Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
AlignFrame | 180 | 1,863 | 730 | ||
PrintThread | 6367 | 9 | 5 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.gui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.Color; | |
25 | import java.awt.Component; | |
26 | import java.awt.Rectangle; | |
27 | import java.awt.Toolkit; | |
28 | import java.awt.datatransfer.Clipboard; | |
29 | import java.awt.datatransfer.DataFlavor; | |
30 | import java.awt.datatransfer.StringSelection; | |
31 | import java.awt.datatransfer.Transferable; | |
32 | import java.awt.dnd.DnDConstants; | |
33 | import java.awt.dnd.DropTargetDragEvent; | |
34 | import java.awt.dnd.DropTargetDropEvent; | |
35 | import java.awt.dnd.DropTargetEvent; | |
36 | import java.awt.dnd.DropTargetListener; | |
37 | import java.awt.event.ActionEvent; | |
38 | import java.awt.event.ActionListener; | |
39 | import java.awt.event.FocusAdapter; | |
40 | import java.awt.event.FocusEvent; | |
41 | import java.awt.event.ItemEvent; | |
42 | import java.awt.event.ItemListener; | |
43 | import java.awt.event.KeyAdapter; | |
44 | import java.awt.event.KeyEvent; | |
45 | import java.awt.event.MouseEvent; | |
46 | import java.awt.print.PageFormat; | |
47 | import java.awt.print.PrinterJob; | |
48 | import java.beans.PropertyChangeEvent; | |
49 | import java.io.File; | |
50 | import java.io.FileWriter; | |
51 | import java.io.IOException; | |
52 | import java.io.OutputStreamWriter; | |
53 | import java.io.PrintWriter; | |
54 | import java.net.URL; | |
55 | import java.util.ArrayList; | |
56 | import java.util.Arrays; | |
57 | import java.util.Deque; | |
58 | import java.util.Enumeration; | |
59 | import java.util.Hashtable; | |
60 | import java.util.List; | |
61 | import java.util.Locale; | |
62 | import java.util.Vector; | |
63 | ||
64 | import javax.swing.AbstractButton; | |
65 | import javax.swing.ButtonGroup; | |
66 | import javax.swing.JCheckBoxMenuItem; | |
67 | import javax.swing.JComponent; | |
68 | import javax.swing.JEditorPane; | |
69 | import javax.swing.JInternalFrame; | |
70 | import javax.swing.JLabel; | |
71 | import javax.swing.JLayeredPane; | |
72 | import javax.swing.JMenu; | |
73 | import javax.swing.JMenuItem; | |
74 | import javax.swing.JPanel; | |
75 | import javax.swing.JProgressBar; | |
76 | import javax.swing.JRadioButtonMenuItem; | |
77 | import javax.swing.JScrollPane; | |
78 | import javax.swing.SwingUtilities; | |
79 | ||
80 | import ext.vamsas.ServiceHandle; | |
81 | import jalview.analysis.AlignmentSorter; | |
82 | import jalview.analysis.AlignmentUtils; | |
83 | import jalview.analysis.CrossRef; | |
84 | import jalview.analysis.Dna; | |
85 | import jalview.analysis.GeneticCodeI; | |
86 | import jalview.analysis.ParseProperties; | |
87 | import jalview.analysis.SequenceIdMatcher; | |
88 | import jalview.api.AlignCalcWorkerI; | |
89 | import jalview.api.AlignExportSettingsI; | |
90 | import jalview.api.AlignViewControllerGuiI; | |
91 | import jalview.api.AlignViewControllerI; | |
92 | import jalview.api.AlignViewportI; | |
93 | import jalview.api.AlignmentViewPanel; | |
94 | import jalview.api.FeatureSettingsControllerI; | |
95 | import jalview.api.FeatureSettingsModelI; | |
96 | import jalview.api.SplitContainerI; | |
97 | import jalview.api.ViewStyleI; | |
98 | import jalview.api.analysis.SimilarityParamsI; | |
99 | import jalview.bin.Cache; | |
100 | import jalview.bin.Console; | |
101 | import jalview.bin.Jalview; | |
102 | import jalview.bin.groovy.JalviewObjectI; | |
103 | import jalview.commands.CommandI; | |
104 | import jalview.commands.EditCommand; | |
105 | import jalview.commands.EditCommand.Action; | |
106 | import jalview.commands.OrderCommand; | |
107 | import jalview.commands.RemoveGapColCommand; | |
108 | import jalview.commands.RemoveGapsCommand; | |
109 | import jalview.commands.SlideSequencesCommand; | |
110 | import jalview.commands.TrimRegionCommand; | |
111 | import jalview.datamodel.AlignExportSettingsAdapter; | |
112 | import jalview.datamodel.AlignedCodonFrame; | |
113 | import jalview.datamodel.Alignment; | |
114 | import jalview.datamodel.AlignmentAnnotation; | |
115 | import jalview.datamodel.AlignmentExportData; | |
116 | import jalview.datamodel.AlignmentI; | |
117 | import jalview.datamodel.AlignmentOrder; | |
118 | import jalview.datamodel.AlignmentView; | |
119 | import jalview.datamodel.ColumnSelection; | |
120 | import jalview.datamodel.ContactMatrixI; | |
121 | import jalview.datamodel.HiddenColumns; | |
122 | import jalview.datamodel.PDBEntry; | |
123 | import jalview.datamodel.SeqCigar; | |
124 | import jalview.datamodel.Sequence; | |
125 | import jalview.datamodel.SequenceGroup; | |
126 | import jalview.datamodel.SequenceI; | |
127 | import jalview.gui.ColourMenuHelper.ColourChangeListener; | |
128 | import jalview.gui.ViewSelectionMenu.ViewSetProvider; | |
129 | import jalview.io.AlignmentProperties; | |
130 | import jalview.io.AnnotationFile; | |
131 | import jalview.io.BackupFiles; | |
132 | import jalview.io.BioJsHTMLOutput; | |
133 | import jalview.io.DataSourceType; | |
134 | import jalview.io.FileFormat; | |
135 | import jalview.io.FileFormatI; | |
136 | import jalview.io.FileFormats; | |
137 | import jalview.io.FileLoader; | |
138 | import jalview.io.FileParse; | |
139 | import jalview.io.FormatAdapter; | |
140 | import jalview.io.HtmlSvgOutput; | |
141 | import jalview.io.IdentifyFile; | |
142 | import jalview.io.JPredFile; | |
143 | import jalview.io.JalviewFileChooser; | |
144 | import jalview.io.JalviewFileView; | |
145 | import jalview.io.JnetAnnotationMaker; | |
146 | import jalview.io.NewickFile; | |
147 | import jalview.io.ScoreMatrixFile; | |
148 | import jalview.io.TCoffeeScoreFile; | |
149 | import jalview.io.exceptions.ImageOutputException; | |
150 | import jalview.io.vcf.VCFLoader; | |
151 | import jalview.jbgui.GAlignFrame; | |
152 | import jalview.project.Jalview2XML; | |
153 | import jalview.schemes.ColourSchemeI; | |
154 | import jalview.schemes.ColourSchemes; | |
155 | import jalview.schemes.ResidueColourScheme; | |
156 | import jalview.schemes.TCoffeeColourScheme; | |
157 | import jalview.util.Constants; | |
158 | import jalview.util.HttpUtils; | |
159 | import jalview.util.ImageMaker.TYPE; | |
160 | import jalview.util.MessageManager; | |
161 | import jalview.util.Platform; | |
162 | import jalview.util.imagemaker.BitmapImageSizing; | |
163 | import jalview.viewmodel.AlignmentViewport; | |
164 | import jalview.viewmodel.ViewportRanges; | |
165 | import jalview.workers.SecondaryStructureConsensusThread; | |
166 | import jalview.ws.DBRefFetcher; | |
167 | import jalview.ws.DBRefFetcher.FetchFinishedListenerI; | |
168 | import jalview.ws.jws1.Discoverer; | |
169 | import jalview.ws.jws2.Jws2Discoverer; | |
170 | import jalview.ws.jws2.jabaws2.Jws2Instance; | |
171 | import jalview.ws.seqfetcher.DbSourceProxy; | |
172 | ||
173 | /** | |
174 | * DOCUMENT ME! | |
175 | * | |
176 | * @author $author$ | |
177 | * @version $Revision$ | |
178 | */ | |
179 | @SuppressWarnings("serial") | |
180 | public class AlignFrame extends GAlignFrame implements DropTargetListener, | |
181 | IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener | |
182 | { | |
183 | ||
184 | public static final int DEFAULT_WIDTH = 700; | |
185 | ||
186 | public static final int DEFAULT_HEIGHT = 500; | |
187 | ||
188 | /* | |
189 | * The currently displayed panel (selected tabbed view if more than one) | |
190 | */ | |
191 | public AlignmentPanel alignPanel; | |
192 | ||
193 | AlignViewport viewport; | |
194 | ||
195 | public AlignViewControllerI avc; | |
196 | ||
197 | List<AlignmentPanel> alignPanels = new ArrayList<>(); | |
198 | ||
199 | /** | |
200 | * Last format used to load or save alignments in this window | |
201 | */ | |
202 | FileFormatI currentFileFormat = null; | |
203 | ||
204 | /** | |
205 | * Current filename for this alignment | |
206 | */ | |
207 | String fileName = null; | |
208 | ||
209 | File fileObject; | |
210 | ||
211 | /** | |
212 | * Creates a new AlignFrame object with specific width and height. | |
213 | * | |
214 | * @param al | |
215 | * @param width | |
216 | * @param height | |
217 | */ | |
218 | 357 | public AlignFrame(AlignmentI al, int width, int height) |
219 | { | |
220 | 357 | this(al, null, width, height); |
221 | } | |
222 | ||
223 | /** | |
224 | * Creates a new AlignFrame object with specific width, height and | |
225 | * sequenceSetId | |
226 | * | |
227 | * @param al | |
228 | * @param width | |
229 | * @param height | |
230 | * @param sequenceSetId | |
231 | */ | |
232 | 0 | public AlignFrame(AlignmentI al, int width, int height, |
233 | String sequenceSetId) | |
234 | { | |
235 | 0 | this(al, null, width, height, sequenceSetId); |
236 | } | |
237 | ||
238 | /** | |
239 | * Creates a new AlignFrame object with specific width, height and | |
240 | * sequenceSetId | |
241 | * | |
242 | * @param al | |
243 | * @param width | |
244 | * @param height | |
245 | * @param sequenceSetId | |
246 | * @param viewId | |
247 | */ | |
248 | 85 | public AlignFrame(AlignmentI al, int width, int height, |
249 | String sequenceSetId, String viewId) | |
250 | { | |
251 | 85 | this(al, null, width, height, sequenceSetId, viewId); |
252 | } | |
253 | ||
254 | /** | |
255 | * new alignment window with hidden columns | |
256 | * | |
257 | * @param al | |
258 | * AlignmentI | |
259 | * @param hiddenColumns | |
260 | * ColumnSelection or null | |
261 | * @param width | |
262 | * Width of alignment frame | |
263 | * @param height | |
264 | * height of frame. | |
265 | */ | |
266 | 357 | public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, |
267 | int height) | |
268 | { | |
269 | 357 | this(al, hiddenColumns, width, height, null); |
270 | } | |
271 | ||
272 | /** | |
273 | * Create alignment frame for al with hiddenColumns, a specific width and | |
274 | * height, and specific sequenceId | |
275 | * | |
276 | * @param al | |
277 | * @param hiddenColumns | |
278 | * @param width | |
279 | * @param height | |
280 | * @param sequenceSetId | |
281 | * (may be null) | |
282 | */ | |
283 | 357 | public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, |
284 | int height, String sequenceSetId) | |
285 | { | |
286 | 357 | this(al, hiddenColumns, width, height, sequenceSetId, null); |
287 | } | |
288 | ||
289 | /** | |
290 | * Create alignment frame for al with hiddenColumns, a specific width and | |
291 | * height, and specific sequenceId | |
292 | * | |
293 | * @param al | |
294 | * @param hiddenColumns | |
295 | * @param width | |
296 | * @param height | |
297 | * @param sequenceSetId | |
298 | * (may be null) | |
299 | * @param viewId | |
300 | * (may be null) | |
301 | */ | |
302 | 442 | public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, |
303 | int height, String sequenceSetId, String viewId) | |
304 | { | |
305 | 442 | setSize(width, height); |
306 | ||
307 | 442 | if (al.getDataset() == null) |
308 | { | |
309 | 342 | al.setDataset(null); |
310 | } | |
311 | ||
312 | 442 | viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); |
313 | ||
314 | 442 | alignPanel = new AlignmentPanel(this, viewport); |
315 | ||
316 | 442 | addAlignmentPanel(alignPanel, true); |
317 | 442 | init(); |
318 | } | |
319 | ||
320 | 5 | public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, |
321 | HiddenColumns hiddenColumns, int width, int height) | |
322 | { | |
323 | 5 | setSize(width, height); |
324 | ||
325 | 5 | if (al.getDataset() == null) |
326 | { | |
327 | 5 | al.setDataset(null); |
328 | } | |
329 | ||
330 | 5 | viewport = new AlignViewport(al, hiddenColumns); |
331 | ||
332 | 5 | if (hiddenSeqs != null && hiddenSeqs.length > 0) |
333 | { | |
334 | 5 | viewport.hideSequence(hiddenSeqs); |
335 | } | |
336 | 5 | alignPanel = new AlignmentPanel(this, viewport); |
337 | 5 | addAlignmentPanel(alignPanel, true); |
338 | 5 | init(); |
339 | } | |
340 | ||
341 | /** | |
342 | * Make a new AlignFrame from existing alignmentPanels | |
343 | * | |
344 | * @param ap | |
345 | * AlignmentPanel | |
346 | * @param av | |
347 | * AlignViewport | |
348 | */ | |
349 | 5 | public AlignFrame(AlignmentPanel ap) |
350 | { | |
351 | 5 | viewport = ap.av; |
352 | 5 | alignPanel = ap; |
353 | 5 | addAlignmentPanel(ap, false); |
354 | 5 | init(); |
355 | } | |
356 | ||
357 | /** | |
358 | * initalise the alignframe from the underlying viewport data and the | |
359 | * configurations | |
360 | */ | |
361 | 452 | void init() |
362 | { | |
363 | 452 | setFrameIcon(null); |
364 | ||
365 | // setBackground(Color.white); // BH 2019 | |
366 | ||
367 | 452 | if (!Jalview.isHeadlessMode()) |
368 | { | |
369 | 389 | progressBar = new ProgressBar(this.statusPanel, this.statusBar); |
370 | } | |
371 | ||
372 | 452 | avc = new jalview.controller.AlignViewController(this, viewport, |
373 | alignPanel); | |
374 | 452 | if (viewport.getAlignmentConservationAnnotation() == null) |
375 | { | |
376 | // BLOSUM62Colour.setEnabled(false); | |
377 | 82 | conservationMenuItem.setEnabled(false); |
378 | 82 | modifyConservation.setEnabled(false); |
379 | // PIDColour.setEnabled(false); | |
380 | // abovePIDThreshold.setEnabled(false); | |
381 | // modifyPID.setEnabled(false); | |
382 | } | |
383 | ||
384 | 452 | String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort"); |
385 | ||
386 | 452 | if (sortby.equals("Id")) |
387 | { | |
388 | 0 | sortIDMenuItem_actionPerformed(null); |
389 | } | |
390 | 452 | else if (sortby.equals("Pairwise Identity")) |
391 | { | |
392 | 0 | sortPairwiseMenuItem_actionPerformed(null); |
393 | } | |
394 | ||
395 | 452 | this.alignPanel.av |
396 | .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); | |
397 | ||
398 | 452 | setMenusFromViewport(viewport); |
399 | 452 | buildSortByAnnotationScoresMenu(); |
400 | 452 | calculateTree.addActionListener(new ActionListener() |
401 | { | |
402 | ||
403 | 0 | @Override |
404 | public void actionPerformed(ActionEvent e) | |
405 | { | |
406 | 0 | openTreePcaDialog(); |
407 | } | |
408 | }); | |
409 | 452 | buildColourMenu(); |
410 | ||
411 | 452 | if (Desktop.desktop != null) |
412 | { | |
413 | 397 | this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); |
414 | 397 | if (!Platform.isJS()) |
415 | { | |
416 | 397 | addServiceListeners(); |
417 | } | |
418 | 397 | setGUINucleotide(); |
419 | } | |
420 | ||
421 | 452 | if (viewport.getWrapAlignment()) |
422 | { | |
423 | 7 | wrapMenuItem_actionPerformed(null); |
424 | } | |
425 | ||
426 | 452 | if (Cache.getDefault("SHOW_OVERVIEW", false)) |
