessage("label.redo_command", new Object[] | |
1651 | { command.getDescription() })); | |
1652 | } | |
1653 | else | |
1654 | { | |
1655 | 0 | redoMenuItem.setEnabled(false); |
1656 | 0 | redoMenuItem.setLabel(MessageManager.getString("action.redo")); |
1657 | } | |
1658 | } | |
1659 | ||
1660 | /** | |
1661 | * TODO: JAL-1104 | |
1662 | */ | |
1663 | 0 | @Override |
1664 | public void addHistoryItem(CommandI command) | |
1665 | { | |
1666 | 0 | if (command.getSize() > 0) |
1667 | { | |
1668 | 0 | viewport.addToHistoryList(command); |
1669 | 0 | viewport.clearRedoList(); |
1670 | 0 | updateEditMenuBar(); |
1671 | 0 | viewport.updateHiddenColumns(); |
1672 | } | |
1673 | } | |
1674 | ||
1675 | /** | |
1676 | * TODO: JAL-1104 DOCUMENT ME! | |
1677 | * | |
1678 | * @param e | |
1679 | * DOCUMENT ME! | |
1680 | */ | |
1681 | 0 | protected void undoMenuItem_actionPerformed() |
1682 | { | |
1683 | 0 | if (viewport.getHistoryList().isEmpty()) |
1684 | { | |
1685 | 0 | return; |
1686 | } | |
1687 | ||
1688 | 0 | CommandI command = viewport.getHistoryList().pop(); |
1689 | 0 | viewport.addToRedoList(command); |
1690 | 0 | command.undoCommand(null); |
1691 | ||
1692 | 0 | AlignmentViewport originalSource = getOriginatingSource(command); |
1693 | // JBPNote Test | |
1694 | 0 | if (originalSource != viewport) |
1695 | { | |
1696 | 0 | System.err |
1697 | .println("Warning: Viewport object mismatch whilst undoing"); | |
1698 | } | |
1699 | 0 | originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = |
1700 | // viewport.getColumnSelection().getHiddenColumns() | |
1701 | // != null; | |
1702 | 0 | updateEditMenuBar(); |
1703 | 0 | originalSource.firePropertyChange("alignment", null, |
1704 | originalSource.getAlignment().getSequences()); | |
1705 | } | |
1706 | ||
1707 | /** | |
1708 | * TODO: JAL-1104 DOCUMENT ME! | |
1709 | * | |
1710 | * @param e | |
1711 | * DOCUMENT ME! | |
1712 | */ | |
1713 | 0 | protected void redoMenuItem_actionPerformed() |
1714 | { | |
1715 | 0 | if (viewport.getRedoList().isEmpty()) |
1716 | { | |
1717 | 0 | return; |
1718 | } | |
1719 | ||
1720 | 0 | CommandI command = viewport.getRedoList().pop(); |
1721 | 0 | viewport.addToHistoryList(command); |
1722 | 0 | command.doCommand(null); |
1723 | ||
1724 | 0 | AlignmentViewport originalSource = getOriginatingSource(command); |
1725 | // JBPNote Test | |
1726 | 0 | if (originalSource != viewport) |
1727 | { | |
1728 | 0 | System.err |
1729 | .println("Warning: Viewport object mismatch whilst re-doing"); | |
1730 | } | |
1731 | 0 | originalSource.updateHiddenColumns(); // sethasHiddenColumns(); = |
1732 | // viewport.getColumnSelection().getHiddenColumns() | |
1733 | // != null; | |
1734 | ||
1735 | 0 | updateEditMenuBar(); |
1736 | 0 | originalSource.firePropertyChange("alignment", null, |
1737 | originalSource.getAlignment().getSequences()); | |
1738 | } | |
1739 | ||
1740 | 0 | AlignmentViewport getOriginatingSource(CommandI command) |
1741 | { | |
1742 | 0 | AlignmentViewport originalSource = null; |
1743 | // For sequence removal and addition, we need to fire | |
1744 | // the property change event FROM the viewport where the | |
1745 | // original alignment was altered | |
1746 | 0 | AlignmentI al = null; |
1747 | 0 | if (command instanceof EditCommand) |
1748 | { | |
1749 | 0 | EditCommand editCommand = (EditCommand) command; |
1750 | 0 | al = editCommand.getAlignment(); |
1751 | 0 | Vector comps = PaintRefresher.components |
1752 | .get(viewport.getSequenceSetId()); | |
1753 | 0 | for (int i = 0; i < comps.size(); i++) |
1754 | { | |
1755 | 0 | if (comps.elementAt(i) instanceof AlignmentPanel) |
1756 | { | |
1757 | 0 | if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) |
1758 | { | |
1759 | 0 | originalSource = ((AlignmentPanel) comps.elementAt(i)).av; |
1760 | 0 | break; |
1761 | } | |
1762 | } | |
1763 | } | |
1764 | } | |
1765 | ||
1766 | 0 | if (originalSource == null) |
1767 | { | |
1768 | // The original view is closed, we must validate | |
1769 | // the current view against the closed view first | |
1770 | 0 | if (al != null) |
1771 | { | |
1772 | 0 | PaintRefresher.validateSequences(al, viewport.getAlignment()); |
1773 | } | |
1774 | ||
1775 | 0 | originalSource = viewport; |
1776 | } | |
1777 | ||
1778 | 0 | return originalSource; |
1779 | } | |
1780 | ||
1781 | /** | |
1782 | * Move the currently selected sequences up or down one position in the | |
1783 | * alignment | |
1784 | * | |
1785 | * @param up | |
1786 | */ | |
1787 | 0 | public void moveSelectedSequences(boolean up) |
1788 | { | |
1789 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
1790 | 0 | if (sg == null) |
1791 | { | |
1792 | 0 | return; |
1793 | } | |
1794 | 0 | viewport.getAlignment().moveSelectedSequencesByOne(sg, |
1795 | 0 | up ? null : viewport.getHiddenRepSequences(), up); |
1796 | 0 | alignPanel.paintAlignment(true, false); |
1797 | ||
1798 | /* | |
1799 | * Also move cDNA/protein complement sequences | |
1800 | */ | |
1801 | 0 | AlignViewportI complement = viewport.getCodingComplement(); |
1802 | 0 | if (complement != null) |
1803 | { | |
1804 | 0 | SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg, |
1805 | viewport, complement); | |
1806 | 0 | complement.getAlignment().moveSelectedSequencesByOne(mappedSelection, |
1807 | 0 | up ? null : complement.getHiddenRepSequences(), up); |
1808 | 0 | getSplitFrame().getComplement(this).alignPanel.paintAlignment(true, |
1809 | false); | |
1810 | } | |
1811 | } | |
1812 | ||
1813 | 0 | synchronized void slideSequences(boolean right, int size) |
1814 | { | |
1815 | 0 | List<SequenceI> sg = new Vector<>(); |
1816 | 0 | if (viewport.cursorMode) |
1817 | { | |
1818 | 0 | sg.add(viewport.getAlignment() |
1819 | .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); | |
1820 | } | |
1821 | 0 | else if (viewport.getSelectionGroup() != null |
1822 | && viewport.getSelectionGroup().getSize() != viewport | |
1823 | .getAlignment().getHeight()) | |
1824 | { | |
1825 | 0 | sg = viewport.getSelectionGroup() |
1826 | .getSequences(viewport.getHiddenRepSequences()); | |
1827 | } | |
1828 | ||
1829 | 0 | if (sg.size() < 1) |
1830 | { | |
1831 | 0 | return; |
1832 | } | |
1833 | ||
1834 | 0 | Vector<SequenceI> invertGroup = new Vector(); |
1835 | ||
1836 | 0 | for (int i = 0; i < viewport.getAlignment().getHeight(); i++) |
1837 | { | |
1838 | 0 | if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) |
1839 | { | |
1840 | 0 | invertGroup.addElement(viewport.getAlignment().getSequenceAt(i)); |
1841 | } | |
1842 | } | |
1843 | ||
1844 | 0 | SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); |
1845 | ||
1846 | 0 | SequenceI[] seqs2 = invertGroup |
1847 | .toArray(new SequenceI[invertGroup.size()]); | |
1848 | 0 | for (int i = 0; i < invertGroup.size(); i++) |
1849 | { | |
1850 | 0 | seqs2[i] = invertGroup.elementAt(i); |
1851 | } | |
1852 | ||
1853 | 0 | SlideSequencesCommand ssc; |
1854 | 0 | if (right) |
1855 | { | |
1856 | 0 | ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, |
1857 | viewport.getGapCharacter()); | |
1858 | } | |
1859 | else | |
1860 | { | |
1861 | 0 | ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, |
1862 | viewport.getGapCharacter()); | |
1863 | } | |
1864 | ||
1865 | 0 | int groupAdjustment = 0; |
1866 | 0 | if (ssc.getGapsInsertedBegin() && right) |
1867 | { | |
1868 | 0 | if (viewport.cursorMode) |
1869 | { | |
1870 | 0 | alignPanel.seqPanel.moveCursor(size, 0); |
1871 | } | |
1872 | else | |
1873 | { | |
1874 | 0 | groupAdjustment = size; |
1875 | } | |
1876 | } | |
1877 | 0 | else if (!ssc.getGapsInsertedBegin() && !right) |
1878 | { | |
1879 | 0 | if (viewport.cursorMode) |
1880 | { | |
1881 | 0 | alignPanel.seqPanel.moveCursor(-size, 0); |
1882 | } | |
1883 | else | |
1884 | { | |
1885 | 0 | groupAdjustment = -size; |
1886 | } | |
1887 | } | |
1888 | ||
1889 | 0 | if (groupAdjustment != 0) |
1890 | { | |
1891 | 0 | viewport.getSelectionGroup().setStartRes( |
1892 | viewport.getSelectionGroup().getStartRes() + groupAdjustment); | |
1893 | 0 | viewport.getSelectionGroup().setEndRes( |
1894 | viewport.getSelectionGroup().getEndRes() + groupAdjustment); | |
1895 | } | |
1896 | ||
1897 | 0 | boolean appendHistoryItem = false; |
1898 | 0 | Deque<CommandI> historyList = viewport.getHistoryList(); |
1899 | 0 | if (historyList != null && historyList.size() > 0 |
1900 | && historyList.peek() instanceof SlideSequencesCommand) | |
1901 | { | |
1902 | 0 | appendHistoryItem = ssc.appendSlideCommand( |
1903 | (SlideSequencesCommand) historyList.peek()); | |
1904 | } | |
1905 | ||
1906 | 0 | if (!appendHistoryItem) |
1907 | { | |
1908 | 0 | addHistoryItem(ssc); |
1909 | } | |
1910 | ||
1911 | 0 | repaint(); |
1912 | } | |
1913 | ||
1914 | static StringBuffer copiedSequences; | |
1915 | ||
1916 | static HiddenColumns copiedHiddenColumns; | |
1917 | ||
1918 | 0 | protected void copy_actionPerformed() |
1919 | { | |
1920 | 0 | if (viewport.getSelectionGroup() == null) |
1921 | { | |
1922 | 0 | return; |
1923 | } | |
1924 | ||
1925 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
1926 | 0 | copiedSequences = new StringBuffer(); |
1927 | 0 | Map<Integer, SequenceI> orderedSeqs = new HashMap<>(); |
1928 | 0 | for (int i = 0; i < sg.getSize(); i++) |
1929 | { | |
1930 | 0 | SequenceI seq = sg.getSequenceAt(i); |
1931 | 0 | int index = viewport.getAlignment().findIndex(seq); |
1932 | 0 | orderedSeqs.put(index, seq); |
1933 | } | |
1934 | ||
1935 | 0 | int index = 0, startRes, endRes; |
1936 | 0 | char ch; |
1937 | ||
1938 | 0 | if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null) |
1939 | { | |
1940 | 0 | int hiddenOffset = viewport.getSelectionGroup().getStartRes(); |
1941 | 0 | int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); |
1942 | ||
1943 | // create new HiddenColumns object with copy of hidden regions | |
1944 | // between startRes and endRes, offset by startRes | |
1945 | 0 | copiedHiddenColumns = new HiddenColumns( |
1946 | viewport.getAlignment().getHiddenColumns(), hiddenOffset, | |
1947 | hiddenCutoff, hiddenOffset); | |
1948 | } | |
1949 | else | |
1950 | { | |
1951 | 0 | copiedHiddenColumns = null; |
1952 | } | |
1953 | ||
1954 | 0 | for (int i = 0; i < sg.getSize(); i++) |
1955 | { | |
1956 | 0 | SequenceI seq = null; |
1957 | ||
1958 | 0 | while (seq == null) |
1959 | { | |
1960 | 0 | if (orderedSeqs.containsKey(index)) |
1961 | { | |
1962 | 0 | seq = orderedSeqs.get(index); |
1963 | 0 | index++; |
1964 | 0 | break; |
1965 | } | |
1966 | else | |
1967 | { | |
1968 | 0 | index++; |
1969 | } | |
1970 | } | |
1971 | ||
1972 | // FIND START RES | |
1973 | // Returns residue following index if gap | |
1974 | 0 | startRes = seq.findPosition(sg.getStartRes()); |
1975 | ||
1976 | // FIND END RES | |
1977 | // Need to find the residue preceeding index if gap | |
1978 | 0 | endRes = 0; |
1979 | ||
1980 | 0 | for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) |
1981 | { | |
1982 | 0 | ch = seq.getCharAt(j); |
1983 | 0 | if (!jalview.util.Comparison.isGap((ch))) |
1984 | { | |
1985 | 0 | endRes++; |
1986 | } | |
1987 | } | |
1988 | ||
1989 | 0 | if (endRes > 0) |
1990 | { | |
1991 | 0 | endRes += seq.getStart() - 1; |
1992 | } | |
1993 | ||
1994 | 0 | copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes |
1995 | + "\t" + seq.getSequenceAsString(sg.getStartRes(), | |
1996 | sg.getEndRes() + 1) | |
1997 | + "\n"); | |
1998 | } | |
1999 | ||
2000 | } | |
2001 | ||
2002 | 0 | protected void pasteNew_actionPerformed() |
2003 | { | |
2004 | 0 | paste(true); |
2005 | } | |
2006 | ||
2007 | 0 | protected void pasteThis_actionPerformed() |
2008 | { | |
2009 | 0 | paste(false); |
2010 | } | |
2011 | ||
2012 | 0 | void paste(boolean newAlignment) |
2013 | { | |
2014 | 0 | try |
2015 | { | |
2016 | 0 | if (copiedSequences == null) |
2017 | { | |
2018 | 0 | return; |
2019 | } | |
2020 | ||
2021 | 0 | StringTokenizer st = new StringTokenizer(copiedSequences.toString(), |
2022 | "\t"); | |
2023 | 0 | Vector seqs = new Vector(); |
2024 | 0 | while (st.hasMoreElements()) |
2025 | { | |
2026 | 0 | String name = st.nextToken(); |
2027 | 0 | int start = Integer.parseInt(st.nextToken()); |
2028 | 0 | int end = Integer.parseInt(st.nextToken()); |
2029 | 0 | seqs.addElement(new Sequence(name, st.nextToken(), start, end)); |
2030 | } | |
2031 | 0 | SequenceI[] newSeqs = new SequenceI[seqs.size()]; |
2032 | 0 | for (int i = 0; i < seqs.size(); i++) |
2033 | { | |
2034 | 0 | newSeqs[i] = (SequenceI) seqs.elementAt(i); |
2035 | } | |
2036 | ||
2037 | 0 | if (newAlignment) |
2038 | { | |
2039 | 0 | String newtitle = MessageManager |