427 | { | |
428 | 28 | this.overviewMenuItem_actionPerformed(null); |
429 | } | |
430 | ||
431 | 452 | addKeyListener(); |
432 | ||
433 | 452 | final List<AlignmentViewPanel> selviews = new ArrayList<>(); |
434 | 452 | final List<AlignmentPanel> origview = new ArrayList<>(); |
435 | 452 | final String menuLabel = MessageManager |
436 | .getString("label.copy_format_from"); | |
437 | 452 | ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, |
438 | new ViewSetProvider() | |
439 | { | |
440 | ||
441 | 0 | @Override |
442 | public AlignmentPanel[] getAllAlignmentPanels() | |
443 | { | |
444 | 0 | origview.clear(); |
445 | 0 | origview.add(alignPanel); |
446 | // make an array of all alignment panels except for this one | |
447 | 0 | List<AlignmentPanel> aps = new ArrayList<>( |
448 | Arrays.asList(Desktop.getAlignmentPanels(null))); | |
449 | 0 | aps.remove(AlignFrame.this.alignPanel); |
450 | 0 | return aps.toArray(new AlignmentPanel[aps.size()]); |
451 | } | |
452 | }, selviews, new ItemListener() | |
453 | { | |
454 | ||
455 | 0 | @Override |
456 | public void itemStateChanged(ItemEvent e) | |
457 | { | |
458 | 0 | if (origview.size() > 0) |
459 | { | |
460 | 0 | final AlignmentPanel ap = origview.get(0); |
461 | ||
462 | /* | |
463 | * Copy the ViewStyle of the selected panel to 'this one'. | |
464 | * Don't change value of 'scaleProteinAsCdna' unless copying | |
465 | * from a SplitFrame. | |
466 | */ | |
467 | 0 | ViewStyleI vs = selviews.get(0).getAlignViewport() |
468 | .getViewStyle(); | |
469 | 0 | boolean fromSplitFrame = selviews.get(0) |
470 | .getAlignViewport().getCodingComplement() != null; | |
471 | 0 | if (!fromSplitFrame) |
472 | { | |
473 | 0 | vs.setScaleProteinAsCdna(ap.getAlignViewport() |
474 | .getViewStyle().isScaleProteinAsCdna()); | |
475 | } | |
476 | 0 | ap.getAlignViewport().setViewStyle(vs); |
477 | ||
478 | /* | |
479 | * Also rescale ViewStyle of SplitFrame complement if there is | |
480 | * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy | |
481 | * the whole ViewStyle (allow cDNA protein to have different | |
482 | * fonts) | |
483 | */ | |
484 | 0 | AlignViewportI complement = ap.getAlignViewport() |
485 | .getCodingComplement(); | |
486 | 0 | if (complement != null && vs.isScaleProteinAsCdna()) |
487 | { | |
488 | 0 | AlignFrame af = Desktop.getAlignFrameFor(complement); |
489 | 0 | ((SplitFrame) af.getSplitViewContainer()) |
490 | .adjustLayout(); | |
491 | 0 | af.setMenusForViewport(); |
492 | } | |
493 | ||
494 | 0 | ap.updateLayout(); |
495 | 0 | ap.setSelected(true); |
496 | 0 | ap.alignFrame.setMenusForViewport(); |
497 | ||
498 | } | |
499 | } | |
500 | }); | |
501 | 452 | if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) |
502 | .indexOf("devel") > -1 | |
503 | || Cache.getDefault("VERSION", "DEVELOPMENT") | |
504 | .toLowerCase(Locale.ROOT).indexOf("test") > -1) | |
505 | { | |
506 | 452 | formatMenu.add(vsel); |
507 | } | |
508 | 452 | addFocusListener(new FocusAdapter() |
509 | { | |
510 | 361 | @Override |
511 | public void focusGained(FocusEvent e) | |
512 | { | |
513 | 361 | Jalview.getInstance().setCurrentAlignFrame(AlignFrame.this); |
514 | } | |
515 | }); | |
516 | ||
517 | } | |
518 | ||
519 | /** | |
520 | * Change the filename and format for the alignment, and enable the 'reload' | |
521 | * button functionality. | |
522 | * | |
523 | * @param file | |
524 | * valid filename | |
525 | * @param format | |
526 | * format of file | |
527 | */ | |
528 | 326 | public void setFileName(String file, FileFormatI format) |
529 | { | |
530 | 326 | fileName = file; |
531 | 326 | setFileFormat(format); |
532 | 326 | reload.setEnabled(true); |
533 | } | |
534 | ||
535 | /** | |
536 | * JavaScript will have this, maybe others. More dependable than a file name | |
537 | * and maintains a reference to the actual bytes loaded. | |
538 | * | |
539 | * @param file | |
540 | */ | |
541 | 241 | public void setFileObject(File file) |
542 | { | |
543 | 241 | this.fileObject = file; |
544 | } | |
545 | ||
546 | /** | |
547 | * Add a KeyListener with handlers for various KeyPressed and KeyReleased | |
548 | * events | |
549 | */ | |
550 | 452 | void addKeyListener() |
551 | { | |
552 | 452 | addKeyListener(new KeyAdapter() |
553 | { | |
554 | 0 | @Override |
555 | public void keyPressed(KeyEvent evt) | |
556 | { | |
557 | 0 | if (viewport.cursorMode |
558 | && ((evt.getKeyCode() >= KeyEvent.VK_0 | |
559 | && evt.getKeyCode() <= KeyEvent.VK_9) | |
560 | || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 | |
561 | && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)) | |
562 | && Character.isDigit(evt.getKeyChar())) | |
563 | { | |
564 | 0 | alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); |
565 | } | |
566 | ||
567 | 0 | switch (evt.getKeyCode()) |
568 | { | |
569 | ||
570 | 0 | case 27: // escape key |
571 | 0 | deselectAllSequenceMenuItem_actionPerformed(null); |
572 | ||
573 | 0 | break; |
574 | ||
575 | 0 | case KeyEvent.VK_DOWN: |
576 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
577 | { | |
578 | 0 | moveSelectedSequences(false); |
579 | } | |
580 | 0 | if (viewport.cursorMode) |
581 | { | |
582 | 0 | alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); |
583 | } | |
584 | 0 | break; |
585 | ||
586 | 0 | case KeyEvent.VK_UP: |
587 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
588 | { | |
589 | 0 | moveSelectedSequences(true); |
590 | } | |
591 | 0 | if (viewport.cursorMode) |
592 | { | |
593 | 0 | alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown()); |
594 | } | |
595 | ||
596 | 0 | break; |
597 | ||
598 | 0 | case KeyEvent.VK_LEFT: |
599 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
600 | { | |
601 | 0 | slideSequences(false, |
602 | alignPanel.getSeqPanel().getKeyboardNo1()); | |
603 | } | |
604 | else | |
605 | { | |
606 | 0 | alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); |
607 | } | |
608 | ||
609 | 0 | break; |
610 | ||
611 | 0 | case KeyEvent.VK_RIGHT: |
612 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
613 | { | |
614 | 0 | slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); |
615 | } | |
616 | else | |
617 | { | |
618 | 0 | alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); |
619 | } | |
620 | 0 | break; |
621 | ||
622 | 0 | case KeyEvent.VK_SPACE: |
623 | 0 | if (viewport.cursorMode) |
624 | { | |
625 | 0 | alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() |
626 | || evt.isShiftDown() || evt.isAltDown()); | |
627 | } | |
628 | 0 | break; |
629 | ||
630 | // case KeyEvent.VK_A: | |
631 | // if (viewport.cursorMode) | |
632 | // { | |
633 | // alignPanel.seqPanel.insertNucAtCursor(false,"A"); | |
634 | // //jalview.bin.Console.outPrintln("A"); | |
635 | // } | |
636 | // break; | |
637 | /* | |
638 | * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { | |
639 | * jalview.bin.Console.outPrintln("closing bracket"); } break; | |
640 | */ | |
641 | 0 | case KeyEvent.VK_DELETE: |
642 | 0 | case KeyEvent.VK_BACK_SPACE: |
643 | 0 | if (!viewport.cursorMode) |
644 | { | |
645 | 0 | cut_actionPerformed(); |
646 | } | |
647 | else | |
648 | { | |
649 | 0 | alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() |
650 | || evt.isShiftDown() || evt.isAltDown()); | |
651 | } | |
652 | ||
653 | 0 | break; |
654 | ||
655 | 0 | case KeyEvent.VK_S: |
656 | 0 | if (viewport.cursorMode) |
657 | { | |
658 | 0 | alignPanel.getSeqPanel().setCursorRow(); |
659 | } | |
660 | 0 | break; |
661 | 0 | case KeyEvent.VK_C: |
662 | 0 | if (viewport.cursorMode && !evt.isControlDown()) |
663 | { | |
664 | 0 | alignPanel.getSeqPanel().setCursorColumn(); |
665 | } | |
666 | 0 | break; |
667 | 0 | case KeyEvent.VK_P: |
668 | 0 | if (viewport.cursorMode) |
669 | { | |
670 | 0 | alignPanel.getSeqPanel().setCursorPosition(); |
671 | } | |
672 | 0 | break; |
673 | ||
674 | 0 | case KeyEvent.VK_ENTER: |
675 | 0 | case KeyEvent.VK_COMMA: |
676 | 0 | if (viewport.cursorMode) |
677 | { | |
678 | 0 | alignPanel.getSeqPanel().setCursorRowAndColumn(); |
679 | } | |
680 | 0 | break; |
681 | ||
682 | 0 | case KeyEvent.VK_Q: |
683 | 0 | if (viewport.cursorMode) |
684 | { | |
685 | 0 | alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); |
686 | } | |
687 | 0 | break; |
688 | 0 | case KeyEvent.VK_M: |
689 | 0 | if (viewport.cursorMode) |
690 | { | |
691 | 0 | alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); |
692 | } | |
693 | 0 | break; |
694 | ||
695 | 0 | case KeyEvent.VK_F2: |
696 | 0 | viewport.cursorMode = !viewport.cursorMode; |
697 | 0 | setStatus(MessageManager |
698 | .formatMessage("label.keyboard_editing_mode", new String[] | |
699 | 0 | { (viewport.cursorMode ? "on" : "off") })); |
700 | 0 | if (viewport.cursorMode) |
701 | { | |
702 | 0 | ViewportRanges ranges = viewport.getRanges(); |
703 | 0 | alignPanel.getSeqPanel().seqCanvas.cursorX = ranges |
704 | .getStartRes(); | |
705 | 0 | alignPanel.getSeqPanel().seqCanvas.cursorY = ranges |
706 | .getStartSeq(); | |
707 | } | |
708 | 0 | alignPanel.getSeqPanel().seqCanvas.repaint(); |
709 | 0 | break; |
710 | ||
711 | 0 | case KeyEvent.VK_F1: |
712 | 0 | try |
713 | { | |
714 | 0 | Help.showHelpWindow(); |
715 | } catch (Exception ex) | |
716 | { | |
717 | 0 | ex.printStackTrace(); |
718 | } | |
719 | 0 | break; |
720 | 0 | case KeyEvent.VK_H: |
721 | { | |
722 | 0 | boolean toggleSeqs = !evt.isControlDown(); |
723 | 0 | boolean toggleCols = !evt.isShiftDown(); |
724 | 0 | toggleHiddenRegions(toggleSeqs, toggleCols); |
725 | 0 | break; |
726 | } | |
727 | 0 | case KeyEvent.VK_B: |
728 | { | |
729 | 0 | boolean toggleSel = evt.isControlDown() || evt.isMetaDown(); |
730 | 0 | boolean modifyExisting = true; // always modify, don't clear |
731 | // evt.isShiftDown(); | |
732 | 0 | boolean invertHighlighted = evt.isAltDown(); |
733 | 0 | avc.markHighlightedColumns(invertHighlighted, modifyExisting, |
734 | toggleSel); | |
735 | 0 | break; |
736 | } | |
737 | 0 | case KeyEvent.VK_PAGE_UP: |
738 | 0 | viewport.getRanges().pageUp(); |
739 | 0 | break; |
740 | 0 | case KeyEvent.VK_PAGE_DOWN: |
741 | 0 | viewport.getRanges().pageDown(); |
742 | 0 | break; |
743 | } | |
744 | } | |
745 | ||
746 | 0 | @Override |
747 | public void keyReleased(KeyEvent evt) | |
748 | { | |
749 | 0 | switch (evt.getKeyCode()) |
750 | { | |
751 | 0 | case KeyEvent.VK_LEFT: |
752 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
753 | { | |
754 | 0 | viewport.firePropertyChange("alignment", null, |
755 | viewport.getAlignment().getSequences()); | |
756 | } | |
757 | 0 | break; |
758 | ||
759 | 0 | case KeyEvent.VK_RIGHT: |
760 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
761 | { | |
762 | 0 | viewport.firePropertyChange("alignment", null, |
763 | viewport.getAlignment().getSequences()); | |
764 | } | |
765 | 0 | break; |
766 | } | |
767 | } | |
768 | }); | |
769 | } | |
770 | ||
771 | 501 | public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) |
772 | { | |
773 | 501 | ap.alignFrame = this; |
774 | 501 | avc = new jalview.controller.AlignViewController(this, viewport, |
775 | alignPanel); | |
776 | ||
777 | 501 | alignPanels.add(ap); |
778 | ||
779 | 501 | PaintRefresher.Register(ap, ap.av.getSequenceSetId()); |
780 | ||
781 | 501 | int aSize = alignPanels.size(); |
782 | ||
783 | 501 | tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null); |
784 | ||
785 | 501 | if (aSize == 1 && ap.av.getViewName() == null) |
786 | { | |
787 | 447 | this.getContentPane().add(ap, BorderLayout.CENTER); |
788 | } | |
789 | else | |
790 | { | |
791 | 54 | if (aSize == 2) |
792 | { | |
793 | 23 | setInitialTabVisible(); |
794 | } | |
795 | ||
796 | 54 | expandViews.setEnabled(true); |
797 | 54 | gatherViews.setEnabled(true); |
798 | 54 | tabbedPane.addTab(ap.av.getViewName(), ap); |
799 | ||
800 | 54 | ap.setVisible(false); |
801 | } | |
802 | ||
803 | 501 | if (newPanel) |
804 | { | |
805 | 457 | if (ap.av.isPadGaps()) |
806 | { | |
807 | 189 | ap.av.getAlignment().padGaps(); |
808 | } | |
809 | 457 | ap.av.updateConservation(ap); |
810 | 457 | ap.av.updateConsensus(ap); |
811 | 457 | ap.av.updateSecondaryStructureConsensus(ap); |
812 | 457 | ap.av.updateStrucConsensus(ap); |
813 | } | |
814 | } | |
815 | ||
816 | 82 | public void setInitialTabVisible() |
817 | { | |
818 | 82 | expandViews.setEnabled(true); |
819 | 82 | gatherViews.setEnabled(true); |
820 | 82 | tabbedPane.setVisible(true); |
821 | 82 | AlignmentPanel first = alignPanels.get(0); |
822 | 82 | tabbedPane.addTab(first.av.getViewName(), first); |
823 | 82 | this.getContentPane().add(tabbedPane, BorderLayout.CENTER); |
824 | } | |
825 | ||
826 | 5719 | public AlignViewport getViewport() |
827 | { | |
828 | 5719 | return viewport; |
829 | } | |
830 | ||
831 | /* Set up intrinsic listeners for dynamically generated GUI bits. */ | |
832 | 397 | private void addServiceListeners() |
833 | { | |
834 | 397 | final java.beans.PropertyChangeListener thisListener; |
835 | 397 | Desktop.instance.addJalviewPropertyChangeListener("services", |
836 | thisListener = new java.beans.PropertyChangeListener() | |
837 | { | |
838 | 2975 | @Override |
839 | public void propertyChange(PropertyChangeEvent evt) | |
840 | { | |
841 | // // jalview.bin.Console.outPrintln("Discoverer property | |
842 | // change."); | |
843 | // if (evt.getPropertyName().equals("services")) | |
844 | { | |
845 | 2975 | SwingUtilities.invokeLater(new Runnable() |
846 | { | |
847 | ||
848 | 2975 | @Override |
849 | public void run() | |
850 | { | |
851 | 2975 | jalview.bin.Console.errPrintln( |
852 | "Rebuild WS Menu for service change"); | |
853 | 2975 | BuildWebServiceMenu(); |
854 | } | |
855 | ||
856 | }); | |
857 | } | |
858 | } | |
859 | }); | |
860 | 397 | addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() |
861 | { | |
862 | 260 | @Override |
863 | public void internalFrameClosed( | |
864 | javax.swing.event.InternalFrameEvent evt) | |
865 | { | |
866 | // jalview.bin.Console.outPrintln("deregistering discoverer listener"); | |
867 | 260 | Desktop.instance.removeJalviewPropertyChangeListener("services", |
868 | thisListener); | |
869 | 260 | closeMenuItem_actionPerformed(true); |
870 | } | |
871 | }); | |
872 | // Finally, build the menu once to get current service state | |
873 | 397 | new Thread(new Runnable() |
874 | { | |
875 | 397 | @Override |
876 | public void run() | |
877 | { | |
878 | 397 | BuildWebServiceMenu(); |
879 | } | |
880 | }).start(); | |
881 | } | |
882 | ||
883 | /** | |
884 | * Configure menu items that vary according to whether the alignment is | |
885 | * nucleotide or protein | |
886 | */ | |
887 | 397 | public void setGUINucleotide() |
888 | { | |
889 | 397 | AlignmentI al = getViewport().getAlignment(); |
890 | 397 | boolean nucleotide = al.isNucleotide(); |
891 | ||
892 | 397 | loadVcf.setVisible(nucleotide); |
893 | 397 | showTranslation.setVisible(nucleotide); |
894 | 397 | showReverse.setVisible(nucleotide); |
895 | 397 | showReverseComplement.setVisible(nucleotide); |
896 | 397 | conservationMenuItem.setEnabled(!nucleotide); |
897 | 397 | modifyConservation |
898 | .setEnabled(!nucleotide && conservationMenuItem.isSelected()); | |
899 | 397 | showGroupConservation.setEnabled(!nucleotide); |
900 | ||
901 | 397 | showComplementMenuItem |
902 | 397 | .setText(nucleotide ? MessageManager.getString("label.protein") |
903 | : MessageManager.getString("label.nucleotide")); | |
904 | } | |
905 | ||
906 | /** | |
907 | * set up menus for the current viewport. This may be called after any | |
908 | * operation that affects the data in the current view (selection changed, | |
909 | * etc) to update the menus to reflect the new state. | |
910 | */ | |
911 | 30 | @Override |
912 | public void setMenusForViewport() | |
913 | { | |
914 | 30 | setMenusFromViewport(viewport); |
915 | } | |
916 | ||
917 | /** | |
918 | * Need to call this method when tabs are selected for multiple views, or when | |
919 | * loading from Jalview2XML.java | |
920 | * | |
921 | * @param av | |
922 | * AlignViewport | |
923 | */ | |
924 | 672 | public void setMenusFromViewport(AlignViewport av) |
925 | { | |
926 | 672 | padGapsMenuitem.setSelected(av.isPadGaps()); |
927 | 672 | colourTextMenuItem.setSelected(av.isShowColourText()); |
928 | 672 | abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); |
929 | 672 | modifyPID.setEnabled(abovePIDThreshold.isSelected()); |
930 | 672 | conservationMenuItem.setSelected(av.getConservationSelected()); |
931 | 672 | modifyConservation.setEnabled(conservationMenuItem.isSelected()); |
932 | 672 | seqLimits.setSelected(av.getShowJVSuffix()); |
933 | 672 | idRightAlign.setSelected(av.isRightAlignIds()); |
934 | 672 | centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); |
935 | 672 | renderGapsMenuItem.setSelected(av.isRenderGaps()); |
936 | 672 | wrapMenuItem.setSelected(av.getWrapAlignment()); |
937 | 672 | scaleAbove.setVisible(av.getWrapAlignment()); |
938 | 672 | scaleLeft.setVisible(av.getWrapAlignment()); |
939 | 672 | scaleRight.setVisible(av.getWrapAlignment()); |
940 | 672 | annotationPanelMenuItem.setState(av.isShowAnnotation()); |
941 | /* | |
942 | * Show/hide annotations only enabled if annotation panel is shown | |
943 | */ | |
944 | 672 | showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
945 | 672 | hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
946 | 672 | showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
947 | 672 | hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
948 | 672 | viewBoxesMenuItem.setSelected(av.getShowBoxes()); |
949 | 672 | viewTextMenuItem.setSelected(av.getShowText()); |
950 | 672 | showNonconservedMenuItem.setSelected(av.getShowUnconserved()); |
951 | 672 | showGroupConsensus.setSelected(av.isShowGroupConsensus()); |
952 | 672 | showGroupConservation.setSelected(av.isShowGroupConservation()); |
953 | 672 | showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); |
954 | 672 | showSequenceLogo.setSelected(av.isShowSequenceLogo()); |
955 | 672 | normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); |
956 | ||
957 | 672 | ColourMenuHelper.setColourSelected(colourMenu, |
958 | av.getGlobalColourScheme()); | |
959 | ||
960 | 672 | showSeqFeatures.setSelected(av.isShowSequenceFeatures()); |
961 | 672 | hiddenMarkers.setState(av.getShowHiddenMarkers()); |
962 | 672 | applyToAllGroups.setState(av.getColourAppliesToAllGroups()); |
963 | 672 | showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); |
964 | 672 | showDbRefsMenuitem.setSelected(av.isShowDBRefs()); |
965 | 672 | autoCalculate.setSelected(av.autoCalculateConsensus); |
966 | 672 | sortByTree.setSelected(av.sortByTree); |
967 | 672 | listenToViewSelections.setSelected(av.followSelection); |
968 | ||
969 | 672 | showProducts.setEnabled(canShowProducts()); |
970 | 672 | setGroovyEnabled(Desktop.getGroovyConsole() != null); |
971 | ||
972 | 672 | updateEditMenuBar(); |
973 | } | |
974 | ||
975 | /** | |
976 | * Set the enabled state of the 'Run Groovy' option in the Calculate menu | |
977 | * | |
978 | * @param b | |
979 | */ | |
980 | 672 | public void setGroovyEnabled(boolean b) |
981 | { | |
982 | 672 | runGroovy.setEnabled(b); |
983 | } | |
984 | ||
985 | private IProgressIndicator progressBar; | |
986 | ||
987 | /* | |
988 | * (non-Javadoc) | |
989 | * | |
990 | * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) | |
991 | */ | |
992 | 581 | @Override |
993 | public void setProgressBar(String message, long id) | |
994 | { | |
995 | 581 | if (!Platform.isHeadless() && progressBar != null) |
996 | 247 | progressBar.setProgressBar(message, id); |
997 | } | |
998 | ||
999 | 0 | @Override |
1000 | public JProgressBar getProgressBar(long id) | |
1001 | { | |
1002 | 0 | if (progressBar != null) |
1003 | 0 | return progressBar.getProgressBar(id); |
1004 | 0 | return null; |
1005 | } | |
1006 | ||
1007 | 0 | public String getMessage(long id) |
1008 | { | |
1009 | 0 | return progressBar.getMessage(id); |
1010 | } | |
1011 | ||
1012 | 0 | public void setProgressBarMessage(long id, String message) |
1013 | { | |
1014 | 0 | progressBar.setProgressBarMessage(id, message); |
1015 | } | |
1016 | ||
1017 | 0 | @Override |
1018 | public void registerHandler(final long id, | |
1019 | final IProgressIndicatorHandler handler) | |
1020 | { | |
1021 | 0 | if (progressBar != null) |
1022 | 0 | progressBar.registerHandler(id, handler); |
1023 | } | |
1024 | ||
1025 | /** | |
1026 | * | |
1027 | * @return true if any progress bars are still active | |
1028 | */ | |
1029 | 15 | @Override |
1030 | public boolean operationInProgress() | |
1031 | { | |
1032 | 15 | return progressBar == null ? false : progressBar.operationInProgress(); |
1033 | } | |
1034 | ||
1035 | /** | |
1036 | * Sets the text of the status bar. Note that setting a null or empty value | |
1037 | * will cause the status bar to be hidden, with possibly undesirable flicker | |
1038 | * of the screen layout. | |
1039 | */ | |
1040 | 398 | @Override |
1041 | public void setStatus(String text) | |
1042 | { | |
1043 | 398 | statusBar.setText(text == null || text.isEmpty() ? " " : text); |
1044 | } | |
1045 | ||
1046 | /* | |
1047 | * Added so Castor Mapping file can obtain Jalview Version | |
1048 | */ | |
1049 | 0 | public String getVersion() |
1050 | { | |
1051 | 0 | return Cache.getProperty("VERSION"); |
1052 | } | |
1053 | ||
1054 | 49 | public FeatureRenderer getFeatureRenderer() |
1055 | { | |
1056 | 49 | return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); |
1057 | } | |
1058 | ||
1059 | 0 | @Override |
1060 | public void fetchSequence_actionPerformed() | |
1061 | { | |
1062 | 0 | new SequenceFetcher(this); |
1063 | } | |
1064 | ||
1065 | 0 | @Override |
1066 | public void addFromFile_actionPerformed(ActionEvent e) | |
1067 | { | |
1068 | 0 | Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); |
1069 | } | |
1070 | ||
1071 | 0 | @Override |
1072 | public void reload_actionPerformed(ActionEvent e) | |
1073 | { | |
1074 | 0 | if (fileName != null) |
1075 | { | |
1076 | // TODO: JAL-1108 - ensure all associated frames are closed regardless of | |
1077 | // originating file's format | |
1078 | // TODO: work out how to recover feature settings for correct view(s) when | |
1079 | // file is reloaded. | |
1080 | 0 | if (FileFormat.Jalview.equals(currentFileFormat)) |
1081 | { | |
1082 | 0 | JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
1083 | 0 | for (int i = 0; i < frames.length; i++) |
1084 | { | |
1085 | 0 | if (frames[i] instanceof AlignFrame && frames[i] != this |
1086 | && ((AlignFrame) frames[i]).fileName != null | |
1087 | && ((AlignFrame) frames[i]).fileName.equals(fileName)) | |
1088 | { | |
1089 | 0 | try |
1090 | { | |
1091 | 0 | frames[i].setSelected(true); |
1092 | 0 | Desktop.instance.closeAssociatedWindows(); |
1093 | } catch (java.beans.PropertyVetoException ex) | |
1094 | { | |
1095 | } | |
1096 | } | |
1097 | ||
1098 | } | |
1099 | 0 | Desktop.instance.closeAssociatedWindows(); |
1100 | ||
1101 | 0 | FileLoader loader = new FileLoader(); |
1102 | 0 | DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName) |
1103 | ? DataSourceType.URL | |
1104 | : DataSourceType.FILE; | |
1105 | 0 | loader.LoadFile(viewport, fileName, protocol, currentFileFormat); |
1106 | } | |
1107 | else | |
1108 | { | |
1109 | 0 | Rectangle bounds = this.getBounds(); |
1110 | ||
1111 | 0 | FileLoader loader = new FileLoader(); |
1112 | ||
1113 | 0 | AlignFrame newframe = null; |
1114 | ||
1115 | 0 | if (fileObject == null) |
1116 | { | |
1117 | ||
1118 | 0 | DataSourceType protocol = HttpUtils.startsWithHttpOrHttps( |
1119 | fileName) ? DataSourceType.URL : DataSourceType.FILE; | |
1120 | 0 | newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, |
1121 | currentFileFormat); | |
1122 | } | |
1123 | else | |
1124 | { | |
1125 | 0 | newframe = loader.LoadFileWaitTillLoaded(fileObject, |
1126 | DataSourceType.FILE, currentFileFormat); | |
1127 | } | |
1128 | ||
1129 | 0 | newframe.setBounds(bounds); |
1130 | 0 | if (featureSettings != null && featureSettings.isShowing()) |
1131 | { | |
1132 | 0 | final Rectangle fspos = featureSettings.frame.getBounds(); |
1133 | // TODO: need a 'show feature settings' function that takes bounds - | |
1134 | // need to refactor Desktop.addFrame | |
1135 | 0 | newframe.featureSettings_actionPerformed(null); |
1136 | 0 | final FeatureSettings nfs = newframe.featureSettings; |
1137 | 0 | SwingUtilities.invokeLater(new Runnable() |
1138 | { | |
1139 | 0 | @Override |
1140 | public void run() | |
1141 | { | |
1142 | 0 | nfs.frame.setBounds(fspos); |
1143 | } | |
1144 | }); | |
1145 | 0 | this.featureSettings.close(); |
1146 | 0 | this.featureSettings = null; |
1147 | } | |
1148 | 0 | this.closeMenuItem_actionPerformed(true); |
1149 | } | |
1150 | } | |
1151 | } | |
1152 | ||
1153 | 0 | @Override |
1154 | public void addFromText_actionPerformed(ActionEvent e) | |
1155 | { | |
1156 | 0 | Desktop.instance |
1157 | .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); | |
1158 | } | |
1159 | ||
1160 | 0 | @Override |
1161 | public void addFromURL_actionPerformed(ActionEvent e) | |
1162 | { | |
1163 | 0 | Desktop.instance.inputURLMenuItem_actionPerformed(viewport); |
1164 | } | |
1165 | ||
1166 | 0 | @Override |
1167 | public void save_actionPerformed(ActionEvent e) | |
1168 | { | |
1169 | 0 | if (fileName == null || (currentFileFormat == null) |
1170 | || HttpUtils.startsWithHttpOrHttps(fileName)) | |
1171 | { | |
1172 | 0 | saveAs_actionPerformed(); |
1173 | } | |
1174 | else | |
1175 | { | |
1176 | 0 | saveAlignment(fileName, currentFileFormat); |
1177 | } | |
1178 | } | |
1179 | ||
1180 | /** | |
1181 | * Saves the alignment to a file with a name chosen by the user, if necessary | |
1182 | * warning if a file would be overwritten | |
1183 | */ | |
1184 | 0 | @Override |
1185 | public void saveAs_actionPerformed() | |
1186 | { | |
1187 | 0 | JalviewFileChooser chooser = JalviewFileChooser.forWrite( |
1188 | Cache.getProperty("LAST_DIRECTORY"), | |
1189 | 0 | currentFileFormat == null ? null : currentFileFormat.getName(), |
1190 | true); | |
1191 | ||
1192 | 0 | chooser.setFileView(new JalviewFileView()); |
1193 | 0 | chooser.setDialogTitle( |
1194 | MessageManager.getString("label.save_alignment_to_file")); | |
1195 | 0 | chooser.setToolTipText(MessageManager.getString("action.save")); |
1196 | ||
1197 | 0 | int value = chooser.showSaveDialog(this); |
1198 | ||
1199 | 0 | if (value != JalviewFileChooser.APPROVE_OPTION) |
1200 | { | |
1201 | 0 | return; |
1202 | } | |
1203 | 0 | currentFileFormat = chooser.getSelectedFormat(); |
1204 | 0 | while (currentFileFormat == null) |
1205 | { | |
1206 | // if the autodetect format from extension failed.. | |
1207 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
1208 | MessageManager | |
1209 | .getString("label.select_file_format_before_saving"), | |
1210 | MessageManager.getString("label.file_format_not_specified"), | |
1211 | JvOptionPane.WARNING_MESSAGE); | |
1212 | 0 | value = chooser.showSaveDialog(this); |
1213 | 0 | if (value != JalviewFileChooser.APPROVE_OPTION) |
1214 | { | |
1215 | 0 | return; |
1216 | } | |
1217 | 0 | currentFileFormat = chooser.getSelectedFormat(); |
1218 | } | |
1219 | ||
1220 | 0 | fileName = chooser.getSelectedFile().getPath(); |
1221 | ||
1222 | 0 | Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); |
1223 | 0 | Cache.setProperty("LAST_DIRECTORY", fileName); |
1224 | 0 | saveAlignment(fileName, currentFileFormat); |
1225 | } | |
1226 | ||
1227 | boolean lastSaveSuccessful = false; | |
1228 | ||
1229 | FileFormatI lastFormatSaved; | |
1230 | ||
1231 | String lastFilenameSaved; | |
1232 | ||
1233 | // globalLastFormatSaved across alignment windows (only for alignments with no | |
1234 | // previous format) | |
1235 | private static FileFormatI globalLastFormatSaved = null; | |
1236 | ||
1237 | 28 | public static void setLastAlignmentSavedFormat(FileFormatI f) |
1238 | { | |
1239 | 28 | globalLastFormatSaved = f; |
1240 | } | |
1241 | ||
1242 | 6 | public static FileFormatI getLastAlignmentSavedFormat() |
1243 | { | |
1244 | 6 | return globalLastFormatSaved; |
1245 | } | |
1246 | ||
1247 | /** | |
1248 | * Raise a dialog or status message for the last call to saveAlignment. | |
1249 | * | |
1250 | * @return true if last call to saveAlignment(file, format) was successful. | |
1251 | */ | |
1252 | 88 | public boolean isSaveAlignmentSuccessful() |
1253 | { | |
1254 | ||
1255 | 88 | if (!lastSaveSuccessful) |
1256 | { | |
1257 | 0 | if (!Platform.isHeadless()) |
1258 | { | |
1259 | 0 | JvOptionPane.showInternalMessageDialog(this, MessageManager |
1260 | .formatMessage("label.couldnt_save_file", new Object[] | |
1261 | { lastFilenameSaved }), | |
1262 | MessageManager.getString("label.error_saving_file"), | |
1263 | JvOptionPane.WARNING_MESSAGE); | |
1264 | } | |
1265 | else | |
1266 | { | |
1267 | 0 | Console.error(MessageManager |
1268 | .formatMessage("label.couldnt_save_file", new Object[] | |
1269 | { lastFilenameSaved })); | |
1270 | } | |
1271 | } | |
1272 | else | |
1273 | { | |
1274 | ||
1275 | 88 | setStatus(MessageManager.formatMessage( |