2040 | .getString("label.copied_sequences"); | |
2041 | 0 | if (getTitle().startsWith( |
2042 | MessageManager.getString("label.copied_sequences"))) | |
2043 | { | |
2044 | 0 | newtitle = getTitle(); |
2045 | } | |
2046 | else | |
2047 | { | |
2048 | 0 | newtitle = newtitle.concat(MessageManager |
2049 | .formatMessage("label.from_msname", new String[] | |
2050 | { getTitle() })); | |
2051 | } | |
2052 | 0 | AlignFrame af = new AlignFrame(new Alignment(newSeqs), |
2053 | viewport.applet, newtitle, false); | |
2054 | 0 | af.viewport.setHiddenColumns(copiedHiddenColumns); |
2055 | ||
2056 | 0 | jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth, |
2057 | frameHeight); | |
2058 | } | |
2059 | else | |
2060 | { | |
2061 | 0 | addSequences(newSeqs); |
2062 | } | |
2063 | ||
2064 | } catch (Exception ex) | |
2065 | { | |
2066 | } // could be anything being pasted in here | |
2067 | ||
2068 | } | |
2069 | ||
2070 | 0 | void addSequences(SequenceI[] seqs) |
2071 | { | |
2072 | 0 | for (int i = 0; i < seqs.length; i++) |
2073 | { | |
2074 | 0 | viewport.getAlignment().addSequence(seqs[i]); |
2075 | } | |
2076 | ||
2077 | // !newAlignment | |
2078 | 0 | addHistoryItem(new EditCommand( |
2079 | MessageManager.getString("label.add_sequences"), Action.PASTE, | |
2080 | seqs, 0, viewport.getAlignment().getWidth(), | |
2081 | viewport.getAlignment())); | |
2082 | ||
2083 | 0 | viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH |
2084 | // 2019.04.18 | |
2085 | 0 | viewport.getAlignment().getWidth(); |
2086 | 0 | viewport.firePropertyChange("alignment", null, |
2087 | viewport.getAlignment().getSequences()); | |
2088 | ||
2089 | } | |
2090 | ||
2091 | 0 | protected void cut_actionPerformed() |
2092 | { | |
2093 | 0 | copy_actionPerformed(); |
2094 | 0 | delete_actionPerformed(); |
2095 | } | |
2096 | ||
2097 | 0 | protected void delete_actionPerformed() |
2098 | { | |
2099 | ||
2100 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
2101 | 0 | if (sg == null) |
2102 | { | |
2103 | 0 | return; |
2104 | } | |
2105 | ||
2106 | 0 | Vector seqs = new Vector(); |
2107 | 0 | SequenceI seq; |
2108 | 0 | for (int i = 0; i < sg.getSize(); i++) |
2109 | { | |
2110 | 0 | seq = sg.getSequenceAt(i); |
2111 | 0 | seqs.addElement(seq); |
2112 | } | |
2113 | ||
2114 | /* | |
2115 | * If the cut affects all sequences, warn, remove highlighted columns | |
2116 | */ | |
2117 | 0 | if (sg.getSize() == viewport.getAlignment().getHeight()) |
2118 | { | |
2119 | 0 | boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) |
2120 | + 1) == viewport.getAlignment().getWidth()) ? true : false; | |
2121 | 0 | if (isEntireAlignWidth) |
2122 | { | |
2123 | 0 | String title = MessageManager.getString("label.delete_all"); |
2124 | 0 | Panel infoPanel = new Panel(); |
2125 | 0 | infoPanel.setLayout(new FlowLayout()); |
2126 | 0 | infoPanel.add( |
2127 | new Label(MessageManager.getString("warn.delete_all"))); | |
2128 | ||
2129 | 0 | final JVDialog dialog = new JVDialog(this, title, true, 400, 200); |
2130 | 0 | dialog.setMainPanel(infoPanel); |
2131 | 0 | dialog.ok.setLabel(MessageManager.getString("action.ok")); |
2132 | 0 | dialog.cancel.setLabel(MessageManager.getString("action.cancel")); |
2133 | 0 | dialog.setVisible(true); |
2134 | ||
2135 | 0 | if (!dialog.accept) |
2136 | { | |
2137 | 0 | return; |
2138 | } | |
2139 | } | |
2140 | 0 | viewport.getColumnSelection().removeElements(sg.getStartRes(), |
2141 | sg.getEndRes() + 1); | |
2142 | } | |
2143 | ||
2144 | 0 | SequenceI[] cut = new SequenceI[seqs.size()]; |
2145 | 0 | for (int i = 0; i < seqs.size(); i++) |
2146 | { | |
2147 | 0 | cut[i] = (SequenceI) seqs.elementAt(i); |
2148 | } | |
2149 | ||
2150 | /* | |
2151 | * //ADD HISTORY ITEM | |
2152 | */ | |
2153 | 0 | addHistoryItem(new EditCommand( |
2154 | MessageManager.getString("label.cut_sequences"), Action.CUT, | |
2155 | cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, | |
2156 | viewport.getAlignment())); | |
2157 | ||
2158 | 0 | viewport.setSelectionGroup(null); |
2159 | 0 | viewport.getAlignment().deleteGroup(sg); |
2160 | ||
2161 | 0 | viewport.firePropertyChange("alignment", null, |
2162 | viewport.getAlignment().getSequences()); | |
2163 | ||
2164 | 0 | if (viewport.getAlignment().getHeight() < 1) |
2165 | { | |
2166 | 0 | this.setVisible(false); |
2167 | } | |
2168 | 0 | viewport.sendSelection(); |
2169 | } | |
2170 | ||
2171 | /** | |
2172 | * group consensus toggled | |
2173 | * | |
2174 | */ | |
2175 | 0 | protected void showGroupConsensus_actionPerformed() |
2176 | { | |
2177 | 0 | viewport.setShowGroupConsensus(showGroupConsensus.getState()); |
2178 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2179 | ||
2180 | } | |
2181 | ||
2182 | /** | |
2183 | * group conservation toggled. | |
2184 | */ | |
2185 | 0 | protected void showGroupConservation_actionPerformed() |
2186 | { | |
2187 | 0 | viewport.setShowGroupConservation(showGroupConservation.getState()); |
2188 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2189 | } | |
2190 | ||
2191 | /* | |
2192 | * (non-Javadoc) | |
2193 | * | |
2194 | * @see | |
2195 | * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt | |
2196 | * .event.ActionEvent) | |
2197 | */ | |
2198 | 0 | protected void showConsensusHistogram_actionPerformed() |
2199 | { | |
2200 | 0 | viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); |
2201 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2202 | } | |
2203 | ||
2204 | /* | |
2205 | * (non-Javadoc) | |
2206 | * | |
2207 | * @see | |
2208 | * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt | |
2209 | * .event.ActionEvent) | |
2210 | */ | |
2211 | 0 | protected void showSequenceLogo_actionPerformed() |
2212 | { | |
2213 | 0 | viewport.setShowSequenceLogo(showSequenceLogo.getState()); |
2214 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2215 | } | |
2216 | ||
2217 | 0 | protected void normSequenceLogo_actionPerformed() |
2218 | { | |
2219 | 0 | showSequenceLogo.setState(true); |
2220 | 0 | viewport.setShowSequenceLogo(true); |
2221 | 0 | viewport.setNormaliseSequenceLogo(normSequenceLogo.getState()); |
2222 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2223 | } | |
2224 | ||
2225 | 0 | protected void applyAutoAnnotationSettings_actionPerformed() |
2226 | { | |
2227 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2228 | } | |
2229 | ||
2230 | 0 | protected void makeGrpsFromSelection_actionPerformed() |
2231 | { | |
2232 | 0 | if (avc.makeGroupsFromSelection()) |
2233 | { | |
2234 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
2235 | 0 | alignPanel.updateAnnotation(); |
2236 | 0 | alignPanel.paintAlignment(true, true); |
2237 | } | |
2238 | } | |
2239 | ||
2240 | 0 | protected void createGroup_actionPerformed() |
2241 | { | |
2242 | 0 | avc.createGroup(); |
2243 | } | |
2244 | ||
2245 | 0 | protected void unGroup_actionPerformed() |
2246 | { | |
2247 | 0 | if (avc.unGroup()) |
2248 | { | |
2249 | 0 | alignPanel.alignmentChanged(); |
2250 | } | |
2251 | } | |
2252 | ||
2253 | 0 | protected void deleteGroups_actionPerformed() |
2254 | { | |
2255 | 0 | if (avc.deleteGroups()) |
2256 | { | |
2257 | 0 | alignPanel.alignmentChanged(); |
2258 | } | |
2259 | } | |
2260 | ||
2261 | 0 | public void selectAllSequenceMenuItem_actionPerformed() |
2262 | { | |
2263 | 0 | SequenceGroup sg = new SequenceGroup(); |
2264 | 0 | for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) |
2265 | { | |
2266 | 0 | sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); |
2267 | } | |
2268 | 0 | sg.setEndRes(viewport.getAlignment().getWidth() - 1); |
2269 | 0 | viewport.setSelectionGroup(sg); |
2270 | // JAL-2034 - should delegate to | |
2271 | // alignPanel to decide if overview needs | |
2272 | // updating. | |
2273 | 0 | alignPanel.paintAlignment(false, false); |
2274 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2275 | 0 | viewport.sendSelection(); |
2276 | } | |
2277 | ||
2278 | 0 | public void deselectAllSequenceMenuItem_actionPerformed() |
2279 | { | |
2280 | 0 | if (viewport.cursorMode) |
2281 | { | |
2282 | 0 | alignPanel.seqPanel.keyboardNo1 = null; |
2283 | 0 | alignPanel.seqPanel.keyboardNo2 = null; |
2284 | } | |
2285 | 0 | viewport.setSelectionGroup(null); |
2286 | 0 | viewport.getColumnSelection().clear(); |
2287 | 0 | viewport.setSelectionGroup(null); |
2288 | 0 | alignPanel.idPanel.idCanvas.searchResults = null; |
2289 | 0 | alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); |
2290 | // JAL-2034 - should delegate to | |
2291 | // alignPanel to decide if overview needs | |
2292 | // updating. | |
2293 | 0 | alignPanel.paintAlignment(false, false); |
2294 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2295 | 0 | viewport.sendSelection(); |
2296 | } | |
2297 | ||
2298 | 0 | public void invertSequenceMenuItem_actionPerformed() |
2299 | { | |
2300 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
2301 | 0 | for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) |
2302 | { | |
2303 | 0 | sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); |
2304 | } | |
2305 | ||
2306 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2307 | 0 | viewport.sendSelection(); |
2308 | } | |
2309 | ||
2310 | 0 | public void invertColSel_actionPerformed() |
2311 | { | |
2312 | 0 | viewport.invertColumnSelection(); |
2313 | 0 | alignPanel.paintAlignment(true, false); |
2314 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2315 | 0 | viewport.sendSelection(); |
2316 | } | |
2317 | ||
2318 | 0 | void trimAlignment(boolean trimLeft) |
2319 | { | |
2320 | 0 | AlignmentI al = viewport.getAlignment(); |
2321 | 0 | ViewportRanges ranges = viewport.getRanges(); |
2322 | 0 | ColumnSelection colSel = viewport.getColumnSelection(); |
2323 | 0 | int column; |
2324 | ||
2325 | 0 | if (!colSel.isEmpty()) |
2326 | { | |
2327 | 0 | if (trimLeft) |
2328 | { | |
2329 | 0 | column = colSel.getMin(); |
2330 | } | |
2331 | else | |
2332 | { | |
2333 | 0 | column = colSel.getMax(); |
2334 | } | |
2335 | ||
2336 | 0 | SequenceI[] seqs; |
2337 | 0 | if (viewport.getSelectionGroup() != null) |
2338 | { | |
2339 | 0 | seqs = viewport.getSelectionGroup() |
2340 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2341 | } | |
2342 | else | |
2343 | { | |
2344 | 0 | seqs = al.getSequencesArray(); |
2345 | } | |
2346 | ||
2347 | 0 | TrimRegionCommand trimRegion; |
2348 | 0 | if (trimLeft) |
2349 | { | |
2350 | 0 | trimRegion = new TrimRegionCommand("Remove Left", true, seqs, |
2351 | column, al); | |
2352 | 0 | ranges.setStartRes(0); |
2353 | } | |
2354 | else | |
2355 | { | |
2356 | 0 | trimRegion = new TrimRegionCommand("Remove Right", false, seqs, |
2357 | column, al); | |
2358 | } | |
2359 | ||
2360 | 0 | setStatus(MessageManager.formatMessage("label.removed_columns", |
2361 | new String[] | |
2362 | { Integer.valueOf(trimRegion.getSize()).toString() })); | |
2363 | 0 | addHistoryItem(trimRegion); |
2364 | ||
2365 | 0 | for (SequenceGroup sg : al.getGroups()) |
2366 | { | |
2367 | 0 | if ((trimLeft && !sg.adjustForRemoveLeft(column)) |
2368 | || (!trimLeft && !sg.adjustForRemoveRight(column))) | |
2369 | { | |
2370 | 0 | al.deleteGroup(sg); |
2371 | } | |
2372 | } | |
2373 | ||
2374 | 0 | viewport.firePropertyChange("alignment", null, al.getSequences()); |
2375 | } | |
2376 | } | |
2377 | ||
2378 | 0 | public void removeGappedColumnMenuItem_actionPerformed() |
2379 | { | |
2380 | 0 | AlignmentI al = viewport.getAlignment(); |
2381 | 0 | ViewportRanges ranges = viewport.getRanges(); |
2382 | 0 | int start = 0; |
2383 | 0 | int end = ranges.getAbsoluteAlignmentWidth() - 1; |
2384 | ||
2385 | 0 | SequenceI[] seqs; |
2386 | 0 | if (viewport.getSelectionGroup() != null) |
2387 | { | |
2388 | 0 | seqs = viewport.getSelectionGroup() |
2389 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2390 | 0 | start = viewport.getSelectionGroup().getStartRes(); |
2391 | 0 | end = viewport.getSelectionGroup().getEndRes(); |
2392 | } | |
2393 | else | |
2394 | { | |
2395 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2396 | } | |
2397 | ||
2398 | 0 | RemoveGapColCommand removeGapCols = new RemoveGapColCommand( |
2399 | "Remove Gapped Columns", seqs, start, end, | |
2400 | viewport.getAlignment()); | |
2401 | ||
2402 | 0 | addHistoryItem(removeGapCols); |
2403 | ||
2404 | 0 | setStatus(MessageManager.formatMessage("label.removed_empty_columns", |
2405 | new String[] | |
2406 | { Integer.valueOf(removeGapCols.getSize()).toString() })); | |
2407 | ||
2408 | // This is to maintain viewport position on first residue | |
2409 | // of first sequence | |