1276 | "label.successfully_saved_to_file_in_format", new Object[] | |
1277 | { lastFilenameSaved, lastFormatSaved })); | |
1278 | ||
1279 | } | |
1280 | 88 | return lastSaveSuccessful; |
1281 | } | |
1282 | ||
1283 | /** | |
1284 | * Saves the alignment to the specified file path, in the specified format, | |
1285 | * which may be an alignment format, or Jalview project format. If the | |
1286 | * alignment has hidden regions, or the format is one capable of including | |
1287 | * non-sequence data (features, annotations, groups), then the user may be | |
1288 | * prompted to specify what to include in the output. | |
1289 | * | |
1290 | * @param file | |
1291 | * @param format | |
1292 | */ | |
1293 | 54 | public void saveAlignment(String file, FileFormatI format) |
1294 | { | |
1295 | 54 | saveAlignment(file, format, false, false); |
1296 | } | |
1297 | ||
1298 | 128 | public void saveAlignment(String file, FileFormatI format, boolean stdout, |
1299 | boolean forceBackup) | |
1300 | { | |
1301 | 128 | lastSaveSuccessful = true; |
1302 | 128 | if (!stdout) |
1303 | { | |
1304 | 116 | lastFilenameSaved = file; |
1305 | } | |
1306 | 128 | lastFormatSaved = format; |
1307 | 128 | globalLastFormatSaved = format; |
1308 | ||
1309 | 128 | if (FileFormat.Jalview.equals(format)) |
1310 | { | |
1311 | 8 | String shortName = title; |
1312 | 8 | if (shortName.indexOf(File.separatorChar) > -1) |
1313 | { | |
1314 | 5 | shortName = shortName |
1315 | .substring(shortName.lastIndexOf(File.separatorChar) + 1); | |
1316 | } | |
1317 | // TODO deal with stdout=true | |
1318 | 8 | lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, |
1319 | shortName); | |
1320 | ||
1321 | 8 | Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); |
1322 | 8 | if (lastSaveSuccessful) |
1323 | { | |
1324 | 8 | this.getViewport().setSavedUpToDate(true); |
1325 | } | |
1326 | ||
1327 | 8 | statusBar.setText(MessageManager.formatMessage( |
1328 | "label.successfully_saved_to_file_in_format", new Object[] | |
1329 | { file, format })); | |
1330 | ||
1331 | 8 | return; |
1332 | } | |
1333 | ||
1334 | 120 | AlignExportSettingsI options = new AlignExportSettingsAdapter(false); |
1335 | 120 | Runnable cancelAction = () -> { |
1336 | 0 | lastSaveSuccessful = false; |
1337 | }; | |
1338 | 120 | Runnable outputAction = () -> { |
1339 | // todo defer this to inside formatSequences (or later) | |
1340 | 120 | AlignmentExportData exportData = viewport.getAlignExportData(options); |
1341 | 120 | String output = new FormatAdapter(alignPanel, options) |
1342 | .formatSequences(format, exportData.getAlignment(), | |
1343 | exportData.getOmitHidden(), | |
1344 | exportData.getStartEndPostions(), | |
1345 | viewport.getAlignment().getHiddenColumns()); | |
1346 | 120 | if (output == null) |
1347 | { | |
1348 | 0 | lastSaveSuccessful = false; |
1349 | } | |
1350 | else | |
1351 | { | |
1352 | // create backupfiles object and get new temp filename destination | |
1353 | 120 | boolean doBackup = forceBackup |
1354 | || (BackupFiles.getEnabled() && !stdout); | |
1355 | 120 | BackupFiles backupfiles = null; |
1356 | 120 | if (doBackup) |
1357 | { | |
1358 | 92 | Console.trace("ALIGNFRAME making backupfiles object for " + file); |
1359 | 92 | backupfiles = new BackupFiles(file); |
1360 | } | |
1361 | 120 | try |
1362 | { | |
1363 | 120 | String tempFilePath = doBackup ? backupfiles.getTempFilePath() |
1364 | : file; | |
1365 | 120 | Console.trace("ALIGNFRAME setting PrintWriter"); |
1366 | 120 | PrintWriter out = stdout |
1367 | ? new PrintWriter(new OutputStreamWriter(System.out)) | |
1368 | : new PrintWriter(new FileWriter(tempFilePath)); | |
1369 | ||
1370 | 120 | if (backupfiles != null) |
1371 | { | |
1372 | 92 | Console.trace("ALIGNFRAME about to write to temp file " |
1373 | + backupfiles.getTempFilePath()); | |
1374 | } | |
1375 | ||
1376 | 120 | out.print(output); |
1377 | 120 | out.flush(); |
1378 | 120 | if (!stdout) |
1379 | { | |
1380 | 108 | Console.trace("ALIGNFRAME about to close file"); |
1381 | 108 | out.close(); |
1382 | 108 | Console.trace("ALIGNFRAME closed file"); |
1383 | } | |
1384 | 120 | AlignFrame.this.setTitle(stdout ? "STDOUT" : file); |
1385 | 120 | if (stdout) |
1386 | { | |
1387 | 12 | statusBar.setText(MessageManager.formatMessage( |
1388 | "label.successfully_printed_to_stdout_in_format", | |
1389 | new Object[] | |
1390 | { format.getName() })); | |
1391 | } | |
1392 | else | |
1393 | { | |
1394 | 108 | statusBar.setText(MessageManager.formatMessage( |
1395 | "label.successfully_saved_to_file_in_format", | |
1396 | new Object[] | |
1397 | { fileName, format.getName() })); | |
1398 | } | |
1399 | 120 | lastSaveSuccessful = true; |
1400 | } catch (IOException e) | |
1401 | { | |
1402 | 0 | lastSaveSuccessful = false; |
1403 | 0 | Console.error( |
1404 | "ALIGNFRAME Something happened writing the temp file"); | |
1405 | 0 | Console.error(e.getMessage()); |
1406 | 0 | Console.debug(Cache.getStackTraceString(e)); |
1407 | } catch (Exception ex) | |
1408 | { | |
1409 | 0 | lastSaveSuccessful = false; |
1410 | 0 | Console.error( |
1411 | "ALIGNFRAME Something unexpected happened writing the temp file"); | |
1412 | 0 | Console.error(ex.getMessage()); |
1413 | 0 | Console.debug(Cache.getStackTraceString(ex)); |
1414 | } | |
1415 | ||
1416 | 120 | if (doBackup) |
1417 | { | |
1418 | 92 | backupfiles.setWriteSuccess(lastSaveSuccessful); |
1419 | 92 | Console.debug("ALIGNFRAME writing temp file was " |
1420 | 92 | + (lastSaveSuccessful ? "" : "NOT ") + "successful"); |
1421 | // do the backup file roll and rename the temp file to actual file | |
1422 | 92 | Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile"); |
1423 | 92 | lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); |
1424 | 92 | Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile " |
1425 | 92 | + (lastSaveSuccessful ? "" : "un") + "successfully"); |
1426 | } | |
1427 | ||
1428 | 120 | Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); |
1429 | 120 | if (lastSaveSuccessful) |
1430 | { | |
1431 | 120 | AlignFrame.this.getViewport().setSavedUpToDate(true); |
1432 | } | |
1433 | } | |
1434 | }; | |
1435 | ||
1436 | /* | |
1437 | * show dialog with export options if applicable; else just do it | |
1438 | */ | |
1439 | 120 | if (AlignExportOptions.isNeeded(viewport, format)) |
1440 | { | |
1441 | 0 | AlignExportOptions choices = new AlignExportOptions( |
1442 | alignPanel.getAlignViewport(), format, options); | |
1443 | 0 | choices.setResponseAction(0, outputAction); |
1444 | 0 | choices.setResponseAction(1, cancelAction); |
1445 | 0 | choices.showDialog(); |
1446 | } | |
1447 | else | |
1448 | { | |
1449 | 120 | try |
1450 | { | |
1451 | 120 | outputAction.run(); |
1452 | } catch (Exception e) | |
1453 | { | |
1454 | // TODO Auto-generated catch block | |
1455 | 0 | e.printStackTrace(); |
1456 | } | |
1457 | } | |
1458 | } | |
1459 | ||
1460 | /** | |
1461 | * Outputs the alignment to textbox in the requested format, if necessary | |
1462 | * first prompting the user for whether to include hidden regions or | |
1463 | * non-sequence data | |
1464 | * | |
1465 | * @param fileFormatName | |
1466 | */ | |
1467 | 0 | @Override |
1468 | protected void outputText_actionPerformed(String fileFormatName) | |
1469 | { | |
1470 | 0 | FileFormatI fileFormat = FileFormats.getInstance() |
1471 | .forName(fileFormatName); | |
1472 | 0 | AlignExportSettingsI options = new AlignExportSettingsAdapter(false); |
1473 | 0 | Runnable outputAction = () -> { |
1474 | // todo defer this to inside formatSequences (or later) | |
1475 | 0 | AlignmentExportData exportData = viewport.getAlignExportData(options); |
1476 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
1477 | 0 | cap.setForInput(null); |
1478 | 0 | try |
1479 | { | |
1480 | 0 | FileFormatI format = fileFormat; |
1481 | 0 | cap.setText(new FormatAdapter(alignPanel, options).formatSequences( |
1482 | format, exportData.getAlignment(), | |
1483 | exportData.getOmitHidden(), | |
1484 | exportData.getStartEndPostions(), | |
1485 | viewport.getAlignment().getHiddenColumns())); | |
1486 | 0 | Desktop.addInternalFrame(cap, MessageManager.formatMessage( |
1487 | "label.alignment_output_command", new Object[] | |
1488 | { fileFormat.getName() }), 600, 500); | |
1489 | } catch (OutOfMemoryError oom) | |
1490 | { | |
1491 | 0 | new OOMWarning("Outputting alignment as " + fileFormat.getName(), |
1492 | oom); | |
1493 | 0 | cap.dispose(); |
1494 | } | |
1495 | }; | |
1496 | ||
1497 | /* | |
1498 | * show dialog with export options if applicable; else just do it | |
1499 | */ | |
1500 | 0 | if (AlignExportOptions.isNeeded(viewport, fileFormat)) |
1501 | { | |
1502 | 0 | AlignExportOptions choices = new AlignExportOptions( |
1503 | alignPanel.getAlignViewport(), fileFormat, options); | |
1504 | 0 | choices.setResponseAction(0, outputAction); |
1505 | 0 | choices.showDialog(); |
1506 | } | |
1507 | else | |
1508 | { | |
1509 | 0 | try |
1510 | { | |
1511 | 0 | outputAction.run(); |
1512 | } catch (Exception e) | |
1513 | { | |
1514 | 0 | e.printStackTrace(); |
1515 | } | |
1516 | } | |
1517 | } | |
1518 | ||
1519 | /** | |
1520 | * DOCUMENT ME! | |
1521 | * | |
1522 | * @param e | |
1523 | * DOCUMENT ME! | |
1524 | */ | |
1525 | 0 | @Override |
1526 | protected void htmlMenuItem_actionPerformed(ActionEvent e) | |
1527 | { | |
1528 | 0 | HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel); |
1529 | 0 | try |
1530 | { | |
1531 | 0 | htmlSVG.exportHTML(null); |
1532 | } catch (ImageOutputException x) | |
1533 | { | |
1534 | // report problem to console and raise dialog | |
1535 | } | |
1536 | } | |
1537 | ||
1538 | 0 | @Override |
1539 | public void bioJSMenuItem_actionPerformed(ActionEvent e) | |
1540 | { | |
1541 | 0 | BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); |
1542 | 0 | try |
1543 | { | |
1544 | 0 | bjs.exportHTML(null); |
1545 | } catch (ImageOutputException x) | |
1546 | { | |
1547 | // report problem to console and raise dialog | |
1548 | } | |
1549 | } | |
1550 | ||
1551 | 0 | public void createImageMap(File file, String image) |
1552 | { | |
1553 | 0 | try |
1554 | { | |
1555 | 0 | alignPanel.makePNGImageMap(file, image); |
1556 | } catch (ImageOutputException x) | |
1557 | { | |
1558 | // report problem to console and raise dialog | |
1559 | } | |
1560 | } | |
1561 | ||
1562 | 0 | @Override |
1563 | public void createPNG_actionPerformed(ActionEvent e) | |
1564 | { | |
1565 | 0 | try |
1566 | { | |
1567 | 0 | createPNG(null); |
1568 | } catch (ImageOutputException ioex) | |
1569 | { | |
1570 | // raise dialog, and report via console | |
1571 | } | |
1572 | } | |
1573 | ||
1574 | 0 | @Override |
1575 | public void createEPS_actionPerformed(ActionEvent e) | |
1576 | { | |
1577 | 0 | try |
1578 | { | |
1579 | 0 | createEPS(null); |
1580 | } catch (ImageOutputException ioex) | |
1581 | { | |
1582 | // raise dialog, and report via console | |
1583 | } | |
1584 | ||
1585 | } | |
1586 | ||
1587 | 0 | @Override |
1588 | public void createSVG_actionPerformed(ActionEvent e) | |
1589 | { | |
1590 | 0 | try |
1591 | { | |
1592 | 0 | createSVG(null); |
1593 | } catch (ImageOutputException ioex) | |
1594 | { | |
1595 | // raise dialog, and report via console | |
1596 | } | |
1597 | ||
1598 | } | |
1599 | ||
1600 | /** | |
1601 | * Creates a PNG image of the alignment and writes it to the given file. If | |
1602 | * the file is null, the user is prompted to choose a file. | |
1603 | * | |
1604 | * @param f | |
1605 | */ | |
1606 | 1 | public void createPNG(File f) throws ImageOutputException |
1607 | { | |
1608 | 1 | createPNG(f, null, BitmapImageSizing.defaultBitmapImageSizing()); |
1609 | } | |
1610 | ||
1611 | 24 | public void createPNG(File f, String renderer, BitmapImageSizing userBis) |
1612 | throws ImageOutputException | |
1613 | { | |
1614 | 24 | alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis); |
1615 | } | |
1616 | ||
1617 | /** | |
1618 | * Creates an EPS image of the alignment and writes it to the given file. If | |
1619 | * the file is null, the user is prompted to choose a file. | |
1620 | * | |
1621 | * @param f | |
1622 | */ | |
1623 | 5 | public void createEPS(File f) throws ImageOutputException |
1624 | { | |
1625 | 5 | createEPS(f, null); |
1626 | } | |
1627 | ||
1628 | 10 | public void createEPS(File f, String renderer) throws ImageOutputException |
1629 | { | |
1630 | 10 | alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer); |
1631 | } | |
1632 | ||
1633 | /** | |
1634 | * Creates an SVG image of the alignment and writes it to the given file. If | |
1635 | * the file is null, the user is prompted to choose a file. | |
1636 | * | |
1637 | * @param f | |
1638 | */ | |
1639 | 1 | public void createSVG(File f) throws ImageOutputException |
1640 | { | |
1641 | 1 | createSVG(f, null); |
1642 | } | |
1643 | ||
1644 | 2 | public void createSVG(File f, String renderer) throws ImageOutputException |
1645 | { | |
1646 | 2 | alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer); |
1647 | } | |
1648 | ||
1649 | 0 | @Override |
1650 | public void pageSetup_actionPerformed(ActionEvent e) | |
1651 | { | |
1652 | 0 | PrinterJob printJob = PrinterJob.getPrinterJob(); |
1653 | 0 | PrintThread.pf = printJob.pageDialog(printJob.defaultPage()); |
1654 | } | |
1655 | ||
1656 | /** | |
1657 | * DOCUMENT ME! | |
1658 | * | |
1659 | * @param e | |
1660 | * DOCUMENT ME! | |
1661 | */ | |
1662 | 0 | @Override |
1663 | public void printMenuItem_actionPerformed(ActionEvent e) | |
1664 | { | |
1665 | // Putting in a thread avoids Swing painting problems | |
1666 | 0 | PrintThread thread = new PrintThread(alignPanel); |
1667 | 0 | thread.start(); |
1668 | } | |
1669 | ||
1670 | 0 | @Override |
1671 | public void exportFeatures_actionPerformed(ActionEvent e) | |
1672 | { | |
1673 | 0 | new AnnotationExporter(alignPanel).exportFeatures(); |
1674 | } | |
1675 | ||
1676 | 0 | @Override |
1677 | public void exportAnnotations_actionPerformed(ActionEvent e) | |
1678 | { | |
1679 | 0 | new AnnotationExporter(alignPanel).exportAnnotations(); |
1680 | } | |
1681 | ||
1682 | 0 | @Override |
1683 | public void associatedData_actionPerformed(ActionEvent e) | |
1684 | { | |
1685 | 0 | final JalviewFileChooser chooser = new JalviewFileChooser( |
1686 | Cache.getProperty("LAST_DIRECTORY")); | |
1687 | 0 | chooser.setFileView(new JalviewFileView()); |
1688 | 0 | String tooltip = MessageManager |
1689 | .getString("label.load_jalview_annotations"); | |
1690 | 0 | chooser.setDialogTitle(tooltip); |