2410 | 0 | SequenceI seq = al.getSequenceAt(0); |
2411 | 0 | int startRes = seq.findPosition(ranges.getStartRes()); |
2412 | // ShiftList shifts; | |
2413 | // viewport.getAlignment().removeGaps(shifts=new ShiftList()); | |
2414 | // edit.alColumnChanges=shifts.getInverse(); | |
2415 | // if (viewport.hasHiddenColumns) | |
2416 | // viewport.getColumnSelection().compensateForEdits(shifts); | |
2417 | 0 | ranges.setStartRes(seq.findIndex(startRes) - 1); |
2418 | 0 | viewport.firePropertyChange("alignment", null, al.getSequences()); |
2419 | ||
2420 | } | |
2421 | ||
2422 | 0 | public void removeAllGapsMenuItem_actionPerformed() |
2423 | { | |
2424 | 0 | AlignmentI al = viewport.getAlignment(); |
2425 | 0 | ViewportRanges ranges = viewport.getRanges(); |
2426 | 0 | int start = 0; |
2427 | 0 | int end = ranges.getAbsoluteAlignmentWidth() - 1; |
2428 | ||
2429 | 0 | SequenceI[] seqs; |
2430 | 0 | if (viewport.getSelectionGroup() != null) |
2431 | { | |
2432 | 0 | seqs = viewport.getSelectionGroup() |
2433 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2434 | 0 | start = viewport.getSelectionGroup().getStartRes(); |
2435 | 0 | end = viewport.getSelectionGroup().getEndRes(); |
2436 | } | |
2437 | else | |
2438 | { | |
2439 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2440 | } | |
2441 | ||
2442 | // This is to maintain viewport position on first residue | |
2443 | // of first sequence | |
2444 | 0 | SequenceI seq = al.getSequenceAt(0); |
2445 | 0 | int startRes = seq.findPosition(ranges.getStartRes()); |
2446 | ||
2447 | 0 | addHistoryItem( |
2448 | new RemoveGapsCommand("Remove Gaps", seqs, start, end, al)); | |
2449 | ||
2450 | 0 | ranges.setStartRes(seq.findIndex(startRes) - 1); |
2451 | ||
2452 | 0 | viewport.firePropertyChange("alignment", null, al.getSequences()); |
2453 | ||
2454 | } | |
2455 | ||
2456 | 0 | public void findMenuItem_actionPerformed() |
2457 | { | |
2458 | 0 | new Finder(alignPanel); |
2459 | } | |
2460 | ||
2461 | /** | |
2462 | * create a new view derived from the current view | |
2463 | * | |
2464 | * @param viewtitle | |
2465 | * @return frame for the new view | |
2466 | */ | |
2467 | 0 | public AlignFrame newView(String viewtitle) |
2468 | { | |
2469 | 0 | AlignmentI newal; |
2470 | 0 | if (viewport.hasHiddenRows()) |
2471 | { | |
2472 | 0 | newal = new Alignment(viewport.getAlignment().getHiddenSequences() |
2473 | .getFullAlignment().getSequencesArray()); | |
2474 | } | |
2475 | else | |
2476 | { | |
2477 | 0 | newal = new Alignment(viewport.getAlignment().getSequencesArray()); |
2478 | } | |
2479 | ||
2480 | 0 | if (viewport.getAlignment().getAlignmentAnnotation() != null) |
2481 | { | |
2482 | 0 | for (int i = 0; i < viewport.getAlignment() |
2483 | .getAlignmentAnnotation().length; i++) | |
2484 | { | |
2485 | 0 | if (!viewport.getAlignment() |
2486 | .getAlignmentAnnotation()[i].autoCalculated) | |
2487 | { | |
2488 | 0 | newal.addAnnotation( |
2489 | viewport.getAlignment().getAlignmentAnnotation()[i]); | |
2490 | } | |
2491 | } | |
2492 | } | |
2493 | ||
2494 | 0 | AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); |
2495 | ||
2496 | 0 | newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId()); |
2497 | 0 | PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); |
2498 | 0 | PaintRefresher.Register(newaf.alignPanel, |
2499 | newaf.alignPanel.av.getSequenceSetId()); | |
2500 | ||
2501 | 0 | PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, |
2502 | newaf.alignPanel.av.getSequenceSetId()); | |
2503 | 0 | PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, |
2504 | newaf.alignPanel.av.getSequenceSetId()); | |
2505 | ||
2506 | 0 | Vector comps = PaintRefresher.components |
2507 | .get(viewport.getSequenceSetId()); | |
2508 | 0 | int viewSize = -1; |
2509 | 0 | for (int i = 0; i < comps.size(); i++) |
2510 | { | |
2511 | 0 | if (comps.elementAt(i) instanceof AlignmentPanel) |
2512 | { | |
2513 | 0 | viewSize++; |
2514 | } | |
2515 | } | |
2516 | ||
2517 | 0 | String title = new String(this.getTitle()); |
2518 | 0 | if (viewtitle != null) |
2519 | { | |
2520 | 0 | title = viewtitle + " ( " + title + ")"; |
2521 | } | |
2522 | else | |
2523 | { | |
2524 | 0 | if (title.indexOf("(View") > -1) |
2525 | { | |
2526 | 0 | title = title.substring(0, title.indexOf("(View")); |
2527 | } | |
2528 | 0 | title += "(View " + viewSize + ")"; |
2529 | } | |
2530 | ||
2531 | 0 | newaf.setTitle(title.toString()); |
2532 | ||
2533 | 0 | newaf.viewport.setHistoryList(viewport.getHistoryList()); |
2534 | 0 | newaf.viewport.setRedoList(viewport.getRedoList()); |
2535 | 0 | return newaf; |
2536 | } | |
2537 | ||
2538 | /** | |
2539 | * | |
2540 | * @return list of feature groups on the view | |
2541 | */ | |
2542 | 0 | public String[] getFeatureGroups() |
2543 | { | |
2544 | 0 | FeatureRenderer fr = null; |
2545 | 0 | if (alignPanel != null |
2546 | && (fr = alignPanel.getFeatureRenderer()) != null) | |
2547 | { | |
2548 | 0 | List<String> gps = fr.getFeatureGroups(); |
2549 | 0 | String[] _gps = gps.toArray(new String[gps.size()]); |
2550 | 0 | return _gps; |
2551 | } | |
2552 | 0 | return null; |
2553 | } | |
2554 | ||
2555 | /** | |
2556 | * get sequence feature groups that are hidden or shown | |
2557 | * | |
2558 | * @param visible | |
2559 | * true is visible | |
2560 | * @return list | |
2561 | */ | |
2562 | 0 | public String[] getFeatureGroupsOfState(boolean visible) |
2563 | { | |
2564 | 0 | FeatureRenderer fr = null; |
2565 | 0 | if (alignPanel != null |
2566 | && (fr = alignPanel.getFeatureRenderer()) != null) | |
2567 | { | |
2568 | 0 | List<String> gps = fr.getGroups(visible); |
2569 | 0 | String[] _gps = gps.toArray(new String[gps.size()]); |
2570 | 0 | return _gps; |
2571 | } | |
2572 | 0 | return null; |
2573 | } | |
2574 | ||
2575 | /** | |
2576 | * Change the display state for the given feature groups | |
2577 | * | |
2578 | * @param groups | |
2579 | * list of group strings | |
2580 | * @param state | |
2581 | * visible or invisible | |
2582 | */ | |
2583 | 0 | public void setFeatureGroupState(String[] groups, boolean state) |
2584 | { | |
2585 | 0 | FeatureRenderer fr = null; |
2586 | 0 | this.sequenceFeatures.setState(true); |
2587 | 0 | viewport.setShowSequenceFeatures(true); |
2588 | 0 | if (alignPanel != null |
2589 | && (fr = alignPanel.getFeatureRenderer()) != null) | |
2590 | { | |
2591 | ||
2592 | 0 | fr.setGroupVisibility(Arrays.asList(groups), state); |
2593 | 0 | alignPanel.seqPanel.seqCanvas.repaint(); |
2594 | 0 | if (alignPanel.overviewPanel != null) |
2595 | { | |
2596 | 0 | alignPanel.overviewPanel.updateOverviewImage(); |
2597 | } | |
2598 | } | |
2599 | } | |
2600 | ||
2601 | 0 | public void seqLimits_itemStateChanged() |
2602 | { | |
2603 | 0 | viewport.setShowJVSuffix(seqLimits.getState()); |
2604 | 0 | alignPanel.fontChanged(); |
2605 | 0 | alignPanel.paintAlignment(true, false); |
2606 | } | |
2607 | ||
2608 | 0 | protected void colourTextMenuItem_actionPerformed() |
2609 | { | |
2610 | 0 | viewport.setColourText(colourTextMenuItem.getState()); |
2611 | 0 | alignPanel.paintAlignment(false, false); |
2612 | } | |
2613 | ||
2614 | 0 | protected void displayNonconservedMenuItem_actionPerformed() |
2615 | { | |
2616 | 0 | viewport.setShowUnconserved(displayNonconservedMenuItem.getState()); |
2617 | 0 | alignPanel.paintAlignment(false, false); |
2618 | } | |
2619 | ||
2620 | 0 | protected void wrapMenuItem_actionPerformed() |
2621 | { | |
2622 | 0 | viewport.setWrapAlignment(wrapMenuItem.getState()); |
2623 | 0 | alignPanel.setWrapAlignment(wrapMenuItem.getState()); |
2624 | 0 | scaleAbove.setEnabled(wrapMenuItem.getState()); |
2625 | 0 | scaleLeft.setEnabled(wrapMenuItem.getState()); |
2626 | 0 | scaleRight.setEnabled(wrapMenuItem.getState()); |
2627 | 0 | alignPanel.paintAlignment(true, false); |
2628 | } | |
2629 | ||
2630 | 0 | public void overviewMenuItem_actionPerformed() |
2631 | { | |
2632 | 0 | if (alignPanel.overviewPanel != null) |
2633 | { | |
2634 | 0 | return; |
2635 | } | |
2636 | ||
2637 | 0 | Frame frame = new Frame(); |
2638 | 0 | final OverviewPanel overview = new OverviewPanel(alignPanel); |
2639 | 0 | frame.add(overview); |
2640 | // +50 must allow for applet frame window | |
2641 | 0 | jalview.bin.JalviewLite.addFrame(frame, MessageManager |
2642 | .formatMessage("label.overview_params", new String[] | |
2643 | { this.getTitle() }), overview.getPreferredSize().width, | |
2644 | overview.getPreferredSize().height + 50); | |
2645 | ||
2646 | 0 | frame.pack(); |
2647 | 0 | final AlignmentPanel ap = alignPanel; |
2648 | 0 | frame.addWindowListener(new WindowAdapter() |
2649 | { | |
2650 | 0 | @Override |
2651 | public void windowClosing(WindowEvent e) | |
2652 | { | |
2653 | 0 | overview.dispose(); |
2654 | 0 | if (ap != null) |
2655 | { | |
2656 | 0 | ap.setOverviewPanel(null); |
2657 | } | |
2658 | }; | |
2659 | }); | |
2660 | ||
2661 | 0 | alignPanel.setOverviewPanel(overview); |
2662 | ||
2663 | } | |
2664 | ||
2665 | 0 | @Override |
2666 | public void changeColour(ColourSchemeI cs) | |
2667 | { | |
2668 | 0 | viewport.setGlobalColourScheme(cs); |
2669 | ||
2670 | 0 | alignPanel.paintAlignment(true, true); |
2671 | } | |
2672 | ||
2673 | 0 | protected void modifyPID_actionPerformed() |
2674 | { | |
2675 | 0 | if (viewport.getAbovePIDThreshold() |
2676 | && viewport.getGlobalColourScheme() != null) | |
2677 | { | |
2678 | 0 | SliderPanel.setPIDSliderSource(alignPanel, |
2679 | viewport.getResidueShading(), alignPanel.getViewName()); | |
2680 | 0 | SliderPanel.showPIDSlider(); |
2681 | } | |
2682 | } | |
2683 | ||
2684 | 0 | protected void modifyConservation_actionPerformed() |
2685 | { | |
2686 | 0 | if (viewport.getConservationSelected() |
2687 | && viewport.getGlobalColourScheme() != null) | |
2688 | { | |
2689 | 0 | SliderPanel.setConservationSlider(alignPanel, |
2690 | viewport.getResidueShading(), alignPanel.getViewName()); | |
2691 | 0 | SliderPanel.showConservationSlider(); |
2692 | } | |
2693 | } | |
2694 | ||
2695 | 0 | protected void conservationMenuItem_actionPerformed() |
2696 | { | |
2697 | 0 | boolean selected = conservationMenuItem.getState(); |
2698 | 0 | modifyConservation.setEnabled(selected); |
2699 | 0 | viewport.setConservationSelected(selected); |
2700 | 0 | viewport.getResidueShading().setConservationApplied(selected); |
2701 | ||
2702 | 0 | changeColour(viewport.getGlobalColourScheme()); |
2703 | ||
2704 | 0 | if (selected) |
2705 | { | |
2706 | 0 | modifyConservation_actionPerformed(); |
2707 | } | |
2708 | else | |
2709 | { | |
2710 | 0 | SliderPanel.hideConservationSlider(); |
2711 | } | |
2712 | } | |
2713 | ||
2714 | 0 | public void abovePIDThreshold_actionPerformed() |
2715 | { | |
2716 | 0 | boolean selected = abovePIDThreshold.getState(); |
2717 | 0 | modifyPID.setEnabled(selected); |
2718 | 0 | viewport.setAbovePIDThreshold(selected); |
2719 | 0 | if (!selected) |
2720 | { | |
2721 | 0 | viewport.getResidueShading().setThreshold(0, |
2722 | viewport.isIgnoreGapsConsensus()); | |
2723 | } | |
2724 | ||
2725 | 0 | changeColour(viewport.getGlobalColourScheme()); |
2726 | ||
2727 | 0 | if (selected) |
2728 | { | |
2729 | 0 | modifyPID_actionPerformed(); |
2730 | } | |
2731 | else | |
2732 | { | |
2733 | 0 | SliderPanel.hidePIDSlider(); |
2734 | } | |
2735 | } | |
2736 | ||
2737 | 0 | public void sortPairwiseMenuItem_actionPerformed() |
2738 | { | |
2739 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2740 | 0 | AlignmentSorter.sortByPID(viewport.getAlignment(), |
2741 | viewport.getAlignment().getSequenceAt(0)); | |
2742 | ||
2743 | 0 | addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, |
2744 | viewport.getAlignment())); | |
2745 | 0 | alignPanel.paintAlignment(true, false); |
2746 | } | |
2747 | ||
2748 | 0 | public void sortIDMenuItem_actionPerformed() |
2749 | { | |
2750 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2751 | 0 | AlignmentSorter.sortByID(viewport.getAlignment()); |
2752 | 0 | addHistoryItem( |
2753 | new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); | |
2754 | 0 | alignPanel.paintAlignment(true, false); |
2755 | } | |
2756 | ||
2757 | 0 | public void sortLengthMenuItem_actionPerformed() |
2758 | { | |
2759 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2760 | 0 | AlignmentSorter.sortByLength(viewport.getAlignment()); |
2761 | 0 | addHistoryItem(new OrderCommand("Length Sort", oldOrder, |
2762 | viewport.getAlignment())); | |
2763 | 0 | alignPanel.paintAlignment(true, false); |
2764 | } | |
2765 | ||
2766 | 0 | public void sortGroupMenuItem_actionPerformed() |
2767 | { | |
2768 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2769 | 0 | AlignmentSorter.sortByGroup(viewport.getAlignment()); |
2770 | 0 | addHistoryItem(new OrderCommand("Group Sort", oldOrder, |
2771 | viewport.getAlignment())); | |
2772 | 0 | alignPanel.paintAlignment(true, false); |
2773 | ||
2774 | } | |
2775 | ||
2776 | 0 | public void removeRedundancyMenuItem_actionPerformed() |
2777 | { | |
2778 | 0 | new RedundancyPanel(alignPanel); |
2779 | } | |
2780 | ||
2781 | 0 | public void pairwiseAlignmentMenuItem_actionPerformed() |
2782 | { | |
2783 | 0 | if (viewport.getSelectionGroup() != null |
2784 | && viewport.getSelectionGroup().getSize() > 1) | |
2785 | { | |
2786 | 0 | Frame frame = new Frame(); |
2787 | 0 | frame.add(new PairwiseAlignPanel(alignPanel)); |
2788 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
2789 | MessageManager.getString("action.pairwise_alignment"), 600, | |
2790 | 500); | |
2791 | } | |
2792 | } | |
2793 | ||
2794 | 0 | public void PCAMenuItem_actionPerformed() |
2795 | { | |
2796 | // are the sequences aligned? | |
2797 | 0 | if (!viewport.getAlignment().isAligned(false)) |
2798 | { | |
2799 | 0 | SequenceI current; |
2800 | 0 | int Width = viewport.getAlignment().getWidth(); |
2801 | ||
2802 | 0 | for (int i = 0; i < viewport.getAlignment().getSequences() |
2803 | .size(); i++) | |
2804 | { | |
2805 | 0 | current = viewport.getAlignment().getSequenceAt(i); |
2806 | ||
2807 | 0 | if (current.getLength() < Width) |
2808 | { | |
2809 | 0 | current.insertCharAt(Width - 1, viewport.getGapCharacter()); |
2810 | } | |
2811 | } | |
2812 | 0 | alignPanel.paintAlignment(false, false); |
2813 | } | |
2814 | ||
2815 | 0 | if ((viewport.getSelectionGroup() != null |
2816 | && viewport.getSelectionGroup().getSize() < 4 | |
2817 | && viewport.getSelectionGroup().getSize() > 0) | |
2818 | || viewport.getAlignment().getHeight() < 4) | |
2819 | { | |
2820 | 0 | return; |
2821 | } | |
2822 | ||
2823 | 0 | try |
2824 | { | |
2825 | 0 | new PCAPanel(viewport); |
2826 | } catch (java.lang.OutOfMemoryError ex) | |
2827 | { | |
2828 | } | |
2829 | ||
2830 | } | |
2831 | ||
2832 | 0 | public void averageDistanceTreeMenuItem_actionPerformed() |
2833 | { | |
2834 | 0 | newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(), |
2835 | "Average distance tree using PID"); | |
2836 | } | |
2837 | ||
2838 | 0 | public void neighbourTreeMenuItem_actionPerformed() |
2839 | { | |
2840 | 0 | newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(), |
2841 | "Neighbour joining tree using PID"); | |
2842 | } | |
2843 | ||
2844 | 0 | protected void njTreeBlosumMenuItem_actionPerformed() |
2845 | { | |
2846 | 0 | newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, |
2847 | ScoreModels.getInstance().getBlosum62().getName(), | |
2848 | "Neighbour joining tree using BLOSUM62"); | |
2849 | } | |
2850 | ||
2851 | 0 | protected void avTreeBlosumMenuItem_actionPerformed() |
2852 | { | |
2853 | 0 | newTreePanel(TreeBuilder.AVERAGE_DISTANCE, |
2854 | ScoreModels.getInstance().getBlosum62().getName(), | |
2855 | "Average distance tree using BLOSUM62"); | |
2856 | } | |
2857 | ||
2858 | 0 | void newTreePanel(String type, String pwType, String title) |
2859 | { | |
2860 | // are the sequences aligned? | |
2861 | 0 | if (!viewport.getAlignment().isAligned(false)) |
2862 | { | |
2863 | 0 | SequenceI current; |
2864 | 0 | int Width = viewport.getAlignment().getWidth(); |
2865 | ||
2866 | 0 | for (int i = 0; i < viewport.getAlignment().getSequences() |
2867 | .size(); i++) | |
2868 | { | |
2869 | 0 | current = viewport.getAlignment().getSequenceAt(i); |
2870 | ||
2871 | 0 | if (current.getLength() < Width) |
2872 | { | |
2873 | 0 | current.insertCharAt(Width - 1, viewport.getGapCharacter()); |
2874 | } | |
2875 | } | |
2876 | 0 | alignPanel.paintAlignment(false, false); |
2877 | ||
2878 | } | |
2879 | ||
2880 | 0 | if ((viewport.getSelectionGroup() != null |
2881 | && viewport.getSelectionGroup().getSize() > 1) | |
2882 | || (viewport.getAlignment().getHeight() > 1)) | |
2883 | { | |
2884 | 0 | final TreePanel tp = new TreePanel(alignPanel, type, pwType); |
2885 | ||
2886 | 0 | addTreeMenuItem(tp, title); |
2887 | ||
2888 | 0 | jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); |
2889 | } | |
2890 | } | |
2891 | ||
2892 | 0 | void loadTree_actionPerformed() |
2893 | { | |
2894 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
2895 | 0 | cap.setText(MessageManager.getString("label.paste_newick_tree_file")); |
2896 | 0 | cap.setTreeImport(); |
2897 | 0 | Frame frame = new Frame(); |
2898 | 0 | frame.add(cap); |
2899 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
2900 | MessageManager.getString("label.paste_newick_file"), 400, 300); | |
2901 | } | |
2902 | ||
2903 | 0 | public void loadTree(jalview.io.NewickFile tree, String treeFile) |
2904 | { | |
2905 | 0 | TreePanel tp = new TreePanel(alignPanel, treeFile, |
2906 | MessageManager.getString("label.load_tree_from_file"), tree); | |
2907 | 0 | jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); |
2908 | 0 | addTreeMenuItem(tp, treeFile); |
2909 | } | |
2910 | ||
2911 | /** | |
2912 | * sort the alignment using the given treePanel | |
2913 | * | |
2914 | * @param treePanel | |
2915 | * tree used to sort view | |
2916 | * @param title | |
2917 | * string used for undo event name | |
2918 | */ | |
2919 | 0 | public void sortByTree(TreePanel treePanel, String title) |
2920 | { | |
2921 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2922 | 0 | AlignmentSorter.sortByTree(viewport.getAlignment(), |
2923 | treePanel.getTree()); | |
2924 | // addHistoryItem(new HistoryItem("Sort", viewport.alignment, | |
2925 | // HistoryItem.SORT)); | |
2926 | 0 | addHistoryItem(new OrderCommand(MessageManager |
2927 | .formatMessage("label.order_by_params", new String[] | |
2928 | { title }), oldOrder, viewport.getAlignment())); | |
2929 | 0 | alignPanel.paintAlignment(true, false); |
2930 | } | |
2931 | ||
2932 | /** | |
2933 | * Do any automatic reordering of the alignment and add the necessary bits to | |
2934 | * the menu structure for the new tree | |
2935 | * | |
2936 | * @param treePanel | |
2937 | * @param title | |
2938 | */ | |
2939 | 0 | protected void addTreeMenuItem(final TreePanel treePanel, |
2940 | final String title) | |
2941 | { | |
2942 | 0 | final MenuItem item = new MenuItem(title); |
2943 | 0 | sortByTreeMenu.add(item); |
2944 | 0 | item.addActionListener(new java.awt.event.ActionListener() |
2945 | { | |
2946 | 0 | @Override |
2947 | public void actionPerformed(ActionEvent evt) | |
2948 | { | |
2949 | 0 | sortByTree(treePanel, title); // treePanel.getTitle()); |
2950 | } | |
2951 | }); | |
2952 | ||
2953 | 0 | treePanel.addWindowListener(new WindowAdapter() |
2954 | { | |
2955 | 0 | @Override |
2956 | public void windowOpened(WindowEvent e) | |
2957 | { | |
2958 | 0 | if (viewport.sortByTree) |
2959 | { | |
2960 | 0 | sortByTree(treePanel, title); |
2961 | } | |
2962 | 0 | super.windowOpened(e); |
2963 | } | |
2964 | ||
2965 | 0 | @Override |
2966 | public void windowClosing(WindowEvent e) | |
2967 | { | |
2968 | 0 | sortByTreeMenu.remove(item); |
2969 | }; | |
2970 | }); | |
2971 | } | |
2972 | ||
2973 | 0 | public boolean sortBy(AlignmentOrder alorder, String undoname) |
2974 | { | |
2975 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2976 | 0 | if (viewport.applet.debug) |
2977 | { | |
2978 | 0 | jalview.bin.Console.errPrintln("Sorting " + alorder.getOrder().size() |
2979 | + " in alignment '" + getTitle() + "'"); | |
2980 | } | |
2981 | 0 | AlignmentSorter.sortBy(viewport.getAlignment(), alorder); |
2982 | 0 | if (undoname != null) |
2983 | { | |
2984 | 0 | addHistoryItem(new OrderCommand(undoname, oldOrder, |
2985 | viewport.getAlignment())); | |
2986 | } | |
2987 | 0 | alignPanel.paintAlignment(true, false); |
2988 | 0 | return true; |
2989 | } | |
2990 | ||
2991 | 0 | protected void documentation_actionPerformed() |
2992 | { | |
2993 | 0 | alignPanel.av.applet.openJalviewHelpUrl(); |
2994 | } | |
2995 | ||
2996 | 0 | protected void about_actionPerformed() |
2997 | { | |
2998 | ||
2999 | class AboutPanel extends Canvas | |
3000 | { | |
3001 | String version; | |
3002 | ||
3003 | String builddate; | |
3004 | ||
3005 | 0 | public AboutPanel(String version, String builddate) |
3006 | { | |
3007 | 0 | this.version = version; |
3008 | 0 | this.builddate = builddate; |
3009 | } | |
3010 | ||
3011 | 0 | @Override |
3012 | public void paint(Graphics g) | |
3013 | { | |
3014 | 0 | g.setColor(Color.white); |
3015 | 0 | g.fillRect(0, 0, getSize().width, getSize().height); |
3016 | 0 | g.setFont(new Font("Helvetica", Font.PLAIN, 12)); |
3017 | 0 | FontMetrics fm = g.getFontMetrics(); |
3018 | 0 | int fh = fm.getHeight(); |
3019 | 0 | int y = 5, x = 7; |
3020 | 0 | g.setColor(Color.black); |
3021 | // TODO: update this text for each release or centrally store it for | |
3022 | // lite and application | |
3023 | 0 | g.setFont(new Font("Helvetica", Font.BOLD, 14)); |
3024 | 0 | g.drawString(MessageManager |
3025 | .formatMessage("label.jalviewLite_release", new String[] | |
3026 | { version }), x, y += fh); | |
3027 | 0 | g.setFont(new Font("Helvetica", Font.BOLD, 12)); |
3028 | 0 | g.drawString(MessageManager.formatMessage("label.jaview_build_date", |
3029 | new String[] | |
3030 | { builddate }), x, y += fh); | |
3031 | 0 | g.setFont(new Font("Helvetica", Font.PLAIN, 12)); |
3032 | 0 | g.drawString(MessageManager.getString("label.jalview_authors_1"), x, |
3033 | y += fh * 1.5); | |
3034 | 0 | g.drawString(MessageManager.getString("label.jalview_authors_2"), |
3035 | x + 50, y += fh + 8); | |
3036 | 0 | g.drawString(MessageManager.getString("label.jalview_dev_managers"), |
3037 | x, y += fh); | |
3038 | 0 | g.drawString(MessageManager |
3039 | .getString("label.jalview_distribution_lists"), x, y += fh); | |
3040 | 0 | g.drawString(MessageManager.getString("label.jalview_please_cite"), |
3041 | x, y += fh + 8); | |
3042 | 0 | g.drawString( |
3043 | MessageManager.getString("label.jalview_cite_1_authors"), x, | |
3044 | y += fh); | |
3045 | 0 | g.drawString(MessageManager.getString("label.jalview_cite_1_title"), |
3046 | x, y += fh); | |
3047 | 0 | g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), |
3048 | x, y += fh); | |
3049 | } | |
3050 | } | |
3051 | ||
3052 | 0 | Frame frame = new Frame(); |
3053 | 0 | frame.add(new AboutPanel(JalviewLite.getVersion(), |
3054 | JalviewLite.getBuildDate())); | |
3055 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
3056 | MessageManager.getString("label.jalview"), 580, 220); | |
3057 | ||
3058 | } | |
3059 | ||
3060 | 0 | public void showURL(String url, String target) |
3061 | { | |
3062 | 0 | if (viewport.applet == null) |
3063 | { | |
3064 | 0 | jalview.bin.Console |
3065 | .outPrintln("Not running as applet - no browser available."); | |
3066 | } | |
3067 | else | |
3068 | { | |
3069 | 0 | viewport.applet.showURL(url, target); |
3070 | } | |
3071 | } | |
3072 | ||
3073 | // //////////////////////////////////////////////////////////////////////////////// | |
3074 | // JBuilder Graphics here | |
3075 | ||
3076 | MenuBar alignFrameMenuBar = new MenuBar(); | |
3077 | ||
3078 | Menu fileMenu = new Menu(MessageManager.getString("action.file")); | |
3079 | ||
3080 | MenuItem loadApplication = new MenuItem( | |
3081 | MessageManager.getString("label.view_full_application")); | |
3082 | ||
3083 | MenuItem loadTree = new MenuItem( | |
3084 | MessageManager.getString("label.load_associated_tree")); | |
3085 | ||
3086 | MenuItem loadAnnotations = new MenuItem( | |
3087 | MessageManager.getString("label.load_features_annotations")); | |
3088 | ||
3089 | MenuItem outputFeatures = new MenuItem( | |
3090 | MessageManager.getString("label.export_features")); | |
3091 | ||
3092 | MenuItem outputAnnotations = new MenuItem( | |
3093 | MessageManager.getString("label.export_annotations")); | |
3094 | ||
3095 | MenuItem closeMenuItem = new MenuItem( | |
3096 | MessageManager.getString("action.close")); | |
3097 | ||
3098 | MenuItem selectAllSequenceMenuItem = new MenuItem( | |
3099 | MessageManager.getString("action.select_all")); | |
3100 | ||
3101 | MenuItem deselectAllSequenceMenuItem = new MenuItem( | |
3102 | MessageManager.getString("action.deselect_all")); | |
3103 | ||
3104 | MenuItem invertSequenceMenuItem = new MenuItem( | |
3105 | MessageManager.getString("action.invert_selection")); | |
3106 | ||
3107 | MenuItem remove2LeftMenuItem = new MenuItem(); | |
3108 | ||
3109 | MenuItem remove2RightMenuItem = new MenuItem(); | |
3110 | ||