1691 | 0 | chooser.setToolTipText(tooltip); |
1692 | 0 | chooser.setResponseHandler(0, () -> { |
1693 | 0 | String choice = chooser.getSelectedFile().getPath(); |
1694 | 0 | Cache.setProperty("LAST_DIRECTORY", choice); |
1695 | 0 | loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); |
1696 | }); | |
1697 | ||
1698 | 0 | chooser.showOpenDialog(this); |
1699 | } | |
1700 | ||
1701 | /** | |
1702 | * Close the current view or all views in the alignment frame. If the frame | |
1703 | * only contains one view then the alignment will be removed from memory. | |
1704 | * | |
1705 | * @param closeAllTabs | |
1706 | */ | |
1707 | 386 | @Override |
1708 | public void closeMenuItem_actionPerformed(boolean closeAllTabs) | |
1709 | { | |
1710 | 386 | if (alignPanels != null && alignPanels.size() < 2) |
1711 | { | |
1712 | 366 | closeAllTabs = true; |
1713 | } | |
1714 | ||
1715 | 386 | Desktop.closeModal(this); |
1716 | ||
1717 | 386 | try |
1718 | { | |
1719 | 386 | if (alignPanels != null) |
1720 | { | |
1721 | 386 | if (closeAllTabs) |
1722 | { | |
1723 | 385 | if (this.isClosed()) |
1724 | { | |
1725 | // really close all the windows - otherwise wait till | |
1726 | // setClosed(true) is called | |
1727 | 512 | for (int i = 0; i < alignPanels.size(); i++) |
1728 | { | |
1729 | 252 | AlignmentPanel ap = alignPanels.get(i); |
1730 | 252 | ap.closePanel(); |
1731 | } | |
1732 | } | |
1733 | } | |
1734 | else | |
1735 | { | |
1736 | 1 | closeView(alignPanel); |
1737 | } | |
1738 | } | |
1739 | 386 | if (closeAllTabs) |
1740 | { | |
1741 | 385 | if (featureSettings != null && featureSettings.isOpen()) |
1742 | { | |
1743 | 0 | featureSettings.close(); |
1744 | 0 | featureSettings = null; |
1745 | } | |
1746 | ||
1747 | /* | |
1748 | * this will raise an INTERNAL_FRAME_CLOSED event and this method will | |
1749 | * be called recursively, with the frame now in 'closed' state | |
1750 | */ | |
1751 | 385 | this.setClosed(true); |
1752 | } | |
1753 | } catch (Exception ex) | |
1754 | { | |
1755 | 0 | ex.printStackTrace(); |
1756 | } | |
1757 | } | |
1758 | ||
1759 | /** | |
1760 | * Close the specified panel and close up tabs appropriately. | |
1761 | * | |
1762 | * @param panelToClose | |
1763 | */ | |
1764 | 1 | public void closeView(AlignmentPanel panelToClose) |
1765 | { | |
1766 | 1 | int index = tabbedPane.getSelectedIndex(); |
1767 | 1 | int closedindex = tabbedPane.indexOfComponent(panelToClose); |
1768 | 1 | alignPanels.remove(panelToClose); |
1769 | 1 | panelToClose.closePanel(); |
1770 | 1 | panelToClose = null; |
1771 | ||
1772 | 1 | tabbedPane.removeTabAt(closedindex); |
1773 | 1 | tabbedPane.validate(); |
1774 | ||
1775 | 1 | if (index > closedindex || index == tabbedPane.getTabCount()) |
1776 | { | |
1777 | // modify currently selected tab index if necessary. | |
1778 | 1 | index--; |
1779 | } | |
1780 | ||
1781 | 1 | this.tabSelectionChanged(index); |
1782 | } | |
1783 | ||
1784 | /** | |
1785 | * DOCUMENT ME! | |
1786 | */ | |
1787 | 1222 | void updateEditMenuBar() |
1788 | { | |
1789 | ||
1790 | 1222 | if (viewport.getHistoryList().size() > 0) |
1791 | { | |
1792 | 1 | undoMenuItem.setEnabled(true); |
1793 | 1 | CommandI command = viewport.getHistoryList().peek(); |
1794 | 1 | undoMenuItem.setText(MessageManager |
1795 | .formatMessage("label.undo_command", new Object[] | |
1796 | { command.getDescription() })); | |
1797 | } | |
1798 | else | |
1799 | { | |
1800 | 1221 | undoMenuItem.setEnabled(false); |
1801 | 1221 | undoMenuItem.setText(MessageManager.getString("action.undo")); |
1802 | } | |
1803 | ||
1804 | 1222 | if (viewport.getRedoList().size() > 0) |
1805 | { | |
1806 | 0 | redoMenuItem.setEnabled(true); |
1807 | ||
1808 | 0 | CommandI command = viewport.getRedoList().peek(); |
1809 | 0 | redoMenuItem.setText(MessageManager |
1810 | .formatMessage("label.redo_command", new Object[] | |
1811 | { command.getDescription() })); | |
1812 | } | |
1813 | else | |
1814 | { | |
1815 | 1222 | redoMenuItem.setEnabled(false); |
1816 | 1222 | redoMenuItem.setText(MessageManager.getString("action.redo")); |
1817 | } | |
1818 | } | |
1819 | ||
1820 | 1 | @Override |
1821 | public void addHistoryItem(CommandI command) | |
1822 | { | |
1823 | 1 | if (command.getSize() > 0) |
1824 | { | |
1825 | 1 | viewport.addToHistoryList(command); |
1826 | 1 | viewport.clearRedoList(); |
1827 | 1 | updateEditMenuBar(); |
1828 | 1 | viewport.updateHiddenColumns(); |
1829 | // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null | |
1830 | // && viewport.getColumnSelection().getHiddenColumns() != null && | |
1831 | // viewport.getColumnSelection() | |
1832 | // .getHiddenColumns().size() > 0); | |
1833 | } | |
1834 | } | |
1835 | ||
1836 | /** | |
1837 | * | |
1838 | * @return alignment objects for all views | |
1839 | */ | |
1840 | 0 | public AlignmentI[] getViewAlignments() |
1841 | { | |
1842 | 0 | if (alignPanels != null) |
1843 | { | |
1844 | 0 | AlignmentI[] als = new AlignmentI[alignPanels.size()]; |
1845 | 0 | int i = 0; |
1846 | 0 | for (AlignmentPanel ap : alignPanels) |
1847 | { | |
1848 | 0 | als[i++] = ap.av.getAlignment(); |
1849 | } | |
1850 | 0 | return als; |
1851 | } | |
1852 | 0 | if (viewport != null) |
1853 | { | |
1854 | 0 | return new AlignmentI[] { viewport.getAlignment() }; |
1855 | } | |
1856 | 0 | return null; |
1857 | } | |
1858 | ||
1859 | /** | |
1860 | * DOCUMENT ME! | |
1861 | * | |
1862 | * @param e | |
1863 | * DOCUMENT ME! | |
1864 | */ | |
1865 | 0 | @Override |
1866 | protected void undoMenuItem_actionPerformed(ActionEvent e) | |
1867 | { | |
1868 | 0 | if (viewport.getHistoryList().isEmpty()) |
1869 | { | |
1870 | 0 | return; |
1871 | } | |
1872 | 0 | CommandI command = viewport.getHistoryList().pop(); |
1873 | 0 | viewport.addToRedoList(command); |
1874 | 0 | command.undoCommand(getViewAlignments()); |
1875 | ||
1876 | 0 | AlignmentViewport originalSource = getOriginatingSource(command); |
1877 | 0 | updateEditMenuBar(); |
1878 | ||
1879 | 0 | if (originalSource != null) |
1880 | { | |
1881 | 0 | if (originalSource != viewport) |
1882 | { | |
1883 | 0 | Console.warn( |
1884 | "Implementation worry: mismatch of viewport origin for undo"); | |
1885 | } | |
1886 | 0 | originalSource.updateHiddenColumns(); |
1887 | // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != | |
1888 | // null | |
1889 | // && viewport.getColumnSelection().getHiddenColumns() != null && | |
1890 | // viewport.getColumnSelection() | |
1891 | // .getHiddenColumns().size() > 0); | |
1892 | 0 | originalSource.firePropertyChange("alignment", null, |
1893 | originalSource.getAlignment().getSequences()); | |
1894 | } | |
1895 | } | |
1896 | ||
1897 | /** | |
1898 | * DOCUMENT ME! | |
1899 | * | |
1900 | * @param e | |
1901 | * DOCUMENT ME! | |
1902 | */ | |
1903 | 0 | @Override |
1904 | protected void redoMenuItem_actionPerformed(ActionEvent e) | |
1905 | { | |
1906 | 0 | if (viewport.getRedoList().size() < 1) |
1907 | { | |
1908 | 0 | return; |
1909 | } | |
1910 | ||
1911 | 0 | CommandI command = viewport.getRedoList().pop(); |
1912 | 0 | viewport.addToHistoryList(command); |
1913 | 0 | command.doCommand(getViewAlignments()); |
1914 | ||
1915 | 0 | AlignmentViewport originalSource = getOriginatingSource(command); |
1916 | 0 | updateEditMenuBar(); |
1917 | ||
1918 | 0 | if (originalSource != null) |
1919 | { | |
1920 | ||
1921 | 0 | if (originalSource != viewport) |
1922 | { | |
1923 | 0 | Console.warn( |
1924 | "Implementation worry: mismatch of viewport origin for redo"); | |
1925 | } | |
1926 | 0 | originalSource.updateHiddenColumns(); |
1927 | // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != | |
1928 | // null | |
1929 | // && viewport.getColumnSelection().getHiddenColumns() != null && | |
1930 | // viewport.getColumnSelection() | |
1931 | // .getHiddenColumns().size() > 0); | |
1932 | 0 | originalSource.firePropertyChange("alignment", null, |
1933 | originalSource.getAlignment().getSequences()); | |
1934 | } | |
1935 | } | |
1936 | ||
1937 | 0 | AlignmentViewport getOriginatingSource(CommandI command) |
1938 | { | |
1939 | 0 | AlignmentViewport originalSource = null; |
1940 | // For sequence removal and addition, we need to fire | |
1941 | // the property change event FROM the viewport where the | |
1942 | // original alignment was altered | |
1943 | 0 | AlignmentI al = null; |
1944 | 0 | if (command instanceof EditCommand) |
1945 | { | |
1946 | 0 | EditCommand editCommand = (EditCommand) command; |
1947 | 0 | al = editCommand.getAlignment(); |
1948 | 0 | List<Component> comps = PaintRefresher.components |
1949 | .get(viewport.getSequenceSetId()); | |
1950 | ||
1951 | 0 | for (Component comp : comps) |
1952 | { | |
1953 | 0 | if (comp instanceof AlignmentPanel) |
1954 | { | |
1955 | 0 | if (al == ((AlignmentPanel) comp).av.getAlignment()) |
1956 | { | |
1957 | 0 | originalSource = ((AlignmentPanel) comp).av; |
1958 | 0 | break; |
1959 | } | |
1960 | } | |
1961 | } | |
1962 | } | |
1963 | ||
1964 | 0 | if (originalSource == null) |
1965 | { | |
1966 | // The original view is closed, we must validate | |
1967 | // the current view against the closed view first | |
1968 | 0 | if (al != null) |
1969 | { | |
1970 | 0 | PaintRefresher.validateSequences(al, viewport.getAlignment()); |
1971 | } | |
1972 | ||
1973 | 0 | originalSource = viewport; |
1974 | } | |
1975 | ||
1976 | 0 | return originalSource; |
1977 | } | |
1978 | ||
1979 | /** | |
1980 | * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection | |
1981 | * or the sequence under cursor in keyboard mode | |
1982 | * | |
1983 | * @param up | |
1984 | * or down (if !up) | |
1985 | */ | |
1986 | 0 | public void moveSelectedSequences(boolean up) |
1987 | { | |
1988 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
1989 | ||
1990 | 0 | if (sg == null) |
1991 | { | |
1992 | 0 | if (viewport.cursorMode) |
1993 | { | |
1994 | 0 | sg = new SequenceGroup(); |
1995 | 0 | sg.addSequence(viewport.getAlignment().getSequenceAt( |
1996 | alignPanel.getSeqPanel().seqCanvas.cursorY), false); | |
1997 | } | |
1998 | else | |
1999 | { | |
2000 | 0 | return; |
2001 | } | |
2002 | } | |
2003 | ||
2004 | 0 | if (sg.getSize() < 1) |
2005 | { | |
2006 | 0 | return; |
2007 | } | |
2008 | ||
2009 | // TODO: JAL-3733 - add an event to the undo buffer for this ! | |
2010 | ||
2011 | 0 | viewport.getAlignment().moveSelectedSequencesByOne(sg, |
2012 | viewport.getHiddenRepSequences(), up); | |
2013 | 0 | alignPanel.paintAlignment(true, false); |
2014 | } | |
2015 | ||
2016 | 0 | synchronized void slideSequences(boolean right, int size) |
2017 | { | |
2018 | 0 | List<SequenceI> sg = new ArrayList<>(); |
2019 | 0 | if (viewport.cursorMode) |
2020 | { | |
2021 | 0 | sg.add(viewport.getAlignment() |
2022 | .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); | |
2023 | } | |
2024 | 0 | else if (viewport.getSelectionGroup() != null |
2025 | && viewport.getSelectionGroup().getSize() != viewport | |
2026 | .getAlignment().getHeight()) | |
2027 | { | |
2028 | 0 | sg = viewport.getSelectionGroup() |
2029 | .getSequences(viewport.getHiddenRepSequences()); | |
2030 | } | |
2031 | ||
2032 | 0 | if (sg.size() < 1) |
2033 | { | |
2034 | 0 | return; |
2035 | } | |
2036 | ||
2037 | 0 | List<SequenceI> invertGroup = new ArrayList<>(); |
2038 | ||
2039 | 0 | for (SequenceI seq : viewport.getAlignment().getSequences()) |
2040 | { | |
2041 | 0 | if (!sg.contains(seq)) |
2042 | { | |
2043 | 0 | invertGroup.add(seq); |
2044 | } | |
2045 | } | |
2046 | ||
2047 | 0 | SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); |
2048 | ||
2049 | 0 | SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; |
2050 | 0 | for (int i = 0; i < invertGroup.size(); i++) |
2051 | { | |
2052 | 0 | seqs2[i] = invertGroup.get(i); |
2053 | } | |
2054 | ||
2055 | 0 | SlideSequencesCommand ssc; |
2056 | 0 | if (right) |
2057 | { | |
2058 | 0 | ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, |
2059 | viewport.getGapCharacter()); | |
2060 | } | |
2061 | else | |
2062 | { | |
2063 | 0 | ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, |
2064 | viewport.getGapCharacter()); | |
2065 | } | |
2066 | ||
2067 | 0 | int groupAdjustment = 0; |
2068 | 0 | if (ssc.getGapsInsertedBegin() && right) |
2069 | { | |
2070 | 0 | if (viewport.cursorMode) |
2071 | { | |
2072 | 0 | alignPanel.getSeqPanel().moveCursor(size, 0); |
2073 | } | |
2074 | else | |
2075 | { | |
2076 | 0 | groupAdjustment = size; |
2077 | } | |
2078 | } | |
2079 | 0 | else if (!ssc.getGapsInsertedBegin() && !right) |
2080 | { | |
2081 | 0 | if (viewport.cursorMode) |
2082 | { | |
2083 | 0 | alignPanel.getSeqPanel().moveCursor(-size, 0); |
2084 | } | |
2085 | else | |
2086 | { | |
2087 | 0 | groupAdjustment = -size; |
2088 | } | |
2089 | } | |
2090 | ||
2091 | 0 | if (groupAdjustment != 0) |
2092 | { | |
2093 | 0 | viewport.getSelectionGroup().setStartRes( |
2094 | viewport.getSelectionGroup().getStartRes() + groupAdjustment); | |
2095 | 0 | viewport.getSelectionGroup().setEndRes( |
2096 | viewport.getSelectionGroup().getEndRes() + groupAdjustment); | |
2097 | } | |
2098 | ||
2099 | /* | |
2100 | * just extend the last slide command if compatible; but not if in | |
2101 | * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) | |
2102 | */ | |
2103 | 0 | boolean appendHistoryItem = false; |
2104 | 0 | Deque<CommandI> historyList = viewport.getHistoryList(); |
2105 | 0 | boolean inSplitFrame = getSplitViewContainer() != null; |
2106 | 0 | if (!inSplitFrame && historyList != null && historyList.size() > 0 |
2107 | && historyList.peek() instanceof SlideSequencesCommand) | |
2108 | { | |
2109 | 0 | appendHistoryItem = ssc.appendSlideCommand( |
2110 | (SlideSequencesCommand) historyList.peek()); | |
2111 | } | |
2112 | ||
2113 | 0 | if (!appendHistoryItem) |
2114 | { | |
2115 | 0 | addHistoryItem(ssc); |
2116 | } | |
2117 | ||
2118 | 0 | repaint(); |
2119 | } | |
2120 | ||
2121 | /** | |
2122 | * DOCUMENT ME! | |
2123 | * | |
2124 | * @param e | |
2125 | * DOCUMENT ME! | |
2126 | */ | |
2127 | 1 | @Override |
2128 | protected void copy_actionPerformed() | |
2129 | { | |
2130 | 1 | if (viewport.getSelectionGroup() == null) |
2131 | { | |
2132 | 0 | return; |
2133 | } | |
2134 | // TODO: preserve the ordering of displayed alignment annotation in any | |
2135 | // internal paste (particularly sequence associated annotation) | |
2136 | 1 | SequenceI[] seqs = viewport.getSelectionAsNewSequence(); |
2137 | 1 | String[] omitHidden = null; |
2138 | ||
2139 | 1 | if (viewport.hasHiddenColumns()) |
2140 | { | |