3111 | MenuItem removeGappedColumnMenuItem = new MenuItem(); | |
3112 | ||
3113 | MenuItem removeAllGapsMenuItem = new MenuItem(); | |
3114 | ||
3115 | CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); | |
3116 | ||
3117 | CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); | |
3118 | ||
3119 | MenuItem sortPairwiseMenuItem = new MenuItem(); | |
3120 | ||
3121 | MenuItem sortIDMenuItem = new MenuItem(); | |
3122 | ||
3123 | MenuItem sortLengthMenuItem = new MenuItem(); | |
3124 | ||
3125 | MenuItem sortGroupMenuItem = new MenuItem(); | |
3126 | ||
3127 | MenuItem removeRedundancyMenuItem = new MenuItem(); | |
3128 | ||
3129 | MenuItem pairwiseAlignmentMenuItem = new MenuItem(); | |
3130 | ||
3131 | MenuItem PCAMenuItem = new MenuItem(); | |
3132 | ||
3133 | MenuItem averageDistanceTreeMenuItem = new MenuItem(); | |
3134 | ||
3135 | MenuItem neighbourTreeMenuItem = new MenuItem(); | |
3136 | ||
3137 | BorderLayout borderLayout1 = new BorderLayout(); | |
3138 | ||
3139 | public Label statusBar = new Label(); | |
3140 | ||
3141 | MenuItem clustalColour = new MenuItem(); | |
3142 | ||
3143 | MenuItem zappoColour = new MenuItem(); | |
3144 | ||
3145 | MenuItem taylorColour = new MenuItem(); | |
3146 | ||
3147 | MenuItem hydrophobicityColour = new MenuItem(); | |
3148 | ||
3149 | MenuItem helixColour = new MenuItem(); | |
3150 | ||
3151 | MenuItem strandColour = new MenuItem(); | |
3152 | ||
3153 | MenuItem turnColour = new MenuItem(); | |
3154 | ||
3155 | MenuItem buriedColour = new MenuItem(); | |
3156 | ||
3157 | MenuItem purinePyrimidineColour = new MenuItem(); | |
3158 | ||
3159 | // MenuItem RNAInteractionColour = new MenuItem(); | |
3160 | ||
3161 | MenuItem RNAHelixColour = new MenuItem(); | |
3162 | ||
3163 | MenuItem userDefinedColour = new MenuItem(); | |
3164 | ||
3165 | MenuItem PIDColour = new MenuItem(); | |
3166 | ||
3167 | MenuItem BLOSUM62Colour = new MenuItem(); | |
3168 | ||
3169 | MenuItem tcoffeeColour = new MenuItem(); | |
3170 | ||
3171 | MenuItem njTreeBlosumMenuItem = new MenuItem(); | |
3172 | ||
3173 | MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); | |
3174 | ||
3175 | CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); | |
3176 | ||
3177 | CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); | |
3178 | ||
3179 | CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); | |
3180 | ||
3181 | MenuItem alProperties = new MenuItem( | |
3182 | MessageManager.getString("label.alignment_props")); | |
3183 | ||
3184 | MenuItem overviewMenuItem = new MenuItem(); | |
3185 | ||
3186 | MenuItem undoMenuItem = new MenuItem(); | |
3187 | ||
3188 | MenuItem redoMenuItem = new MenuItem(); | |
3189 | ||
3190 | CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); | |
3191 | ||
3192 | MenuItem noColourmenuItem = new MenuItem(); | |
3193 | ||
3194 | CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); | |
3195 | ||
3196 | CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); | |
3197 | ||
3198 | MenuItem findMenuItem = new MenuItem(); | |
3199 | ||
3200 | CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); | |
3201 | ||
3202 | MenuItem nucleotideColour = new MenuItem(); | |
3203 | ||
3204 | MenuItem deleteGroups = new MenuItem(); | |
3205 | ||
3206 | MenuItem grpsFromSelection = new MenuItem(); | |
3207 | ||
3208 | MenuItem createGroup = new MenuItem(); | |
3209 | ||
3210 | MenuItem unGroup = new MenuItem(); | |
3211 | ||
3212 | MenuItem delete = new MenuItem(); | |
3213 | ||
3214 | MenuItem copy = new MenuItem(); | |
3215 | ||
3216 | MenuItem cut = new MenuItem(); | |
3217 | ||
3218 | Menu pasteMenu = new Menu(); | |
3219 | ||
3220 | MenuItem pasteNew = new MenuItem(); | |
3221 | ||
3222 | MenuItem pasteThis = new MenuItem(); | |
3223 | ||
3224 | CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); | |
3225 | ||
3226 | MenuItem font = new MenuItem(); | |
3227 | ||
3228 | CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); | |
3229 | ||
3230 | CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); | |
3231 | ||
3232 | CheckboxMenuItem scaleRight = new CheckboxMenuItem(); | |
3233 | ||
3234 | MenuItem modifyPID = new MenuItem(); | |
3235 | ||
3236 | MenuItem modifyConservation = new MenuItem(); | |
3237 | ||
3238 | CheckboxMenuItem autoCalculate = null; | |
3239 | ||
3240 | CheckboxMenuItem sortByTree = new CheckboxMenuItem( | |
3241 | "Sort Alignment With New Tree", true); | |
3242 | ||
3243 | Menu sortByTreeMenu = new Menu(); | |
3244 | ||
3245 | MenuItem inputText = new MenuItem(); | |
3246 | ||
3247 | MenuItem documentation = new MenuItem(); | |
3248 | ||
3249 | MenuItem about = new MenuItem(); | |
3250 | ||
3251 | CheckboxMenuItem seqLimits = new CheckboxMenuItem(); | |
3252 | ||
3253 | CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem(); | |
3254 | ||
3255 | CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); | |
3256 | ||
3257 | CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem(); | |
3258 | ||
3259 | CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem(); | |
3260 | ||
3261 | CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem(); | |
3262 | ||
3263 | CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem(); | |
3264 | ||
3265 | CheckboxMenuItem showGroupConservation = new CheckboxMenuItem(); | |
3266 | ||
3267 | CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem(); | |
3268 | ||
3269 | /** | |
3270 | * Initialise menus and other items | |
3271 | * | |
3272 | * @throws Exception | |
3273 | */ | |
3274 | 0 | private void jbInit() throws Exception |
3275 | { | |
3276 | 0 | setMenuBar(alignFrameMenuBar); |
3277 | ||
3278 | /* | |
3279 | * Configure File menu items and actions | |
3280 | */ | |
3281 | 0 | inputText |
3282 | .setLabel(MessageManager.getString("label.input_from_textbox")); | |
3283 | 0 | inputText.addActionListener(this); |
3284 | 0 | Menu outputTextboxMenu = new Menu( |
3285 | MessageManager.getString("label.out_to_textbox")); | |
3286 | 0 | for (String ff : FileFormats.getInstance().getWritableFormats(true)) |
3287 | { | |
3288 | 0 | MenuItem item = new MenuItem(ff); |
3289 | ||
3290 | 0 | item.addActionListener(new java.awt.event.ActionListener() |
3291 | { | |
3292 | 0 | @Override |
3293 | public void actionPerformed(ActionEvent e) | |
3294 | { | |
3295 | 0 | outputText_actionPerformed(e); |
3296 | } | |
3297 | }); | |
3298 | ||
3299 | 0 | outputTextboxMenu.add(item); |
3300 | } | |
3301 | 0 | closeMenuItem.addActionListener(this); |
3302 | 0 | loadApplication.addActionListener(this); |
3303 | 0 | loadTree.addActionListener(this); |
3304 | 0 | loadAnnotations.addActionListener(this); |
3305 | 0 | outputFeatures.addActionListener(this); |
3306 | 0 | outputAnnotations.addActionListener(this); |
3307 | ||
3308 | /* | |
3309 | * Configure Edit menu items and actions | |
3310 | */ | |
3311 | 0 | undoMenuItem.setEnabled(false); |
3312 | 0 | undoMenuItem.setLabel(MessageManager.getString("action.undo")); |
3313 | 0 | undoMenuItem.addActionListener(this); |
3314 | 0 | redoMenuItem.setEnabled(false); |
3315 | 0 | redoMenuItem.setLabel(MessageManager.getString("action.redo")); |
3316 | 0 | redoMenuItem.addActionListener(this); |
3317 | 0 | copy.setLabel(MessageManager.getString("action.copy")); |
3318 | 0 | copy.addActionListener(this); |
3319 | 0 | cut.setLabel(MessageManager.getString("action.cut")); |
3320 | 0 | cut.addActionListener(this); |
3321 | 0 | delete.setLabel(MessageManager.getString("action.delete")); |
3322 | 0 | delete.addActionListener(this); |
3323 | 0 | pasteMenu.setLabel(MessageManager.getString("action.paste")); |
3324 | 0 | pasteNew.setLabel(MessageManager.getString("label.to_new_alignment")); |
3325 | 0 | pasteNew.addActionListener(this); |
3326 | 0 | pasteThis.setLabel(MessageManager.getString("label.to_this_alignment")); |
3327 | 0 | pasteThis.addActionListener(this); |
3328 | 0 | remove2LeftMenuItem |
3329 | .setLabel(MessageManager.getString("action.remove_left")); | |
3330 | 0 | remove2LeftMenuItem.addActionListener(this); |
3331 | 0 | remove2RightMenuItem |
3332 | .setLabel(MessageManager.getString("action.remove_right")); | |
3333 | 0 | remove2RightMenuItem.addActionListener(this); |
3334 | 0 | removeGappedColumnMenuItem.setLabel( |
3335 | MessageManager.getString("action.remove_empty_columns")); | |
3336 | 0 | removeGappedColumnMenuItem.addActionListener(this); |
3337 | 0 | removeAllGapsMenuItem |
3338 | .setLabel(MessageManager.getString("action.remove_all_gaps")); | |
3339 | 0 | removeAllGapsMenuItem.addActionListener(this); |
3340 | 0 | removeRedundancyMenuItem |
3341 | .setLabel(MessageManager.getString("action.remove_redundancy")); | |
3342 | 0 | removeRedundancyMenuItem.addActionListener(this); |
3343 | ||
3344 | /* | |
3345 | * Configure Select menu items and actions | |
3346 | */ | |
3347 | 0 | findMenuItem.setLabel(MessageManager.getString("action.find")); |
3348 | 0 | findMenuItem.addActionListener(this); |
3349 | 0 | selectAllSequenceMenuItem.addActionListener(this); |
3350 | 0 | deselectAllSequenceMenuItem.addActionListener(this); |
3351 | 0 | invertSequenceMenuItem.setLabel( |
3352 | MessageManager.getString("action.invert_sequence_selection")); | |
3353 | 0 | invertSequenceMenuItem.addActionListener(this); |
3354 | 0 | invertColSel.setLabel( |
3355 | MessageManager.getString("action.invert_column_selection")); | |
3356 | 0 | invertColSel.addActionListener(this); |
3357 | 0 | deleteGroups |
3358 | .setLabel(MessageManager.getString("action.undefine_groups")); | |
3359 | 0 | deleteGroups.addActionListener(this); |
3360 | 0 | grpsFromSelection.setLabel( |
3361 | MessageManager.getString("action.make_groups_selection")); | |
3362 | 0 | grpsFromSelection.addActionListener(this); |
3363 | 0 | createGroup.setLabel(MessageManager.getString("action.create_group")); |
3364 | 0 | createGroup.addActionListener(this); |
3365 | 0 | unGroup.setLabel(MessageManager.getString("action.remove_group")); |
3366 | 0 | unGroup.addActionListener(this); |
3367 | ||
3368 | 0 | annotationColumnSelection.setLabel( |
3369 | MessageManager.getString("action.select_by_annotation")); | |
3370 | 0 | annotationColumnSelection.addActionListener(this); |
3371 | ||
3372 | /* | |
3373 | * Configure View menu items and actions | |
3374 | */ | |
3375 | 0 | newView.setLabel(MessageManager.getString("action.new_view")); |
3376 | 0 | newView.addActionListener(this); |
3377 | 0 | Menu showMenu = new Menu(MessageManager.getString("action.show")); |
3378 | 0 | showColumns.setLabel(MessageManager.getString("label.all_columns")); |
3379 | 0 | showSeqs.setLabel(MessageManager.getString("label.all_sequences")); |
3380 | 0 | Menu hideMenu = new Menu(MessageManager.getString("action.hide")); |
3381 | 0 | hideColumns |
3382 | .setLabel(MessageManager.getString("label.selected_columns")); | |
3383 | 0 | hideSequences |
3384 | .setLabel(MessageManager.getString("label.selected_sequences")); | |
3385 | 0 | hideAllButSelection.setLabel( |
3386 | MessageManager.getString("label.all_but_selected_region")); | |
3387 | 0 | hideAllSelection |
3388 | .setLabel(MessageManager.getString("label.selected_region")); | |
3389 | 0 | showAllHidden.setLabel( |
3390 | MessageManager.getString("label.all_sequences_columns")); | |
3391 | 0 | showColumns.addActionListener(this); |
3392 | 0 | showSeqs.addActionListener(this); |
3393 | 0 | hideColumns.addActionListener(this); |
3394 | 0 | hideSequences.addActionListener(this); |
3395 | 0 | hideAllButSelection.addActionListener(this); |
3396 | 0 | hideAllSelection.addActionListener(this); |
3397 | 0 | showAllHidden.addActionListener(this); |
3398 | 0 | featureSettings |
3399 | .setLabel(MessageManager.getString("action.feature_settings")); | |
3400 | 0 | featureSettings.addActionListener(this); |
3401 | 0 | sequenceFeatures.setLabel( |
3402 | MessageManager.getString("label.show_sequence_features")); | |
3403 | 0 | sequenceFeatures.addItemListener(this); |
3404 | 0 | sequenceFeatures.setState(false); |
3405 | 0 | followMouseOverFlag.setLabel( |
3406 | MessageManager.getString("label.automatic_scrolling")); | |
3407 | 0 | followMouseOverFlag.addItemListener(this); |
3408 | 0 | alProperties.addActionListener(this); |
3409 | 0 | overviewMenuItem |
3410 | .setLabel(MessageManager.getString("label.overview_window")); | |
3411 | 0 | overviewMenuItem.addActionListener(this); |
3412 | ||
3413 | /* | |
3414 | * Configure Annotations menu items and actions | |
3415 | */ | |
3416 | 0 | annotationPanelMenuItem |
3417 | .setLabel(MessageManager.getString("label.show_annotations")); | |
3418 | 0 | annotationPanelMenuItem.addItemListener(this); |
3419 | 0 | showGroupConsensus |