2141 | 0 | omitHidden = viewport.getViewAsString(true); |
2142 | } | |
2143 | ||
2144 | 1 | String output = new FormatAdapter().formatSequences(FileFormat.Fasta, |
2145 | seqs, omitHidden, null); | |
2146 | ||
2147 | 1 | StringSelection ss = new StringSelection(output); |
2148 | ||
2149 | 1 | try |
2150 | { | |
2151 | 1 | jalview.gui.Desktop.internalCopy = true; |
2152 | // Its really worth setting the clipboard contents | |
2153 | // to empty before setting the large StringSelection!! | |
2154 | 1 | Toolkit.getDefaultToolkit().getSystemClipboard() |
2155 | .setContents(new StringSelection(""), null); | |
2156 | ||
2157 | 1 | Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, |
2158 | Desktop.instance); | |
2159 | } catch (OutOfMemoryError er) | |
2160 | { | |
2161 | 0 | new OOMWarning("copying region", er); |
2162 | 0 | return; |
2163 | } | |
2164 | ||
2165 | 1 | HiddenColumns hiddenColumns = null; |
2166 | 1 | if (viewport.hasHiddenColumns()) |
2167 | { | |
2168 | 0 | int hiddenOffset = viewport.getSelectionGroup().getStartRes(); |
2169 | 0 | int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); |
2170 | ||
2171 | // create new HiddenColumns object with copy of hidden regions | |
2172 | // between startRes and endRes, offset by startRes | |
2173 | 0 | hiddenColumns = new HiddenColumns( |
2174 | viewport.getAlignment().getHiddenColumns(), hiddenOffset, | |
2175 | hiddenCutoff, hiddenOffset); | |
2176 | } | |
2177 | ||
2178 | 1 | Desktop.jalviewClipboard = new Object[] { seqs, |
2179 | viewport.getAlignment().getDataset(), hiddenColumns }; | |
2180 | 1 | setStatus(MessageManager.formatMessage( |
2181 | "label.copied_sequences_to_clipboard", new Object[] | |
2182 | { Integer.valueOf(seqs.length).toString() })); | |
2183 | } | |
2184 | ||
2185 | /** | |
2186 | * DOCUMENT ME! | |
2187 | * | |
2188 | * @param e | |
2189 | * DOCUMENT ME! | |
2190 | */ | |
2191 | 0 | @Override |
2192 | protected void pasteNew_actionPerformed(ActionEvent e) | |
2193 | { | |
2194 | 0 | paste(true); |
2195 | } | |
2196 | ||
2197 | /** | |
2198 | * DOCUMENT ME! | |
2199 | * | |
2200 | * @param e | |
2201 | * DOCUMENT ME! | |
2202 | */ | |
2203 | 0 | @Override |
2204 | protected void pasteThis_actionPerformed(ActionEvent e) | |
2205 | { | |
2206 | 0 | paste(false); |
2207 | } | |
2208 | ||
2209 | /** | |
2210 | * Paste contents of Jalview clipboard | |
2211 | * | |
2212 | * @param newAlignment | |
2213 | * true to paste to a new alignment, otherwise add to this. | |
2214 | */ | |
2215 | 0 | void paste(boolean newAlignment) |
2216 | { | |
2217 | 0 | boolean externalPaste = true; |
2218 | 0 | try |
2219 | { | |
2220 | 0 | Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); |
2221 | 0 | Transferable contents = c.getContents(this); |
2222 | ||
2223 | 0 | if (contents == null) |
2224 | { | |
2225 | 0 | return; |
2226 | } | |
2227 | ||
2228 | 0 | String str; |
2229 | 0 | FileFormatI format; |
2230 | 0 | try |
2231 | { | |
2232 | 0 | str = (String) contents.getTransferData(DataFlavor.stringFlavor); |
2233 | 0 | if (str.length() < 1) |
2234 | { | |
2235 | 0 | return; |
2236 | } | |
2237 | ||
2238 | 0 | format = new IdentifyFile().identify(str, DataSourceType.PASTE); |
2239 | ||
2240 | } catch (OutOfMemoryError er) | |
2241 | { | |
2242 | 0 | new OOMWarning("Out of memory pasting sequences!!", er); |
2243 | 0 | return; |
2244 | } | |
2245 | ||
2246 | 0 | SequenceI[] sequences; |
2247 | 0 | boolean annotationAdded = false; |
2248 | 0 | AlignmentI alignment = null; |
2249 | ||
2250 | 0 | if (Desktop.jalviewClipboard != null) |
2251 | { | |
2252 | // The clipboard was filled from within Jalview, we must use the | |
2253 | // sequences | |
2254 | // And dataset from the copied alignment | |
2255 | 0 | SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; |
2256 | // be doubly sure that we create *new* sequence objects. | |
2257 | 0 | sequences = new SequenceI[newseq.length]; |
2258 | 0 | for (int i = 0; i < newseq.length; i++) |
2259 | { | |
2260 | 0 | sequences[i] = new Sequence(newseq[i]); |
2261 | } | |
2262 | 0 | alignment = new Alignment(sequences); |
2263 | 0 | externalPaste = false; |
2264 | } | |
2265 | else | |
2266 | { | |
2267 | // parse the clipboard as an alignment. | |
2268 | 0 | alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE, |
2269 | format); | |
2270 | 0 | sequences = alignment.getSequencesArray(); |
2271 | } | |
2272 | ||
2273 | 0 | int alwidth = 0; |
2274 | 0 | ArrayList<Integer> newGraphGroups = new ArrayList<>(); |
2275 | 0 | int fgroup = -1; |
2276 | ||
2277 | 0 | if (newAlignment) |
2278 | { | |
2279 | ||
2280 | 0 | if (Desktop.jalviewClipboard != null) |
2281 | { | |
2282 | // dataset is inherited | |
2283 | 0 | alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); |
2284 | } | |
2285 | else | |
2286 | { | |
2287 | // new dataset is constructed | |
2288 | 0 | alignment.setDataset(null); |
2289 | } | |
2290 | 0 | alwidth = alignment.getWidth() + 1; |
2291 | } | |
2292 | else | |
2293 | { | |
2294 | 0 | AlignmentI pastedal = alignment; // preserve pasted alignment object |
2295 | // Add pasted sequences and dataset into existing alignment. | |
2296 | 0 | alignment = viewport.getAlignment(); |
2297 | 0 | alwidth = alignment.getWidth() + 1; |
2298 | // decide if we need to import sequences from an existing dataset | |
2299 | 0 | boolean importDs = Desktop.jalviewClipboard != null |
2300 | && Desktop.jalviewClipboard[1] != alignment.getDataset(); | |
2301 | // importDs==true instructs us to copy over new dataset sequences from | |
2302 | // an existing alignment | |
2303 | 0 | Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to |
2304 | // create | |
2305 | // minimum dataset set | |
2306 | ||
2307 | 0 | for (int i = 0; i < sequences.length; i++) |
2308 | { | |
2309 | 0 | if (importDs) |
2310 | { | |
2311 | 0 | newDs.addElement(null); |
2312 | } | |
2313 | 0 | SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple |
2314 | // paste | |
2315 | 0 | if (importDs && ds != null) |
2316 | { | |
2317 | 0 | if (!newDs.contains(ds)) |
2318 | { | |
2319 | 0 | newDs.setElementAt(ds, i); |
2320 | 0 | ds = new Sequence(ds); |
2321 | // update with new dataset sequence | |
2322 | 0 | sequences[i].setDatasetSequence(ds); |
2323 | } | |
2324 | else | |
2325 | { | |
2326 | 0 | ds = sequences[newDs.indexOf(ds)].getDatasetSequence(); |
2327 | } | |
2328 | } | |
2329 | else | |
2330 | { | |
2331 | // copy and derive new dataset sequence | |
2332 | 0 | sequences[i] = sequences[i].deriveSequence(); |
2333 | 0 | alignment.getDataset() |
2334 | .addSequence(sequences[i].getDatasetSequence()); | |
2335 | // TODO: avoid creation of duplicate dataset sequences with a | |
2336 | // 'contains' method using SequenceI.equals()/SequenceI.contains() | |
2337 | } | |
2338 | 0 | alignment.addSequence(sequences[i]); // merges dataset |
2339 | } | |
2340 | 0 | if (newDs != null) |
2341 | { | |
2342 | 0 | newDs.clear(); // tidy up |
2343 | } | |
2344 | 0 | if (alignment.getAlignmentAnnotation() != null) |
2345 | { | |
2346 | 0 | for (AlignmentAnnotation alan : alignment |
2347 | .getAlignmentAnnotation()) | |
2348 | { | |
2349 | 0 | if (alan.graphGroup > fgroup) |
2350 | { | |
2351 | 0 | fgroup = alan.graphGroup; |
2352 | } | |
2353 | } | |
2354 | } | |
2355 | 0 | if (pastedal.getAlignmentAnnotation() != null) |
2356 | { | |
2357 | // Add any annotation attached to alignment. | |
2358 | 0 | AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation(); |
2359 | 0 | for (int i = 0; i < alann.length; i++) |
2360 | { | |
2361 | 0 | annotationAdded = true; |
2362 | 0 | if (alann[i].sequenceRef == null && !alann[i].autoCalculated) |
2363 | { | |
2364 | 0 | AlignmentAnnotation newann = new AlignmentAnnotation( |
2365 | alann[i]); | |
2366 | 0 | if (newann.graphGroup > -1) |
2367 | { | |
2368 | 0 | if (newGraphGroups.size() <= newann.graphGroup |
2369 | || newGraphGroups.get(newann.graphGroup) == null) | |
2370 | { | |
2371 | 0 | for (int q = newGraphGroups |
2372 | 0 | .size(); q <= newann.graphGroup; q++) |
2373 | { | |
2374 | 0 | newGraphGroups.add(q, null); |
2375 | } | |
2376 | 0 | newGraphGroups.set(newann.graphGroup, |
2377 | Integer.valueOf(++fgroup)); | |
2378 | } | |
2379 | 0 | newann.graphGroup = newGraphGroups.get(newann.graphGroup) |
2380 | .intValue(); | |
2381 | } | |
2382 | ||
2383 | 0 | newann.padAnnotation(alwidth); |
2384 | 0 | alignment.addAnnotation(newann); |
2385 | } | |
2386 | } | |
2387 | } | |
2388 | } | |
2389 | 0 | if (!newAlignment) |
2390 | { | |
2391 | // ///// | |
2392 | // ADD HISTORY ITEM | |
2393 | // | |
2394 | 0 | addHistoryItem(new EditCommand( |
2395 | MessageManager.getString("label.add_sequences"), | |
2396 | Action.PASTE, sequences, 0, alignment.getWidth(), | |
2397 | alignment)); | |
2398 | } | |
2399 | // Add any annotations attached to sequences | |
2400 | 0 | for (int i = 0; i < sequences.length; i++) |
2401 | { | |
2402 | 0 | if (sequences[i].getAnnotation() != null) |
2403 | { | |
2404 | 0 | AlignmentAnnotation newann; |
2405 | 0 | for (int a = 0; a < sequences[i].getAnnotation().length; a++) |
2406 | { | |
2407 | 0 | annotationAdded = true; |
2408 | 0 | newann = sequences[i].getAnnotation()[a]; |
2409 | 0 | newann.adjustForAlignment(); |
2410 | 0 | newann.padAnnotation(alwidth); |
2411 | 0 | if (newann.graphGroup > -1) |
2412 | { | |
2413 | 0 | if (newann.graphGroup > -1) |
2414 | { | |
2415 | 0 | if (newGraphGroups.size() <= newann.graphGroup |
2416 | || newGraphGroups.get(newann.graphGroup) == null) | |
2417 | { | |
2418 | 0 | for (int q = newGraphGroups |
2419 | 0 | .size(); q <= newann.graphGroup; q++) |
2420 | { | |
2421 | 0 | newGraphGroups.add(q, null); |
2422 | } | |
2423 | 0 | newGraphGroups.set(newann.graphGroup, |
2424 | Integer.valueOf(++fgroup)); | |
2425 | } | |
2426 | 0 | newann.graphGroup = newGraphGroups.get(newann.graphGroup) |
2427 | .intValue(); | |
2428 | } | |
2429 | } | |
2430 | // annotation was duplicated earlier | |
2431 | 0 | alignment.addAnnotation(sequences[i].getAnnotation()[a]); |
2432 | // take care of contact matrix too | |
2433 | 0 | ContactMatrixI cm = sequences[i] |
2434 | .getContactMatrixFor(sequences[i].getAnnotation()[a]); | |
2435 | 0 | if (cm != null) |
2436 | { | |
2437 | 0 | alignment.addContactListFor(sequences[i].getAnnotation()[a], |
2438 | cm); | |
2439 | } | |
2440 | ||
2441 | 0 | alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], |
2442 | a); | |
2443 | } | |
2444 | } | |
2445 | } | |
2446 | 0 | if (!newAlignment) |
2447 | { | |
2448 | ||
2449 | // propagate alignment changed. | |
2450 | 0 | viewport.getRanges().setEndSeq(alignment.getHeight() - 1); |
2451 | 0 | if (annotationAdded) |
2452 | { | |
2453 | // Duplicate sequence annotation in all views. | |
2454 | 0 | AlignmentI[] alview = this.getViewAlignments(); |
2455 | 0 | for (int i = 0; i < sequences.length; i++) |
2456 | { | |
2457 | 0 | AlignmentAnnotation sann[] = sequences[i].getAnnotation(); |
2458 | 0 | if (sann == null) |
2459 | { | |
2460 | 0 | continue; |
2461 | } | |
2462 | 0 | for (int avnum = 0; avnum < alview.length; avnum++) |
2463 | { | |
2464 | 0 | if (alview[avnum] != alignment) |
2465 | { | |
2466 | // duplicate in a view other than the one with input focus | |
2467 | 0 | int avwidth = alview[avnum].getWidth() + 1; |
2468 | // this relies on sann being preserved after we | |
2469 | // modify the sequence's annotation array for each duplication | |
2470 | 0 | for (int a = 0; a < sann.length; a++) |
2471 | { | |
2472 | 0 | AlignmentAnnotation newann = new AlignmentAnnotation( |
2473 | sann[a]); | |
2474 | 0 | sequences[i].addAlignmentAnnotation(newann); |
2475 | 0 | newann.padAnnotation(avwidth); |
2476 | 0 | alview[avnum].addAnnotation(newann); // annotation was |
2477 | // duplicated earlier | |
2478 | // TODO JAL-1145 graphGroups are not updated for sequence | |
2479 | // annotation added to several views. This may cause | |
2480 | // strangeness | |
2481 | 0 | alview[avnum].setAnnotationIndex(newann, a); |
2482 | } | |
2483 | } | |
2484 | } | |
2485 | } | |
2486 | 0 | buildSortByAnnotationScoresMenu(); |
2487 | } | |
2488 | 0 | viewport.firePropertyChange("alignment", null, |
2489 | alignment.getSequences()); | |
2490 | 0 | if (alignPanels != null) |
2491 | { | |
2492 | 0 | for (AlignmentPanel ap : alignPanels) |
2493 | { | |
2494 | 0 | ap.validateAnnotationDimensions(false); |
2495 | } | |
2496 | } | |
2497 | else | |
2498 | { | |
2499 | 0 | alignPanel.validateAnnotationDimensions(false); |
2500 | } | |
2501 | ||
2502 | } | |
2503 | else | |
2504 | { | |
2505 | 0 | AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, |
2506 | DEFAULT_HEIGHT); | |
2507 | 0 | String newtitle = new String("Copied sequences"); |
2508 | ||
2509 | 0 | if (Desktop.jalviewClipboard != null |
2510 | && Desktop.jalviewClipboard[2] != null) | |
2511 | { | |
2512 | 0 | HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; |
2513 | 0 | af.viewport.setHiddenColumns(hc); |
2514 | } | |
2515 | ||
2516 | // >>>This is a fix for the moment, until a better solution is | |
2517 | // found!!<<< | |
2518 | 0 | af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() |
2519 | .transferSettings(alignPanel.getSeqPanel().seqCanvas | |
2520 | .getFeatureRenderer()); | |
2521 | ||
2522 | // TODO: maintain provenance of an alignment, rather than just make the | |
2523 | // title a concatenation of operations. | |
2524 | 0 | if (!externalPaste) |
2525 | { | |
2526 | 0 | if (title.startsWith("Copied sequences")) |
2527 | { | |
2528 | 0 | newtitle = title; |
2529 | } | |
2530 | else | |
2531 | { | |
2532 | 0 | newtitle = newtitle.concat("- from " + title); |
2533 | } | |
2534 | } | |
2535 | else | |
2536 | { | |
2537 | 0 | newtitle = new String("Pasted sequences"); |
2538 | } | |
2539 | ||
2540 | 0 | Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, |
2541 | DEFAULT_HEIGHT); | |
2542 | ||
2543 | } | |
2544 | ||
2545 | } catch (Exception ex) | |
2546 | { | |
2547 | 0 | ex.printStackTrace(); |
2548 | 0 | jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); |
2549 | // could be anything being pasted in here | |
2550 | } | |
2551 | ||
2552 | } | |
2553 | ||
2554 | 0 | @Override |
2555 | protected void expand_newalign(ActionEvent e) | |
2556 | { | |
2557 | 0 | try |
2558 | { | |
2559 | 0 | AlignmentI alignment = AlignmentUtils |
2560 | .expandContext(getViewport().getAlignment(), -1); | |
2561 | 0 | AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, |
2562 | DEFAULT_HEIGHT); | |
2563 | 0 | String newtitle = new String("Flanking alignment"); |
2564 | ||
2565 | 0 | if (Desktop.jalviewClipboard != null |
2566 | && Desktop.jalviewClipboard[2] != null) | |
2567 | { | |
2568 | 0 | HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; |
2569 | 0 | af.viewport.setHiddenColumns(hc); |
2570 | } | |
2571 | ||
2572 | // >>>This is a fix for the moment, until a better solution is | |
2573 | // found!!<<< | |
2574 | 0 | af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() |
2575 | .transferSettings(alignPanel.getSeqPanel().seqCanvas | |
2576 | .getFeatureRenderer()); | |
2577 | ||
2578 | // TODO: maintain provenance of an alignment, rather than just make the | |
2579 | // title a concatenation of operations. | |
2580 | { | |
2581 | 0 | if (title.startsWith("Copied sequences")) |
2582 | { | |
2583 | 0 | newtitle = title; |
2584 | } | |
2585 | else | |
2586 | { | |
2587 | 0 | newtitle = newtitle.concat("- from " + title); |
2588 | } | |
2589 | } | |
2590 | ||
2591 | 0 | Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); |
2592 | ||
2593 | } catch (Exception ex) | |
2594 | { | |
2595 | 0 | ex.printStackTrace(); |
2596 | 0 | jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); |
2597 | // could be anything being pasted in here | |
2598 | } catch (OutOfMemoryError oom) | |
2599 | { | |
2600 | 0 | new OOMWarning("Viewing flanking region of alignment", oom); |
2601 | } | |
2602 | } | |
2603 | ||
2604 | /** | |
2605 | * Action Cut (delete and copy) the selected region | |
2606 | */ | |
2607 | 0 | @Override |
2608 | protected void cut_actionPerformed() | |
2609 | { | |
2610 | 0 | copy_actionPerformed(); |
2611 | 0 | delete_actionPerformed(); |
2612 | } | |
2613 | ||
2614 | /** | |
2615 | * Performs menu option to Delete the currently selected region | |
2616 | */ | |
2617 | 0 | @Override |
2618 | protected void delete_actionPerformed() | |
2619 | { | |
2620 | ||
2621 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
2622 | 0 | if (sg == null) |
2623 | { | |
2624 | 0 | return; |
2625 | } | |
2626 | ||
2627 | 0 | Runnable okAction = () -> { |
2628 | 0 | SequenceI[] cut = sg.getSequences() |
2629 | .toArray(new SequenceI[sg.getSize()]); | |
2630 | ||
2631 | 0 | addHistoryItem(new EditCommand( |
2632 | MessageManager.getString("label.cut_sequences"), Action.CUT, | |
2633 | cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, | |
2634 | viewport.getAlignment())); | |
2635 | ||
2636 | 0 | viewport.setSelectionGroup(null); |
2637 | 0 | viewport.sendSelection(); |
2638 | 0 | viewport.getAlignment().deleteGroup(sg); |
2639 | ||
2640 | 0 | viewport.firePropertyChange("alignment", null, |
2641 | viewport.getAlignment().getSequences()); | |
2642 | 0 | if (viewport.getAlignment().getHeight() < 1) |
2643 | { | |
2644 | 0 | try |
2645 | { | |
2646 | 0 | AlignFrame.this.setClosed(true); |
2647 | } catch (Exception ex) | |
2648 | { | |
2649 | } | |
2650 | } | |
2651 | }; | |
2652 | ||
2653 | /* | |
2654 | * If the cut affects all sequences, prompt for confirmation | |
2655 | */ | |
2656 | 0 | boolean wholeHeight = sg.getSize() == viewport.getAlignment() |
2657 | .getHeight(); | |
2658 | 0 | boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes()) |
2659 | + 1) == viewport.getAlignment().getWidth()) ? true : false; | |
2660 | 0 | if (wholeHeight && wholeWidth) |
2661 | { | |
2662 | 0 | JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); |
2663 | 0 | dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION |
2664 | 0 | Object[] options = new Object[] { |
2665 | MessageManager.getString("action.ok"), | |
2666 | MessageManager.getString("action.cancel") }; | |
2667 | 0 | dialog.showDialog(MessageManager.getString("warn.delete_all"), |
2668 | MessageManager.getString("label.delete_all"), | |
2669 | JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, | |
2670 | options, options[0]); | |
2671 | } | |
2672 | else | |
2673 | { | |
2674 | 0 | try |
2675 | { | |
2676 | 0 | okAction.run(); |
2677 | } catch (Exception e) | |
2678 | { | |
2679 | 0 | e.printStackTrace(); |
2680 | } | |
2681 | } | |
2682 | } | |
2683 | ||
2684 | /** | |
2685 | * DOCUMENT ME! | |
2686 | * | |
2687 | * @param e | |
2688 | * DOCUMENT ME! | |
2689 | */ | |
2690 | 0 | @Override |
2691 | protected void deleteGroups_actionPerformed(ActionEvent e) | |
2692 | { | |
2693 | 0 | if (avc.deleteGroups()) |
2694 | { | |
2695 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
2696 | 0 | alignPanel.updateAnnotation(); |
2697 | 0 | alignPanel.paintAlignment(true, true); |
2698 | } | |
2699 | } | |
2700 | ||
2701 | /** | |
2702 | * DOCUMENT ME! | |
2703 | * | |
2704 | * @param e | |
2705 | * DOCUMENT ME! | |
2706 | */ | |
2707 | 6 | @Override |
2708 | public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) | |
2709 | { | |
2710 | 6 | SequenceGroup sg = new SequenceGroup( |
2711 | viewport.getAlignment().getSequences()); | |
2712 | ||
2713 | 6 | sg.setEndRes(viewport.getAlignment().getWidth() - 1); |
2714 | 6 | viewport.setSelectionGroup(sg); |
2715 | 6 | viewport.isSelectionGroupChanged(true); |
2716 | 6 | viewport.sendSelection(); |
2717 | // JAL-2034 - should delegate to | |
2718 | // alignPanel to decide if overview needs | |
2719 | // updating. | |
2720 | 6 | alignPanel.paintAlignment(false, false); |
2721 | 6 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2722 | } | |
2723 | ||
2724 | /** | |
2725 | * DOCUMENT ME! | |
2726 | * | |
2727 | * @param e | |
2728 | * DOCUMENT ME! | |
2729 | */ | |
2730 | 2 | @Override |
2731 | public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) | |
2732 | { | |
2733 | 2 | if (viewport.cursorMode) |
2734 | { | |
2735 | 0 | alignPanel.getSeqPanel().keyboardNo1 = null; |
2736 | 0 | alignPanel.getSeqPanel().keyboardNo2 = null; |
2737 | } | |
2738 | 2 | viewport.setSelectionGroup(null); |
2739 | 2 | viewport.getColumnSelection().clear(); |
2740 | 2 | viewport.setSearchResults(null); |
2741 | 2 | alignPanel.getIdPanel().getIdCanvas().searchResults = null; |
2742 | // JAL-2034 - should delegate to | |
2743 | // alignPanel to decide if overview needs | |
2744 | // updating. | |
2745 | 2 | alignPanel.paintAlignment(false, false); |
2746 | 2 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2747 | 2 | viewport.sendSelection(); |
2748 | } | |
2749 | ||
2750 | /** | |
2751 | * DOCUMENT ME! | |
2752 | * | |
2753 | * @param e | |
2754 | * DOCUMENT ME! | |
2755 | */ | |
2756 | 0 | @Override |
2757 | public void invertSequenceMenuItem_actionPerformed(ActionEvent e) | |
2758 | { | |
2759 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
2760 | ||
2761 | 0 | if (sg == null) |
2762 | { | |
2763 | 0 | selectAllSequenceMenuItem_actionPerformed(null); |
2764 | ||
2765 | 0 | return; |
2766 | } | |
2767 | ||
2768 | 0 | for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) |
2769 | { | |
2770 | 0 | sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); |
2771 | } | |
2772 | // JAL-2034 - should delegate to | |
2773 | // alignPanel to decide if overview needs | |
2774 | // updating. | |
2775 | ||
2776 | 0 | alignPanel.paintAlignment(true, false); |
2777 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2778 | 0 | viewport.sendSelection(); |
2779 | } | |
2780 | ||
2781 | 0 | @Override |
2782 | public void invertColSel_actionPerformed(ActionEvent e) | |
2783 | { | |
2784 | 0 | viewport.invertColumnSelection(); |
2785 | 0 | alignPanel.paintAlignment(true, false); |
2786 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2787 | 0 | viewport.sendSelection(); |
2788 | } | |
2789 | ||
2790 | /** | |
2791 | * DOCUMENT ME! | |
2792 | * | |
2793 | * @param e | |
2794 | * DOCUMENT ME! | |
2795 | */ | |
2796 | 0 | @Override |
2797 | public void remove2LeftMenuItem_actionPerformed(ActionEvent e) | |
2798 | { | |
2799 | 0 | trimAlignment(true); |
2800 | } | |
2801 | ||
2802 | /** | |
2803 | * DOCUMENT ME! | |
2804 | * | |
2805 | * @param e | |
2806 | * DOCUMENT ME! | |
2807 | */ | |
2808 | 0 | @Override |
2809 | public void remove2RightMenuItem_actionPerformed(ActionEvent e) | |
2810 | { | |
2811 | 0 | trimAlignment(false); |
2812 | } | |
2813 | ||
2814 | 0 | void trimAlignment(boolean trimLeft) |
2815 | { | |
2816 | 0 | ColumnSelection colSel = viewport.getColumnSelection(); |
2817 | 0 | int column; |
2818 | ||
2819 | 0 | if (!colSel.isEmpty()) |
2820 | { | |
2821 | 0 | if (trimLeft) |
2822 | { | |
2823 | 0 | column = colSel.getMin(); |
2824 | } | |
2825 | else | |
2826 | { | |
2827 | 0 | column = colSel.getMax(); |
2828 | } | |
2829 | ||
2830 | 0 | SequenceI[] seqs; |
2831 | 0 | if (viewport.getSelectionGroup() != null) |
2832 | { | |
2833 | 0 | seqs = viewport.getSelectionGroup() |
2834 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2835 | } | |
2836 | else | |
2837 | { | |
2838 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2839 | } | |
2840 | ||
2841 | 0 | TrimRegionCommand trimRegion; |
2842 | 0 | if (trimLeft) |
2843 | { | |
2844 | 0 | trimRegion = new TrimRegionCommand("Remove Left", true, seqs, |
2845 | column, viewport.getAlignment()); | |
2846 | 0 | viewport.getRanges().setStartRes(0); |
2847 | } | |
2848 | else | |
2849 | { | |
2850 | 0 | trimRegion = new TrimRegionCommand("Remove Right", false, seqs, |
2851 | column, viewport.getAlignment()); | |
2852 | } | |
2853 | ||
2854 | 0 | setStatus(MessageManager.formatMessage("label.removed_columns", |
2855 | new String[] | |
2856 | { Integer.valueOf(trimRegion.getSize()).toString() })); | |
2857 | ||
2858 | 0 | addHistoryItem(trimRegion); |
2859 | ||
2860 | 0 | for (SequenceGroup sg : viewport.getAlignment().getGroups()) |
2861 | { | |
2862 | 0 | if ((trimLeft && !sg.adjustForRemoveLeft(column)) |
2863 | || (!trimLeft && !sg.adjustForRemoveRight(column))) | |
2864 | { | |
2865 | 0 | viewport.getAlignment().deleteGroup(sg); |
2866 | } | |
2867 | } | |
2868 | ||
2869 | 0 | viewport.firePropertyChange("alignment", null, |
2870 | viewport.getAlignment().getSequences()); | |
2871 | } | |
2872 | } | |
2873 | ||
2874 | /** | |
2875 | * DOCUMENT ME! | |
2876 | * | |
2877 | * @param e | |
2878 | * DOCUMENT ME! | |
2879 | */ | |
2880 | 0 | @Override |
2881 | public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) | |
2882 | { | |
2883 | 0 | int start = 0, end = viewport.getAlignment().getWidth() - 1; |
2884 | ||
2885 | 0 | SequenceI[] seqs; |
2886 | 0 | if (viewport.getSelectionGroup() != null) |
2887 | { | |
2888 | 0 | seqs = viewport.getSelectionGroup() |
2889 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2890 | 0 | start = viewport.getSelectionGroup().getStartRes(); |
2891 | 0 | end = viewport.getSelectionGroup().getEndRes(); |
2892 | } | |
2893 | else | |
2894 | { | |
2895 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2896 | } | |
2897 | ||
2898 | 0 | RemoveGapColCommand removeGapCols = new RemoveGapColCommand( |
2899 | "Remove Gapped Columns", seqs, start, end, | |
2900 | viewport.getAlignment()); | |
2901 | ||
2902 | 0 | addHistoryItem(removeGapCols); |
2903 | ||
2904 | 0 | setStatus(MessageManager.formatMessage("label.removed_empty_columns", |
2905 | new Object[] | |
2906 | { Integer.valueOf(removeGapCols.getSize()).toString() })); | |
2907 | ||
2908 | // This is to maintain viewport position on first residue | |
2909 | // of first sequence | |
2910 | 0 | SequenceI seq = viewport.getAlignment().getSequenceAt(0); |
2911 | 0 | ViewportRanges ranges = viewport.getRanges(); |
2912 | 0 | int startRes = seq.findPosition(ranges.getStartRes()); |
2913 | // ShiftList shifts; | |
2914 | // viewport.getAlignment().removeGaps(shifts=new ShiftList()); | |
2915 | // edit.alColumnChanges=shifts.getInverse(); | |
2916 | // if (viewport.hasHiddenColumns) | |
2917 | // viewport.getColumnSelection().compensateForEdits(shifts); | |
2918 | 0 | ranges.setStartRes(seq.findIndex(startRes) - 1); |
2919 | 0 | viewport.firePropertyChange("alignment", null, |
2920 | viewport.getAlignment().getSequences()); | |
2921 | ||
2922 | } | |
2923 | ||
2924 | /** | |
2925 | * DOCUMENT ME! | |
2926 | * | |
2927 | * @param e | |
2928 | * DOCUMENT ME! | |
2929 | */ | |
2930 | 0 | @Override |
2931 | public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) | |
2932 | { | |
2933 | 0 | int start = 0, end = viewport.getAlignment().getWidth() - 1; |
2934 | ||
2935 | 0 | SequenceI[] seqs; |
2936 | 0 | if (viewport.getSelectionGroup() != null) |
2937 | { | |
2938 | 0 | seqs = viewport.getSelectionGroup() |
2939 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2940 | 0 | start = viewport.getSelectionGroup().getStartRes(); |
2941 | 0 | end = viewport.getSelectionGroup().getEndRes(); |
2942 | } | |
2943 | else | |
2944 | { | |
2945 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2946 | } | |
2947 | ||
2948 | // This is to maintain viewport position on first residue | |
2949 | // of first sequence | |
2950 | 0 | SequenceI seq = viewport.getAlignment().getSequenceAt(0); |
2951 | 0 | int startRes = seq.findPosition(viewport.getRanges().getStartRes()); |
2952 | ||
2953 | 0 | addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, |
2954 | viewport.getAlignment())); | |
2955 | ||
2956 | 0 | viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); |
2957 | ||
2958 | 0 | viewport.firePropertyChange("alignment", null, |
2959 | viewport.getAlignment().getSequences()); | |
2960 | ||
2961 | } | |
2962 | ||
2963 | /** | |
2964 | * DOCUMENT ME! | |
2965 | * | |
2966 | * @param e | |
2967 | * DOCUMENT ME! | |
2968 | */ | |
2969 | 0 | @Override |
2970 | public void padGapsMenuitem_actionPerformed(ActionEvent e) | |
2971 | { | |
2972 | 0 | viewport.setPadGaps(padGapsMenuitem.isSelected()); |
2973 | 0 | viewport.firePropertyChange("alignment", null, |
2974 | viewport.getAlignment().getSequences()); | |
2975 | } | |
2976 | ||
2977 | /** | |
2978 | * Opens a Finder dialog | |
2979 | * | |
2980 | * @param e | |
2981 | */ | |
2982 | 0 | @Override |
2983 | public void findMenuItem_actionPerformed(ActionEvent e) | |
2984 | { | |
2985 | 0 | new Finder(alignPanel, false, null); |
2986 | } | |
2987 | ||
2988 | /** | |
2989 | * Create a new view of the current alignment. | |
2990 | */ | |
2991 | 7 | @Override |
2992 | public void newView_actionPerformed(ActionEvent e) | |
2993 | { | |
2994 | 7 | newView(null, true); |
2995 | } | |
2996 | ||
2997 | /** | |
2998 | * Creates and shows a new view of the current alignment. | |
2999 | * | |
3000 | * @param viewTitle | |
3001 | * title of newly created view; if null, one will be generated | |
3002 | * @param copyAnnotation | |
3003 | * if true then duplicate all annnotation, groups and settings | |
3004 | * @return new alignment panel, already displayed. | |
3005 | */ | |