3420 | .setLabel(MessageManager.getString("label.group_consensus")); | |
3421 | 0 | showGroupConservation |
3422 | .setLabel(MessageManager.getString("label.group_conservation")); | |
3423 | 0 | showConsensusHistogram.setLabel( |
3424 | MessageManager.getString("label.show_consensus_histogram")); | |
3425 | 0 | showSequenceLogo.setLabel( |
3426 | MessageManager.getString("label.show_consensus_logo")); | |
3427 | 0 | normSequenceLogo.setLabel( |
3428 | MessageManager.getString("label.norm_consensus_logo")); | |
3429 | 0 | applyAutoAnnotationSettings |
3430 | .setLabel(MessageManager.getString("label.apply_all_groups")); | |
3431 | 0 | applyAutoAnnotationSettings.setState(true); |
3432 | 0 | Menu autoAnnMenu = new Menu( |
3433 | MessageManager.getString("label.autocalculated_annotation")); | |
3434 | ||
3435 | 0 | Menu selectSS = new Menu(MessageManager |
3436 | .getString("label.select_secondary_structure_source")); | |
3437 | 0 | showGroupConsensus.addItemListener(this); |
3438 | 0 | showGroupConservation.addItemListener(this); |
3439 | 0 | showConsensusHistogram.addItemListener(this); |
3440 | 0 | showSequenceLogo.addItemListener(this); |
3441 | 0 | normSequenceLogo.addItemListener(this); |
3442 | 0 | applyAutoAnnotationSettings.addItemListener(this); |
3443 | 0 | showAlignmentAnnotations = new CheckboxMenuItem( |
3444 | MessageManager.getString("label.show_all_al_annotations")); | |
3445 | 0 | showSequenceAnnotations = new CheckboxMenuItem( |
3446 | MessageManager.getString("label.show_all_seq_annotations")); | |
3447 | 0 | sortAnnBySequence = new CheckboxMenuItem( |
3448 | MessageManager.getString("label.sort_annotations_by_sequence")); | |
3449 | 0 | sortAnnByLabel = new CheckboxMenuItem( |
3450 | MessageManager.getString("label.sort_annotations_by_label")); | |
3451 | 0 | showAutoFirst = new CheckboxMenuItem( |
3452 | MessageManager.getString("label.show_first")); | |
3453 | 0 | showAutoFirst.setState(false); // pending applet parameter |
3454 | 0 | setShowAutoCalculatedAbove(showAutoFirst.getState()); |
3455 | 0 | showAutoLast = new CheckboxMenuItem( |
3456 | MessageManager.getString("label.show_last")); | |
3457 | 0 | showAutoLast.setState(!showAutoFirst.getState()); |
3458 | 0 | showAlignmentAnnotations.addItemListener(this); |
3459 | 0 | showSequenceAnnotations.addItemListener(this); |
3460 | 0 | sortAnnBySequence.addItemListener(this); |
3461 | 0 | sortAnnByLabel.addItemListener(this); |
3462 | 0 | showAutoFirst.addItemListener(this); |
3463 | 0 | showAutoLast.addItemListener(this); |
3464 | ||
3465 | /* | |
3466 | * Configure Format menu items and actions | |
3467 | */ | |
3468 | 0 | font.setLabel(MessageManager.getString("action.font")); |
3469 | 0 | font.addActionListener(this); |
3470 | 0 | scaleAbove.setLabel(MessageManager.getString("action.scale_above")); |
3471 | 0 | scaleAbove.setState(true); |
3472 | 0 | scaleAbove.setEnabled(false); |
3473 | 0 | scaleAbove.addItemListener(this); |
3474 | 0 | scaleLeft.setEnabled(false); |
3475 | 0 | scaleLeft.setState(true); |
3476 | 0 | scaleLeft.setLabel(MessageManager.getString("action.scale_left")); |
3477 | 0 | scaleLeft.addItemListener(this); |
3478 | 0 | scaleRight.setEnabled(false); |
3479 | 0 | scaleRight.setState(true); |
3480 | 0 | scaleRight.setLabel(MessageManager.getString("action.scale_right")); |
3481 | 0 | scaleRight.addItemListener(this); |
3482 | 0 | viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes")); |
3483 | 0 | viewBoxesMenuItem.setState(true); |
3484 | 0 | viewBoxesMenuItem.addItemListener(this); |
3485 | 0 | viewTextMenuItem.setLabel(MessageManager.getString("action.text")); |
3486 | 0 | viewTextMenuItem.setState(true); |
3487 | 0 | viewTextMenuItem.addItemListener(this); |
3488 | 0 | colourTextMenuItem |
3489 | .setLabel(MessageManager.getString("label.colour_text")); | |
3490 | 0 | colourTextMenuItem.addItemListener(this); |
3491 | 0 | displayNonconservedMenuItem |
3492 | .setLabel(MessageManager.getString("label.show_non_conserved")); | |
3493 | 0 | displayNonconservedMenuItem.addItemListener(this); |
3494 | 0 | wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); |
3495 | 0 | wrapMenuItem.addItemListener(this); |
3496 | 0 | renderGapsMenuItem |
3497 | .setLabel(MessageManager.getString("action.show_gaps")); | |
3498 | 0 | renderGapsMenuItem.setState(true); |
3499 | 0 | renderGapsMenuItem.addItemListener(this); |
3500 | 0 | centreColumnLabelFlag.setLabel( |
3501 | MessageManager.getString("label.centre_column_labels")); | |
3502 | 0 | centreColumnLabelFlag.addItemListener(this); |
3503 | 0 | seqLimits.setState(true); |
3504 | 0 | seqLimits.setLabel( |
3505 | MessageManager.getString("label.show_sequence_limits")); | |
3506 | 0 | seqLimits.addItemListener(this); |
3507 | ||
3508 | /* | |
3509 | * Configure Colour menu items and actions | |
3510 | */ | |
3511 | 0 | applyToAllGroups.setLabel( |
3512 | MessageManager.getString("label.apply_colour_to_all_groups")); | |
3513 | 0 | applyToAllGroups.setState(true); |
3514 | 0 | applyToAllGroups.addItemListener(this); |
3515 | 0 | clustalColour.setLabel( |
3516 | MessageManager.getString("label.colourScheme_clustal")); | |
3517 | 0 | clustalColour.addActionListener(this); |
3518 | 0 | zappoColour |
3519 | .setLabel(MessageManager.getString("label.colourScheme_zappo")); | |
3520 | 0 | zappoColour.addActionListener(this); |
3521 | 0 | taylorColour.setLabel( |
3522 | MessageManager.getString("label.colourScheme_taylor")); | |
3523 | 0 | taylorColour.addActionListener(this); |
3524 | 0 | hydrophobicityColour.setLabel( |
3525 | MessageManager.getString("label.colourScheme_hydrophobic")); | |
3526 | 0 | hydrophobicityColour.addActionListener(this); |
3527 | 0 | helixColour.setLabel( |
3528 | MessageManager.getString("label.colourScheme_helixpropensity")); | |
3529 | 0 | helixColour.addActionListener(this); |
3530 | 0 | strandColour.setLabel(MessageManager |
3531 | .getString("label.colourScheme_strandpropensity")); | |
3532 | 0 | strandColour.addActionListener(this); |
3533 | 0 | turnColour.setLabel( |
3534 | MessageManager.getString("label.colourScheme_turnpropensity")); | |
3535 | 0 | turnColour.addActionListener(this); |
3536 | 0 | buriedColour.setLabel( |
3537 | MessageManager.getString("label.colourScheme_buriedindex")); | |
3538 | 0 | buriedColour.addActionListener(this); |
3539 | 0 | purinePyrimidineColour.setLabel(MessageManager |
3540 | .getString("label.colourScheme_purine/pyrimidine")); | |
3541 | 0 | purinePyrimidineColour.addActionListener(this); |
3542 | // RNAInteractionColour.setLabel(MessageManager | |
3543 | // .getString("label.rna_interaction")); | |
3544 | // RNAInteractionColour.addActionListener(this); | |
3545 | 0 | RNAHelixColour.setLabel( |
3546 | MessageManager.getString("label.colourScheme_rnahelices")); | |
3547 | 0 | RNAHelixColour.addActionListener(this); |
3548 | 0 | userDefinedColour |
3549 | .setLabel(MessageManager.getString("action.user_defined")); | |
3550 | 0 | userDefinedColour.addActionListener(this); |
3551 | 0 | PIDColour.setLabel( |
3552 | MessageManager.getString("label.colourScheme_%identity")); | |
3553 | 0 | PIDColour.addActionListener(this); |
3554 | 0 | BLOSUM62Colour.setLabel( |
3555 | MessageManager.getString("label.colourScheme_blosum62")); | |
3556 | 0 | BLOSUM62Colour.addActionListener(this); |
3557 | 0 | tcoffeeColour.setLabel( |
3558 | MessageManager.getString("label.colourScheme_t-coffeescores")); | |
3559 | // it will be enabled only if a score file is provided | |
3560 | 0 | tcoffeeColour.setEnabled(false); |
3561 | 0 | tcoffeeColour.addActionListener(this); |
3562 | 0 | conservationMenuItem |
3563 | .setLabel(MessageManager.getString("action.by_conservation")); | |
3564 | 0 | conservationMenuItem.addItemListener(this); |
3565 | 0 | noColourmenuItem.setLabel(MessageManager.getString("label.none")); |
3566 | 0 | noColourmenuItem.addActionListener(this); |
3567 | 0 | abovePIDThreshold.setLabel( |
3568 | MessageManager.getString("label.above_identity_threshold")); | |
3569 | 0 | abovePIDThreshold.addItemListener(this); |
3570 | 0 | nucleotideColour.setLabel( |
3571 | MessageManager.getString("label.colourScheme_nucleotide")); | |
3572 | 0 | nucleotideColour.addActionListener(this); |
3573 | 0 | modifyPID.setLabel( |
3574 | MessageManager.getString("label.modify_identity_threshold")); | |
3575 | 0 | modifyPID.setEnabled(abovePIDThreshold.getState()); |
3576 | 0 | modifyPID.addActionListener(this); |
3577 | 0 | modifyConservation.setLabel(MessageManager |
3578 | .getString("label.modify_conservation_threshold")); | |
3579 | 0 | modifyConservation.setEnabled(conservationMenuItem.getState()); |
3580 | 0 | modifyConservation.addActionListener(this); |
3581 | 0 | annotationColour |
3582 | .setLabel(MessageManager.getString("action.by_annotation")); | |
3583 | 0 | annotationColour.addActionListener(this); |
3584 | ||
3585 | /* | |
3586 | * Configure Calculate menu items and actions | |
3587 | */ | |
3588 | 0 | sortPairwiseMenuItem |
3589 | .setLabel(MessageManager.getString("action.by_pairwise_id")); | |
3590 | 0 | sortPairwiseMenuItem.addActionListener(this); |
3591 | 0 | sortIDMenuItem.setLabel(MessageManager.getString("action.by_id")); |
3592 | 0 | sortIDMenuItem.addActionListener(this); |
3593 | 0 | sortLengthMenuItem |
3594 | .setLabel(MessageManager.getString("action.by_length")); | |
3595 | 0 | sortLengthMenuItem.addActionListener(this); |
3596 | 0 | sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group")); |
3597 | 0 | sortGroupMenuItem.addActionListener(this); |
3598 | 0 | pairwiseAlignmentMenuItem.setLabel( |
3599 | MessageManager.getString("action.pairwise_alignment")); | |
3600 | 0 | pairwiseAlignmentMenuItem.addActionListener(this); |
3601 | 0 | PCAMenuItem.setLabel( |
3602 | MessageManager.getString("label.principal_component_analysis")); | |
3603 | 0 | PCAMenuItem.addActionListener(this); |
3604 | 0 | autoCalculate = new CheckboxMenuItem( |
3605 | MessageManager.getString("label.autocalculate_consensus"), | |
3606 | true); | |
3607 | 0 | averageDistanceTreeMenuItem.setLabel( |
3608 | MessageManager.getString("label.average_distance_identity")); | |
3609 | 0 | averageDistanceTreeMenuItem.addActionListener(this); |
3610 | 0 | neighbourTreeMenuItem.setLabel( |
3611 | MessageManager.getString("label.neighbour_joining_identity")); | |
3612 | 0 | neighbourTreeMenuItem.addActionListener(this); |
3613 | 0 | avDistanceTreeBlosumMenuItem.setLabel( |
3614 | MessageManager.getString("label.average_distance_blosum62")); | |
3615 | 0 | avDistanceTreeBlosumMenuItem.addActionListener(this); |
3616 | 0 | njTreeBlosumMenuItem |
3617 | .setLabel(MessageManager.getString("label.neighbour_blosum62")); | |
3618 | 0 | njTreeBlosumMenuItem.addActionListener(this); |
3619 | 0 | sortByTreeMenu |
3620 | .setLabel(MessageManager.getString("action.by_tree_order")); | |
3621 | 0 | Menu sortMenu = new Menu(MessageManager.getString("action.sort")); |
3622 | 0 | Menu calculateTreeMenu = new Menu( |
3623 | MessageManager.getString("action.calculate_tree")); | |
3624 | 0 | autoCalculate.addItemListener(this); |
3625 | 0 | sortByTree.addItemListener(this); |
3626 | ||
3627 | /* | |
3628 | * Configure Help menu items and actions | |
3629 | */ | |
3630 | 0 | Menu helpMenu = new Menu(MessageManager.getString("action.help")); |
3631 | 0 | documentation.setLabel(MessageManager.getString("label.documentation")); |
3632 | 0 | documentation.addActionListener(this); |
3633 | 0 | about.setLabel(MessageManager.getString("label.about")); |
3634 | 0 | about.addActionListener(this); |
3635 | ||
3636 | /* | |
3637 | * Add top level menus to frame | |
3638 | */ | |
3639 | 0 | alignFrameMenuBar.add(fileMenu); |
3640 | 0 | Menu editMenu = new Menu(MessageManager.getString("action.edit")); |
3641 | 0 | alignFrameMenuBar.add(editMenu); |
3642 | 0 | Menu selectMenu = new Menu(MessageManager.getString("action.select")); |
3643 | 0 | alignFrameMenuBar.add(selectMenu); |
3644 | 0 | Menu viewMenu = new Menu(MessageManager.getString("action.view")); |
3645 | 0 | alignFrameMenuBar.add(viewMenu); |
3646 | 0 | Menu annotationsMenu = new Menu( |
3647 | MessageManager.getString("action.annotations")); | |
3648 | 0 | alignFrameMenuBar.add(annotationsMenu); |
3649 | 0 | Menu formatMenu = new Menu(MessageManager.getString("action.format")); |
3650 | 0 | alignFrameMenuBar.add(formatMenu); |
3651 | 0 | Menu colourMenu = new Menu(MessageManager.getString("action.colour")); |
3652 | 0 | alignFrameMenuBar.add(colourMenu); |
3653 | 0 | Menu calculateMenu = new Menu( |
3654 | MessageManager.getString("action.calculate")); | |
3655 | 0 | alignFrameMenuBar.add(calculateMenu); |
3656 | 0 | alignFrameMenuBar.add(helpMenu); |
3657 | ||
3658 | /* | |
3659 | * File menu | |
3660 | */ | |
3661 | 0 | fileMenu.add(inputText); |
3662 | 0 | fileMenu.add(loadTree); |
3663 | 0 | fileMenu.add(loadAnnotations); |
3664 | 0 | fileMenu.addSeparator(); |
3665 | 0 | fileMenu.add(outputTextboxMenu); |
3666 | 0 | fileMenu.add(outputFeatures); |
3667 | 0 | fileMenu.add(outputAnnotations); |
3668 | 0 | if (jalviewServletURL != null) |
3669 | { | |
3670 | 0 | fileMenu.add(loadApplication); |
3671 | } | |
3672 | 0 | fileMenu.addSeparator(); |
3673 | 0 | fileMenu.add(closeMenuItem); |
3674 | ||
3675 | /* | |
3676 | * Edit menu | |
3677 | */ | |
3678 | 0 | editMenu.add(undoMenuItem); |
3679 | 0 | editMenu.add(redoMenuItem); |
3680 | 0 | editMenu.add(cut); |
3681 | 0 | editMenu.add(copy); |
3682 | 0 | pasteMenu.add(pasteNew); |
3683 | 0 | pasteMenu.add(pasteThis); |
3684 | 0 | editMenu.add(pasteMenu); |
3685 | 0 | editMenu.add(delete); |
3686 | 0 | editMenu.addSeparator(); |
3687 | 0 | editMenu.add(remove2LeftMenuItem); |
3688 | 0 | editMenu.add(remove2RightMenuItem); |
3689 | 0 | editMenu.add(removeGappedColumnMenuItem); |
3690 | 0 | editMenu.add(removeAllGapsMenuItem); |
3691 | 0 | editMenu.add(removeRedundancyMenuItem); |
3692 | ||
3693 | /* | |
3694 | * Select menu | |
3695 | */ | |
3696 | 0 | selectMenu.add(findMenuItem); |
3697 | 0 | selectMenu.addSeparator(); |
3698 | 0 | selectMenu.add(selectAllSequenceMenuItem); |
3699 | 0 | selectMenu.add(deselectAllSequenceMenuItem); |
3700 | 0 | selectMenu.add(invertSequenceMenuItem); |
3701 | 0 | selectMenu.add(invertColSel); |
3702 | 0 | selectMenu.add(createGroup); |
3703 | 0 | selectMenu.add(unGroup); |
3704 | 0 | selectMenu.add(grpsFromSelection); |
3705 | 0 | selectMenu.add(deleteGroups); |
3706 | 0 | selectMenu.add(annotationColumnSelection); |
3707 | ||
3708 | /* | |
3709 | * View menu | |
3710 | */ | |
3711 | 0 | viewMenu.add(newView); |
3712 | 0 | viewMenu.addSeparator(); |
3713 | 0 | showMenu.add(showColumns); |
3714 | 0 | showMenu.add(showSeqs); |
3715 | 0 | showMenu.add(showAllHidden); |
3716 | 0 | viewMenu.add(showMenu); |
3717 | 0 | hideMenu.add(hideColumns); |
3718 | 0 | hideMenu.add(hideSequences); |
3719 | 0 | hideMenu.add(hideAllSelection); |
3720 | 0 | hideMenu.add(hideAllButSelection); |
3721 | 0 | viewMenu.add(hideMenu); |
3722 | 0 | viewMenu.addSeparator(); |
3723 | 0 | viewMenu.add(followMouseOverFlag); |
3724 | 0 | viewMenu.addSeparator(); |
3725 | 0 | viewMenu.add(sequenceFeatures); |
3726 | 0 | viewMenu.add(featureSettings); |
3727 | 0 | viewMenu.addSeparator(); |
3728 | 0 | viewMenu.add(alProperties); |
3729 | 0 | viewMenu.addSeparator(); |
3730 | 0 | viewMenu.add(overviewMenuItem); |
3731 | ||
3732 | /* | |
3733 | * Annotations menu | |
3734 | */ | |
3735 | 0 | annotationsMenu.add(annotationPanelMenuItem); |
3736 | 0 | annotationsMenu.addSeparator(); |
3737 | 0 | annotationsMenu.add(showAlignmentAnnotations); |
3738 | 0 | annotationsMenu.add(showSequenceAnnotations); |
3739 | 0 | annotationsMenu.add(sortAnnBySequence); |
3740 | 0 | annotationsMenu.add(sortAnnByLabel); |
3741 | 0 | annotationsMenu.addSeparator(); |
3742 | 0 | autoAnnMenu.add(showAutoFirst); |
3743 | 0 | autoAnnMenu.add(showAutoLast); |
3744 | 0 | autoAnnMenu.addSeparator(); |
3745 | 0 | autoAnnMenu.add(applyAutoAnnotationSettings); |
3746 | 0 | autoAnnMenu.add(showConsensusHistogram); |
3747 | 0 | autoAnnMenu.add(showSequenceLogo); |
3748 | 0 | autoAnnMenu.add(normSequenceLogo); |
3749 | 0 | autoAnnMenu.addSeparator(); |
3750 | 0 | autoAnnMenu.add(showGroupConservation); |
3751 | 0 | autoAnnMenu.add(showGroupConsensus); |
3752 | 0 | annotationsMenu.add(autoAnnMenu); |
3753 | ||
3754 | /* | |
3755 | * Format menu | |
3756 | */ | |
3757 | 0 | formatMenu.add(font); |
3758 | 0 | formatMenu.add(seqLimits); |
3759 | 0 | formatMenu.add(wrapMenuItem); |
3760 | 0 | formatMenu.add(scaleAbove); |
3761 | 0 | formatMenu.add(scaleLeft); |
3762 | 0 | formatMenu.add(scaleRight); |
3763 | 0 | formatMenu.add(viewBoxesMenuItem); |
3764 | 0 | formatMenu.add(viewTextMenuItem); |
3765 | 0 | formatMenu.add(colourTextMenuItem); |
3766 | 0 | formatMenu.add(displayNonconservedMenuItem); |
3767 | 0 | formatMenu.add(renderGapsMenuItem); |
3768 | 0 | formatMenu.add(centreColumnLabelFlag); |
3769 | ||
3770 | /* | |
3771 | * Colour menu | |
3772 | */ | |
3773 | 0 | colourMenu.add(applyToAllGroups); |
3774 | 0 | colourMenu.addSeparator(); |
3775 | 0 | colourMenu.add(noColourmenuItem); |
3776 | 0 | colourMenu.add(clustalColour); |
3777 | 0 | colourMenu.add(BLOSUM62Colour); |
3778 | 0 | colourMenu.add(PIDColour); |
3779 | 0 | colourMenu.add(zappoColour); |
3780 | 0 | colourMenu.add(taylorColour); |
3781 | 0 | colourMenu.add(hydrophobicityColour); |
3782 | 0 | colourMenu.add(helixColour); |
3783 | 0 | colourMenu.add(strandColour); |
3784 | 0 | colourMenu.add(turnColour); |
3785 | 0 | colourMenu.add(buriedColour); |
3786 | 0 | colourMenu.add(nucleotideColour); |
3787 | 0 | colourMenu.add(purinePyrimidineColour); |
3788 | // colourMenu.add(RNAInteractionColour); | |
3789 | 0 | colourMenu.add(tcoffeeColour); |
3790 | 0 | colourMenu.add(userDefinedColour); |
3791 | 0 | colourMenu.addSeparator(); |
3792 | 0 | colourMenu.add(conservationMenuItem); |
3793 | 0 | colourMenu.add(modifyConservation); |
3794 | 0 | colourMenu.add(abovePIDThreshold); |
3795 | 0 | colourMenu.add(modifyPID); |
3796 | 0 | colourMenu.add(annotationColour); |
3797 | 0 | colourMenu.add(RNAHelixColour); |
3798 | ||
3799 | /* | |
3800 | * Calculate menu | |
3801 | */ | |
3802 | 0 | sortMenu.add(sortIDMenuItem); |
3803 | 0 | sortMenu.add(sortLengthMenuItem); |
3804 | 0 | sortMenu.add(sortByTreeMenu); |
3805 | 0 | sortMenu.add(sortGroupMenuItem); |
3806 | 0 | sortMenu.add(sortPairwiseMenuItem); |
3807 | 0 | calculateMenu.add(sortMenu); |
3808 | 0 | calculateTreeMenu.add(averageDistanceTreeMenuItem); |
3809 | 0 | calculateTreeMenu.add(neighbourTreeMenuItem); |
3810 | 0 | calculateTreeMenu.add(avDistanceTreeBlosumMenuItem); |
3811 | 0 | calculateTreeMenu.add(njTreeBlosumMenuItem); |
3812 | 0 | calculateMenu.add(calculateTreeMenu); |
3813 | 0 | calculateMenu.addSeparator(); |
3814 | 0 | calculateMenu.add(pairwiseAlignmentMenuItem); |
3815 | 0 | calculateMenu.add(PCAMenuItem); |
3816 | 0 | calculateMenu.add(autoCalculate); |
3817 | 0 | calculateMenu.add(sortByTree); |
3818 | ||
3819 | /* | |
3820 | * Help menu | |
3821 | */ | |
3822 | 0 | helpMenu.add(documentation); |
3823 | 0 | helpMenu.add(about); |
3824 | ||
3825 | /* | |
3826 | * Status bar | |
3827 | */ | |
3828 | 0 | statusBar.setBackground(Color.white); |
3829 | 0 | statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
3830 | 0 | setStatus(MessageManager.getString("label.status_bar")); |
3831 | 0 | this.add(statusBar, BorderLayout.SOUTH); |
3832 | } | |
3833 | ||
3834 | 0 | @Override |
3835 | public void setStatus(String string) | |
3836 | { | |
3837 | 0 | statusBar.setText(string); |
3838 | }; | |
3839 | ||
3840 | MenuItem featureSettings = new MenuItem(); | |
3841 | ||
3842 | CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); | |
3843 | ||
3844 | MenuItem annotationColour = new MenuItem(); | |
3845 | ||
3846 | MenuItem annotationColumnSelection = new MenuItem(); | |
3847 | ||
3848 | MenuItem invertColSel = new MenuItem(); | |
3849 | ||
3850 | MenuItem showColumns = new MenuItem(); | |
3851 | ||
3852 | MenuItem showSeqs = new MenuItem(); | |
3853 | ||
3854 | MenuItem hideColumns = new MenuItem(); | |
3855 | ||
3856 | MenuItem hideSequences = new MenuItem(); | |
3857 | ||
3858 | MenuItem hideAllButSelection = new MenuItem(); | |
3859 | ||
3860 | MenuItem hideAllSelection = new MenuItem(); | |
3861 | ||
3862 | MenuItem showAllHidden = new MenuItem(); | |
3863 | ||
3864 | MenuItem newView = new MenuItem(); | |
3865 | ||
3866 | private CheckboxMenuItem showAlignmentAnnotations; | |
3867 | ||
3868 | private CheckboxMenuItem showSequenceAnnotations; | |
3869 | ||
3870 | private CheckboxMenuItem sortAnnBySequence; | |
3871 | ||
3872 | private CheckboxMenuItem sortAnnByLabel; | |
3873 | ||
3874 | private CheckboxMenuItem showAutoFirst; | |
3875 | ||
3876 | private CheckboxMenuItem showAutoLast; | |
3877 | ||
3878 | private SplitFrame splitFrame; | |
3879 | ||
3880 | /** | |
3881 | * Attach the alignFrame panels after embedding menus, if necessary. This used | |
3882 | * to be called setEmbedded, but is now creates the dropdown menus in a | |
3883 | * platform independent manner to avoid OSX/Mac menu appendage daftness. | |
3884 | * | |
3885 | * @param reallyEmbedded | |
3886 | * true to attach the view to the applet area on the page rather than | |
3887 | * in a new window | |
3888 | */ | |
3889 | 0 | public void createAlignFrameWindow(boolean reallyEmbedded) |
3890 | { | |
3891 | 0 | if (reallyEmbedded) |
3892 | { | |
3893 | 0 | embedAlignFrameInApplet(viewport.applet); |
3894 | } | |
3895 | else | |
3896 | { | |
3897 | // ////// | |
3898 | // test and embed menu bar if necessary. | |
3899 | // | |
3900 | 0 | if (embedMenuIfNeeded(alignPanel)) |
3901 | { | |
3902 | /* | |
3903 | * adjust for status bar height too. ? pointless as overridden by layout | |
3904 | * manager | |
3905 | */ | |
3906 | 0 | alignPanel.setSize(getSize().width, |
3907 | getSize().height - statusBar.getHeight()); | |
3908 | } | |
3909 | 0 | add(statusBar, BorderLayout.SOUTH); |
3910 | 0 | add(alignPanel, BorderLayout.CENTER); |
3911 | // and register with the applet so it can pass external API calls to us | |
3912 | 0 | jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth, |
3913 | frameHeight); | |
3914 | } | |
3915 | } | |
3916 | ||
3917 | /** | |
3918 | * Add the components of this AlignFrame to the applet container. | |
3919 | * | |
3920 | * @param theApplet | |
3921 | */ | |
3922 | 0 | public void embedAlignFrameInApplet(final JalviewLite theApplet) |
3923 | { | |
3924 | // //// | |
3925 | // Explicitly build the embedded menu panel for the on-page applet | |
3926 | // | |
3927 | // view cannot be closed if its actually on the page | |
3928 | 0 | fileMenu.remove(closeMenuItem); |
3929 | 0 | fileMenu.remove(3); // Remove Separator |
3930 | // construct embedded menu, using default font | |
3931 | 0 | embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false); |
3932 | // and actually add the components to the applet area | |
3933 | 0 | theApplet.setLayout(new BorderLayout()); |
3934 | 0 | theApplet.add(embeddedMenu, BorderLayout.NORTH); |
3935 | 0 | theApplet.add(statusBar, BorderLayout.SOUTH); |
3936 | // TODO should size be left to the layout manager? | |
3937 | 0 | alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height |
3938 | - embeddedMenu.getHeight() - statusBar.getHeight()); | |
3939 | 0 | theApplet.add(alignPanel, BorderLayout.CENTER); |
3940 | 0 | final AlignFrame me = this; |
3941 | 0 | theApplet.addFocusListener(new FocusListener() |
3942 | { | |
3943 | ||
3944 | 0 | @Override |
3945 | public void focusLost(FocusEvent e) | |
3946 | { | |
3947 | 0 | if (theApplet.currentAlignFrame == me) |
3948 | { | |
3949 | 0 | theApplet.currentAlignFrame = null; |
3950 | } | |
3951 | } | |
3952 | ||
3953 | 0 | @Override |
3954 | public void focusGained(FocusEvent e) | |
3955 | { | |
3956 | 0 | theApplet.currentAlignFrame = me; |
3957 | } | |
3958 | }); | |
3959 | 0 | theApplet.validate(); |
3960 | } | |
3961 | ||
3962 | /** | |
3963 | * create a new binding between structures in an existing jmol viewer instance | |
3964 | * and an alignpanel with sequences that have existing PDBFile entries. Note, | |
3965 | * this does not open a new Jmol window, or modify the display of the | |
3966 | * structures in the original jmol window. Note This method doesn't work | |
3967 | * without an additional javascript library to exchange messages between the | |
3968 | * distinct applets. See http://issues.jalview.org/browse/JAL-621 | |
3969 | * | |
3970 | * @param jmolViewer | |
3971 | * JmolViewer instance | |
3972 | * @param sequenceIds | |
3973 | * - sequence Ids to search for associations | |
3974 | */ | |
3975 | 0 | public SequenceStructureBinding addStructureViewInstance( |
3976 | Object jmolviewer, String[] sequenceIds) | |
3977 | { | |
3978 | 0 | Viewer viewer = null; |
3979 | 0 | try |
3980 | { | |
3981 | 0 | viewer = (Viewer) jmolviewer; |
3982 | } catch (ClassCastException ex) | |
3983 | { | |
3984 | 0 | jalview.bin.Console.errPrintln( |
3985 | "Unsupported viewer object :" + jmolviewer.getClass()); | |
3986 | } | |
3987 | 0 | if (viewer == null) |
3988 | { | |
3989 | 0 | jalview.bin.Console |
3990 | .errPrintln("Can't use this object as a structure viewer:" | |
3991 | + jmolviewer.getClass()); | |
3992 | 0 | return null; |
3993 | } | |
3994 | 0 | SequenceI[] seqs = null; |
3995 | 0 | if (sequenceIds == null || sequenceIds.length == 0) |
3996 | { | |
3997 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
3998 | } | |
3999 | else | |
4000 | { | |
4001 | 0 | Vector sqi = new Vector(); |
4002 | 0 | AlignmentI al = viewport.getAlignment(); |
4003 | 0 | for (int sid = 0; sid < sequenceIds.length; sid++) |
4004 | { | |
4005 | 0 | SequenceI sq = al.findName(sequenceIds[sid]); |
4006 | 0 | if (sq != null) |
4007 | { | |
4008 | 0 | sqi.addElement(sq); |
4009 | } | |
4010 | } | |
4011 | 0 | if (sqi.size() > 0) |
4012 | { | |
4013 | 0 | seqs = new SequenceI[sqi.size()]; |
4014 | 0 | for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++) |
4015 | { | |
4016 | 0 | seqs[sid] = (SequenceI) sqi.elementAt(sid); |
4017 | } | |
4018 | } | |
4019 | else | |
4020 | { | |
4021 | 0 | return null; |
4022 | } | |
4023 | } | |
4024 | 0 | AAStructureBindingModel jmv = null; |
4025 | // TODO: search for a jmv that involves viewer | |
4026 | 0 | if (jmv == null) |
4027 | { // create a new viewer/jalview binding. | |
4028 | 0 | jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs }); |
4029 | } | |
4030 | 0 | return jmv; |
4031 | ||
4032 | } | |
4033 | ||
4034 | /** | |
4035 | * bind a pdb file to a sequence in the current view | |
4036 | * | |
4037 | * @param sequenceId | |
4038 | * - sequenceId within the dataset. | |
4039 | * @param pdbEntryString | |
4040 | * - the short name for the PDB file | |
4041 | * @param pdbFile | |
4042 | * - pdb file - either a URL or a valid PDB file. | |
4043 | * @return true if binding was as success TODO: consider making an exception | |
4044 | * structure for indicating when PDB parsing or sequenceId location | |
4045 | * fails. | |
4046 | */ | |
4047 | 0 | public boolean addPdbFile(String sequenceId, String pdbEntryString, |
4048 | String pdbFile) | |
4049 | { | |
4050 | 0 | SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId); |
4051 | 0 | boolean needtoadd = false; |
4052 | 0 | if (toaddpdb != null) |
4053 | { | |
4054 | 0 | Vector pdbe = toaddpdb.getAllPDBEntries(); |
4055 | 0 | PDBEntry pdbentry = null; |
4056 | 0 | if (pdbe != null && pdbe.size() > 0) |
4057 | { | |
4058 | 0 | for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++) |
4059 | { | |
4060 | 0 | pdbentry = (PDBEntry) pdbe.elementAt(pe); |
4061 | 0 | if (!pdbentry.getId().equals(pdbEntryString) |
4062 | && !pdbentry.getFile().equals(pdbFile)) | |
4063 | { | |
4064 | 0 | pdbentry = null; |
4065 | } | |
4066 | else | |
4067 | { | |
4068 | 0 | continue; |
4069 | } | |
4070 | } | |
4071 | } | |
4072 | 0 | if (pdbentry == null) |
4073 | { | |
4074 | 0 | pdbentry = new PDBEntry(); |
4075 | 0 | pdbentry.setId(pdbEntryString); |
4076 | 0 | pdbentry.setFile(pdbFile); |
4077 | 0 | needtoadd = true; // add this new entry to sequence. |
4078 | } | |
4079 | // resolve data source | |
4080 | // TODO: this code should be a refactored to an io package | |
4081 | 0 | DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile, |
4082 | FileFormat.PDB); | |
4083 | 0 | if (protocol == null) |
4084 | { | |
4085 | 0 | return false; |
4086 | } | |
4087 | 0 | if (needtoadd) |
4088 | { | |
4089 | 0 | pdbentry.setProperty("protocol", protocol); |
4090 | 0 | toaddpdb.addPDBId(pdbentry); |
4091 | 0 | alignPanel.getStructureSelectionManager() |
4092 | .registerPDBEntry(pdbentry); | |
4093 | } | |
4094 | } | |
4095 | 0 | return true; |
4096 | } | |
4097 | ||
4098 | 0 | private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains) |
4099 | { | |
4100 | 0 | if (seqs != null) |
4101 | { | |
4102 | 0 | Vector sequences = new Vector(); |
4103 | 0 | for (int i = 0; i < seqs.length; i++) |
4104 | { | |
4105 | 0 | if (seqs[i] != null) |
4106 | { | |
4107 | 0 | sequences |
4108 | .addElement(new Object[] | |
4109 | 0 | { seqs[i], (chains != null) ? chains[i] : null }); |
4110 | } | |
4111 | } | |
4112 | 0 | seqs = new SequenceI[sequences.size()]; |
4113 | 0 | chains = new String[sequences.size()]; |
4114 | 0 | for (int i = 0, isize = sequences.size(); i < isize; i++) |
4115 | { | |
4116 | 0 | Object[] oj = (Object[]) sequences.elementAt(i); |
4117 | ||
4118 | 0 | seqs[i] = (SequenceI) oj[0]; |
4119 | 0 | chains[i] = (String) oj[1]; |
4120 | } | |
4121 | } | |
4122 | 0 | return new Object[] { seqs, chains }; |
4123 | ||
4124 | } | |
4125 | ||
4126 | 0 | public void newStructureView(JalviewLite applet, PDBEntry pdb, |
4127 | SequenceI[] seqs, String[] chains, DataSourceType protocol) | |
4128 | { | |
4129 | // Scrub any null sequences from the array | |
4130 | 0 | Object[] sqch = cleanSeqChainArrays(seqs, chains); |
4131 | 0 | seqs = (SequenceI[]) sqch[0]; |
4132 | 0 | chains = (String[]) sqch[1]; |
4133 | 0 | if (seqs == null || seqs.length == 0) |
4134 | { | |
4135 | 0 | jalview.bin.Console.errPrintln( |
4136 | "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); | |
4137 | } | |
4138 | 0 | if (protocol == null) |
4139 | { | |
4140 | 0 | String sourceType = (String) pdb.getProperty("protocol"); |
4141 | 0 | try |
4142 | { | |
4143 | 0 | protocol = DataSourceType.valueOf(sourceType); |
4144 | } catch (IllegalArgumentException e) | |
4145 | { | |
4146 | // ignore | |
4147 | } | |
4148 | 0 | if (protocol == null) |
4149 | { | |
4150 | 0 | jalview.bin.Console |
4151 | .errPrintln("Couldn't work out protocol to open structure: " | |
4152 | + pdb.getId()); | |
4153 | 0 | return; |
4154 | } | |
4155 | } | |
4156 | 0 | if (applet.useXtrnalSviewer) |
4157 | { | |
4158 | // register the association(s) and quit, don't create any windows. | |
4159 | 0 | if (StructureSelectionManager.getStructureSelectionManager(applet) |
4160 | .setMapping(seqs, chains, pdb.getFile(), protocol, | |
4161 | null) == null) | |
4162 | { | |
4163 | 0 | jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile() |
4164 | + " (" + protocol + ") to any sequences"); | |
4165 | } | |
4166 | 0 | return; |
4167 | } | |
4168 | 0 | if (applet.isAlignPdbStructures() && applet.jmolAvailable) |
4169 | { | |
4170 | // can only do alignments with Jmol | |
4171 | // find the last jmol window assigned to this alignment | |
4172 | 0 | AppletJmol ajm = null, tajm; |
4173 | 0 | Vector jmols = applet.getAppletWindow(AppletJmol.class); |
4174 | 0 | for (int i = 0, iSize = jmols.size(); i < iSize; i++) |
4175 | { | |
4176 | 0 | tajm = (AppletJmol) jmols.elementAt(i); |
4177 | 0 | if (tajm.ap.alignFrame == this) |
4178 | { | |
4179 | 0 | ajm = tajm; |
4180 | 0 | break; |
4181 | } | |
4182 | } | |
4183 | 0 | if (ajm != null) |
4184 | { | |
4185 | 0 | jalview.bin.Console.errPrintln( |
4186 | "Incremental adding and aligning structure to existing Jmol view not yet implemented."); | |
4187 | // try and add the pdb structure | |
4188 | // ajm.addS | |
4189 | 0 | ajm = null; |
4190 | } | |
4191 | } | |
4192 | // otherwise, create a new window | |
4193 | 0 | if (applet.jmolAvailable) |
4194 | { | |
4195 | 0 | new AppletJmol(pdb, seqs, chains, alignPanel, protocol); |
4196 | 0 | applet.lastFrameX += 40; |
4197 | 0 | applet.lastFrameY += 40; |
4198 | } | |
4199 | else | |
4200 | { | |
4201 | 0 | new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol); |
4202 | } | |
4203 | ||
4204 | } | |
4205 | ||
4206 | 0 | public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb, |
4207 | SequenceI[][] seqs, String[][] chains, String[] protocols) | |
4208 | { | |
4209 | // TODO Auto-generated method stub | |
4210 | 0 | jalview.bin.Console |
4211 | .errPrintln("Aligned Structure View: Not yet implemented."); | |
4212 | } | |
4213 | ||
4214 | /** | |
4215 | * modify the current selection, providing the user has not made a selection | |
4216 | * already. | |
4217 | * | |
4218 | * @param sel | |
4219 | * - sequences from this alignment | |
4220 | * @param csel | |
4221 | * - columns to be selected on the alignment | |
4222 | */ | |
4223 | 0 | public void select(SequenceGroup sel, ColumnSelection csel, |
4224 | HiddenColumns hidden) | |
4225 | { | |
4226 | 0 | alignPanel.seqPanel.selection(sel, csel, hidden, null); |
4227 | } | |
4228 | ||
4229 | 0 | public void scrollTo(int row, int column) |
4230 | { | |
4231 | 0 | alignPanel.seqPanel.scrollTo(row, column); |
4232 | } | |
4233 | ||
4234 | 0 | public void scrollToRow(int row) |
4235 | { | |
4236 | 0 | alignPanel.seqPanel.scrollToRow(row); |
4237 | } | |
4238 | ||
4239 | 0 | public void scrollToColumn(int column) |
4240 | { | |
4241 | 0 | alignPanel.seqPanel.scrollToColumn(column); |
4242 | } | |
4243 | ||
4244 | /** | |
4245 | * @return the alignments unique ID. | |
4246 | */ | |
4247 | 0 | public String getSequenceSetId() |
4248 | { | |
4249 | 0 | return viewport.getSequenceSetId(); |
4250 | } | |
4251 | ||
4252 | /** | |
4253 | * Load the (T-Coffee) score file from the specified url | |
4254 | * | |
4255 | * @param source | |
4256 | * File/URL/T-COFFEE score file contents | |
4257 | * @throws IOException | |
4258 | * @return true if alignment was annotated with data from source | |
4259 | */ | |
4260 | 0 | public boolean loadScoreFile(String source) throws IOException |
4261 | { | |
4262 | ||
4263 | 0 | TCoffeeScoreFile file = new TCoffeeScoreFile(source, |
4264 | AppletFormatAdapter.checkProtocol(source)); | |
4265 | 0 | if (!file.isValid()) |
4266 | { | |
4267 | // TODO: raise dialog for gui | |
4268 | 0 | jalview.bin.Console.errPrintln("Problems parsing T-Coffee scores: " |
4269 | + file.getWarningMessage()); | |
4270 | 0 | jalview.bin.Console.errPrintln("Origin was:\n" + source); |
4271 | 0 | return false; |
4272 | } | |
4273 | ||
4274 | /* | |
4275 | * check that the score matrix matches the alignment dimensions | |
4276 | */ | |
4277 | 0 | AlignmentI aln; |
4278 | 0 | if ((aln = viewport.getAlignment()) != null |
4279 | && (aln.getHeight() != file.getHeight() | |
4280 | || aln.getWidth() != file.getWidth())) | |
4281 | { | |
4282 | // TODO: raise a dialog box here rather than bomb out. | |
4283 | 0 | jalview.bin.Console.errPrintln( |
4284 | "The scores matrix does not match the alignment dimensions"); | |
4285 | ||
4286 | } | |
4287 | ||
4288 | // TODO add parameter to indicate if matching should be done | |
4289 | 0 | if (file.annotateAlignment(alignPanel.getAlignment(), false)) |
4290 | { | |
4291 | 0 | alignPanel.fontChanged(); |
4292 | 0 | tcoffeeColour.setEnabled(true); |
4293 | // switch to this color | |
4294 | 0 | changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); |
4295 | 0 | return true; |
4296 | } | |
4297 | else | |
4298 | { | |
4299 | 0 | jalview.bin.Console.errPrintln("Problems resolving T-Coffee scores:"); |
4300 | 0 | if (file.getWarningMessage() != null) |
4301 | { | |
4302 | 0 | jalview.bin.Console.errPrintln(file.getWarningMessage()); |
4303 | } | |
4304 | } | |
4305 | 0 | return false; |
4306 | } | |
4307 | ||
4308 | 0 | public SplitFrame getSplitFrame() |
4309 | { | |
4310 | 0 | return this.splitFrame; |
4311 | } | |
4312 | ||
4313 | 0 | public void setSplitFrame(SplitFrame sf) |
4314 | { | |
4315 | 0 | this.splitFrame = sf; |
4316 | } | |
4317 | ||
4318 | // may not need this | |
4319 | 0 | @Override |
4320 | public void setShowSeqFeatures(boolean b) | |
4321 | { | |
4322 | // showSeqFeatures.setSelected(b); | |
4323 | 0 | viewport.setShowSequenceFeatures(b); |
4324 | ||
4325 | } | |
4326 | ||
4327 | 0 | @Override |
4328 | public void setMenusForViewport() | |
4329 | { | |
4330 | // setMenusFromViewport(viewport); | |
4331 | ||
4332 | } | |
4333 | ||
4334 | 0 | @Override |
4335 | public void refreshFeatureUI(boolean enableIfNecessary) | |
4336 | { | |
4337 | 0 | if (enableIfNecessary) |
4338 | { | |
4339 | 0 | sequenceFeatures.setState(true); |
4340 | 0 | alignPanel.av.setShowSequenceFeatures(true); |
4341 | } | |
4342 | } | |
4343 | ||
4344 | 0 | @Override |
4345 | public FeatureSettingsControllerI getFeatureSettingsUI() | |
4346 | { | |
4347 | 0 | return alignPanel.av.featureSettings; |
4348 | } | |
4349 | ||
4350 | 0 | @Override |
4351 | public FeatureSettingsControllerI showFeatureSettingsUI() | |
4352 | { | |
4353 | 0 | return new FeatureSettings(alignPanel); |
4354 | } | |
4355 | ||
4356 | private Rectangle fs_bounds = null; | |
4357 | ||
4358 | 0 | @Override |
4359 | public void setFeatureSettingsGeometry(Rectangle bounds) | |
4360 | { | |
4361 | 0 | fs_bounds = bounds; |
4362 | } | |
4363 | ||
4364 | 0 | @Override |
4365 | public Rectangle getFeatureSettingsGeometry() | |
4366 | { | |
4367 | 0 | return fs_bounds; |
4368 | } | |
4369 | ||
4370 | } |