3006 | 10 | public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) |
3007 | { | |
3008 | /* | |
3009 | * Create a new AlignmentPanel (with its own, new Viewport) | |
3010 | */ | |
3011 | 10 | AlignmentPanel newap = new jalview.project.Jalview2XML() |
3012 | .copyAlignPanel(alignPanel); | |
3013 | 10 | if (!copyAnnotation) |
3014 | { | |
3015 | /* | |
3016 | * remove all groups and annotation except for the automatic stuff | |
3017 | */ | |
3018 | 0 | newap.av.getAlignment().deleteAllGroups(); |
3019 | 0 | newap.av.getAlignment().deleteAllAnnotations(false); |
3020 | } | |
3021 | ||
3022 | 10 | newap.av.setGatherViewsHere(false); |
3023 | ||
3024 | 10 | if (viewport.getViewName() == null) |
3025 | { | |
3026 | 9 | viewport.setViewName( |
3027 | MessageManager.getString("label.view_name_original")); | |
3028 | } | |
3029 | ||
3030 | /* | |
3031 | * Views share the same edits undo and redo stacks | |
3032 | */ | |
3033 | 10 | newap.av.setHistoryList(viewport.getHistoryList()); |
3034 | 10 | newap.av.setRedoList(viewport.getRedoList()); |
3035 | ||
3036 | /* | |
3037 | * copy any visualisation settings that are not saved in the project | |
3038 | */ | |
3039 | 10 | newap.av.setColourAppliesToAllGroups( |
3040 | viewport.getColourAppliesToAllGroups()); | |
3041 | ||
3042 | /* | |
3043 | * Views share the same mappings; need to deregister any new mappings | |
3044 | * created by copyAlignPanel, and register the new reference to the shared | |
3045 | * mappings | |
3046 | */ | |
3047 | 10 | newap.av.replaceMappings(viewport.getAlignment()); |
3048 | ||
3049 | /* | |
3050 | * start up cDNA consensus (if applicable) now mappings are in place | |
3051 | */ | |
3052 | 10 | if (newap.av.initComplementConsensus()) |
3053 | { | |
3054 | 0 | newap.refresh(true); // adjust layout of annotations |
3055 | } | |
3056 | ||
3057 | 10 | newap.av.setViewName(getNewViewName(viewTitle)); |
3058 | ||
3059 | 10 | addAlignmentPanel(newap, true); |
3060 | 10 | newap.alignmentChanged(); |
3061 | ||
3062 | 10 | if (alignPanels.size() == 2) |
3063 | { | |
3064 | 9 | viewport.setGatherViewsHere(true); |
3065 | } | |
3066 | 10 | tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); |
3067 | ||
3068 | 10 | return newap; |
3069 | } | |
3070 | ||
3071 | /** | |
3072 | * Make a new name for the view, ensuring it is unique within the current | |
3073 | * sequenceSetId. (This used to be essential for Jalview Project archives, but | |
3074 | * these now use viewId. Unique view names are still desirable for usability.) | |
3075 | * | |
3076 | * @param viewTitle | |
3077 | * @return | |
3078 | */ | |
3079 | 10 | protected String getNewViewName(String viewTitle) |
3080 | { | |
3081 | 10 | int index = Desktop.getViewCount(viewport.getSequenceSetId()); |
3082 | 10 | boolean addFirstIndex = false; |
3083 | 10 | if (viewTitle == null || viewTitle.trim().length() == 0) |
3084 | { | |
3085 | 7 | viewTitle = MessageManager.getString("action.view"); |
3086 | 7 | addFirstIndex = true; |
3087 | } | |
3088 | else | |
3089 | { | |
3090 | 3 | index = 1;// we count from 1 if given a specific name |
3091 | } | |
3092 | 10 | String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); |
3093 | ||
3094 | 10 | List<Component> comps = PaintRefresher.components |
3095 | .get(viewport.getSequenceSetId()); | |
3096 | ||
3097 | 10 | List<String> existingNames = getExistingViewNames(comps); |
3098 | ||
3099 | 10 | while (existingNames.contains(newViewName)) |
3100 | { | |
3101 | 0 | newViewName = viewTitle + " " + (++index); |
3102 | } | |
3103 | 10 | return newViewName; |
3104 | } | |
3105 | ||
3106 | /** | |
3107 | * Returns a list of distinct view names found in the given list of | |
3108 | * components. View names are held on the viewport of an AlignmentPanel. | |
3109 | * | |
3110 | * @param comps | |
3111 | * @return | |
3112 | */ | |
3113 | 10 | protected List<String> getExistingViewNames(List<Component> comps) |
3114 | { | |
3115 | 10 | List<String> existingNames = new ArrayList<>(); |
3116 | 10 | for (Component comp : comps) |
3117 | { | |
3118 | 63 | if (comp instanceof AlignmentPanel) |
3119 | { | |
3120 | 21 | AlignmentPanel ap = (AlignmentPanel) comp; |
3121 | 21 | if (!existingNames.contains(ap.av.getViewName())) |
3122 | { | |
3123 | 20 | existingNames.add(ap.av.getViewName()); |
3124 | } | |
3125 | } | |
3126 | } | |
3127 | 10 | return existingNames; |
3128 | } | |
3129 | ||
3130 | /** | |
3131 | * Explode tabbed views into separate windows. | |
3132 | */ | |
3133 | 0 | @Override |
3134 | public void expandViews_actionPerformed(ActionEvent e) | |
3135 | { | |
3136 | 0 | Desktop.explodeViews(this); |
3137 | } | |
3138 | ||
3139 | /** | |
3140 | * Gather views in separate windows back into a tabbed presentation. | |
3141 | */ | |
3142 | 0 | @Override |
3143 | public void gatherViews_actionPerformed(ActionEvent e) | |
3144 | { | |
3145 | 0 | Desktop.instance.gatherViews(this); |
3146 | } | |
3147 | ||
3148 | /** | |
3149 | * DOCUMENT ME! | |
3150 | * | |
3151 | * @param e | |
3152 | * DOCUMENT ME! | |
3153 | */ | |
3154 | 0 | @Override |
3155 | public void font_actionPerformed(ActionEvent e) | |
3156 | { | |
3157 | 0 | new FontChooser(alignPanel); |
3158 | } | |
3159 | ||
3160 | /** | |
3161 | * DOCUMENT ME! | |
3162 | * | |
3163 | * @param e | |
3164 | * DOCUMENT ME! | |
3165 | */ | |
3166 | 0 | @Override |
3167 | protected void seqLimit_actionPerformed(ActionEvent e) | |
3168 | { | |
3169 | 0 | viewport.setShowJVSuffix(seqLimits.isSelected()); |
3170 | ||
3171 | 0 | alignPanel.getIdPanel().getIdCanvas() |
3172 | .setPreferredSize(alignPanel.calculateIdWidth()); | |
3173 | 0 | alignPanel.paintAlignment(true, false); |
3174 | } | |
3175 | ||
3176 | 0 | @Override |
3177 | public void idRightAlign_actionPerformed(ActionEvent e) | |
3178 | { | |
3179 | 0 | viewport.setRightAlignIds(idRightAlign.isSelected()); |
3180 | 0 | alignPanel.paintAlignment(false, false); |
3181 | } | |
3182 | ||
3183 | 0 | @Override |
3184 | public void centreColumnLabels_actionPerformed(ActionEvent e) | |
3185 | { | |
3186 | 0 | viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); |
3187 | 0 | alignPanel.paintAlignment(false, false); |
3188 | } | |
3189 | ||
3190 | /* | |
3191 | * (non-Javadoc) | |
3192 | * | |
3193 | * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() | |
3194 | */ | |
3195 | 0 | @Override |
3196 | protected void followHighlight_actionPerformed() | |
3197 | { | |
3198 | /* | |
3199 | * Set the 'follow' flag on the Viewport (and scroll to position if now | |
3200 | * true). | |
3201 | */ | |
3202 | 0 | final boolean state = this.followHighlightMenuItem.getState(); |
3203 | 0 | viewport.setFollowHighlight(state); |
3204 | 0 | if (state) |
3205 | { | |
3206 | 0 | alignPanel.scrollToPosition(viewport.getSearchResults()); |
3207 | } | |
3208 | } | |
3209 | ||
3210 | /** | |
3211 | * DOCUMENT ME! | |
3212 | * | |
3213 | * @param e | |
3214 | * DOCUMENT ME! | |
3215 | */ | |
3216 | 0 | @Override |
3217 | protected void colourTextMenuItem_actionPerformed(ActionEvent e) | |
3218 | { | |
3219 | 0 | viewport.setColourText(colourTextMenuItem.isSelected()); |
3220 | 0 | alignPanel.paintAlignment(false, false); |
3221 | } | |
3222 | ||
3223 | /** | |
3224 | * DOCUMENT ME! | |
3225 | * | |
3226 | * @param e | |
3227 | * DOCUMENT ME! | |
3228 | */ | |
3229 | 7 | @Override |
3230 | public void wrapMenuItem_actionPerformed(ActionEvent e) | |
3231 | { | |
3232 | 7 | setWrapFormat(wrapMenuItem.isSelected(), false); |
3233 | } | |
3234 | ||
3235 | 8 | public void setWrapFormat(boolean b, boolean setMenuItem) |
3236 | { | |
3237 | 8 | scaleAbove.setVisible(b); |
3238 | 8 | scaleLeft.setVisible(b); |
3239 | 8 | scaleRight.setVisible(b); |
3240 | 8 | viewport.setWrapAlignment(b); |
3241 | 8 | alignPanel.updateLayout(); |
3242 | 8 | if (setMenuItem) |
3243 | { | |
3244 | 0 | wrapMenuItem.setSelected(b); |
3245 | } | |
3246 | } | |
3247 | ||
3248 | 0 | @Override |
3249 | public void showAllSeqs_actionPerformed(ActionEvent e) | |
3250 | { | |
3251 | 0 | viewport.showAllHiddenSeqs(); |
3252 | } | |
3253 | ||
3254 | 0 | @Override |
3255 | public void showAllColumns_actionPerformed(ActionEvent e) | |
3256 | { | |
3257 | 0 | viewport.showAllHiddenColumns(); |
3258 | 0 | alignPanel.paintAlignment(true, true); |
3259 | 0 | viewport.sendSelection(); |
3260 | } | |
3261 | ||
3262 | 0 | @Override |
3263 | public void hideSelSequences_actionPerformed(ActionEvent e) | |
3264 | { | |
3265 | 0 | viewport.hideAllSelectedSeqs(); |
3266 | } | |
3267 | ||
3268 | /** | |
3269 | * called by key handler and the hide all/show all menu items | |
3270 | * | |
3271 | * @param toggleSeqs | |
3272 | * @param toggleCols | |
3273 | */ | |
3274 | 0 | protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) |
3275 | { | |
3276 | ||
3277 | 0 | boolean hide = false; |
3278 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
3279 | 0 | if (!toggleSeqs && !toggleCols) |
3280 | { | |
3281 | // Hide everything by the current selection - this is a hack - we do the | |
3282 | // invert and then hide | |
3283 | // first check that there will be visible columns after the invert. | |
3284 | 0 | if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 |
3285 | && sg.getStartRes() <= sg.getEndRes())) | |
3286 | { | |
3287 | // now invert the sequence set, if required - empty selection implies | |
3288 | // that no hiding is required. | |
3289 | 0 | if (sg != null) |
3290 | { | |
3291 | 0 | invertSequenceMenuItem_actionPerformed(null); |
3292 | 0 | sg = viewport.getSelectionGroup(); |
3293 | 0 | toggleSeqs = true; |
3294 | ||
3295 | } | |
3296 | 0 | viewport.expandColSelection(sg, true); |
3297 | // finally invert the column selection and get the new sequence | |
3298 | // selection. | |
3299 | 0 | invertColSel_actionPerformed(null); |
3300 | 0 | toggleCols = true; |
3301 | } | |
3302 | } | |
3303 | ||
3304 | 0 | if (toggleSeqs) |
3305 | { | |
3306 | 0 | if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) |
3307 | { | |
3308 | 0 | hideSelSequences_actionPerformed(null); |
3309 | 0 | hide = true; |
3310 | } | |
3311 | 0 | else if (!(toggleCols && viewport.hasSelectedColumns())) |
3312 | { | |
3313 | 0 | showAllSeqs_actionPerformed(null); |
3314 | } | |
3315 | } | |
3316 | ||
3317 | 0 | if (toggleCols) |
3318 | { | |
3319 | 0 | if (viewport.hasSelectedColumns()) |
3320 | { | |
3321 | 0 | hideSelColumns_actionPerformed(null); |
3322 | 0 | if (!toggleSeqs) |
3323 | { | |
3324 | 0 | viewport.setSelectionGroup(sg); |
3325 | } | |
3326 | } | |
3327 | 0 | else if (!hide) |
3328 | { | |
3329 | 0 | showAllColumns_actionPerformed(null); |
3330 | } | |
3331 | } | |
3332 | } | |
3333 | ||
3334 | /* | |
3335 | * (non-Javadoc) | |
3336 | * | |
3337 | * @see | |
3338 | * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. | |
3339 | * event.ActionEvent) | |
3340 | */ | |
3341 | 0 | @Override |
3342 | public void hideAllButSelection_actionPerformed(ActionEvent e) | |
3343 | { | |
3344 | 0 | toggleHiddenRegions(false, false); |
3345 | 0 | viewport.sendSelection(); |
3346 | } | |
3347 | ||
3348 | /* | |
3349 | * (non-Javadoc) | |
3350 | * | |
3351 | * @see | |
3352 | * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event | |
3353 | * .ActionEvent) | |
3354 | */ | |
3355 | 0 | @Override |
3356 | public void hideAllSelection_actionPerformed(ActionEvent e) | |
3357 | { | |
3358 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
3359 | 0 | viewport.expandColSelection(sg, false); |
3360 | 0 | viewport.hideAllSelectedSeqs(); |
3361 | 0 | viewport.hideSelectedColumns(); |
3362 | 0 | alignPanel.updateLayout(); |
3363 | 0 | alignPanel.paintAlignment(true, true); |
3364 | 0 | viewport.sendSelection(); |
3365 | } | |
3366 | ||
3367 | /* | |
3368 | * (non-Javadoc) | |
3369 | * | |
3370 | * @see | |
3371 | * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. | |
3372 | * ActionEvent) | |
3373 | */ | |
3374 | 0 | @Override |
3375 | public void showAllhidden_actionPerformed(ActionEvent e) | |
3376 | { | |
3377 | 0 | viewport.showAllHiddenColumns(); |
3378 | 0 | viewport.showAllHiddenSeqs(); |
3379 | 0 | alignPanel.paintAlignment(true, true); |
3380 | 0 | viewport.sendSelection(); |
3381 | } | |
3382 | ||
3383 | 2 | @Override |
3384 | public void hideSelColumns_actionPerformed(ActionEvent e) | |
3385 | { | |
3386 | 2 | viewport.hideSelectedColumns(); |
3387 | 2 | alignPanel.updateLayout(); |
3388 | 2 | alignPanel.paintAlignment(true, true); |
3389 | 2 | viewport.sendSelection(); |
3390 | } | |
3391 | ||
3392 | 0 | @Override |
3393 | public void hiddenMarkers_actionPerformed(ActionEvent e) | |
3394 | { | |
3395 | 0 | viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); |
3396 | 0 | repaint(); |
3397 | } | |
3398 | ||
3399 | /** | |
3400 | * DOCUMENT ME! | |
3401 | * | |
3402 | * @param e | |
3403 | * DOCUMENT ME! | |
3404 | */ | |
3405 | 0 | @Override |
3406 | protected void scaleAbove_actionPerformed(ActionEvent e) | |
3407 | { | |
3408 | 0 | viewport.setScaleAboveWrapped(scaleAbove.isSelected()); |
3409 | 0 | alignPanel.updateLayout(); |
3410 | 0 | alignPanel.paintAlignment(true, false); |
3411 | } | |
3412 | ||
3413 | /** | |
3414 | * DOCUMENT ME! | |
3415 | * | |
3416 | * @param e | |
3417 | * DOCUMENT ME! | |
3418 | */ | |
3419 | 0 | @Override |
3420 | protected void scaleLeft_actionPerformed(ActionEvent e) | |
3421 | { | |
3422 | 0 | viewport.setScaleLeftWrapped(scaleLeft.isSelected()); |
3423 | 0 | alignPanel.updateLayout(); |
3424 | 0 | alignPanel.paintAlignment(true, false); |
3425 | } | |
3426 | ||
3427 | /** | |
3428 | * DOCUMENT ME! | |
3429 | * | |
3430 | * @param e | |
3431 | * DOCUMENT ME! | |
3432 | */ | |
3433 | 0 | @Override |
3434 | protected void scaleRight_actionPerformed(ActionEvent e) | |
3435 | { | |
3436 | 0 | viewport.setScaleRightWrapped(scaleRight.isSelected()); |
3437 | 0 | alignPanel.updateLayout(); |
3438 | 0 | alignPanel.paintAlignment(true, false); |
3439 | } | |
3440 | ||
3441 | /** | |
3442 | * DOCUMENT ME! | |
3443 | * | |
3444 | * @param e | |
3445 | * DOCUMENT ME! | |
3446 | */ | |
3447 | 0 | @Override |
3448 | public void viewBoxesMenuItem_actionPerformed(ActionEvent e) | |
3449 | { | |
3450 | 0 | viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); |
3451 | 0 | alignPanel.paintAlignment(false, false); |
3452 | } | |
3453 | ||
3454 | /** | |
3455 | * DOCUMENT ME! | |
3456 | * | |
3457 | * @param e | |
3458 | * DOCUMENT ME! | |
3459 | */ | |
3460 | 0 | @Override |
3461 | public void viewTextMenuItem_actionPerformed(ActionEvent e) | |
3462 | { | |
3463 | 0 | viewport.setShowText(viewTextMenuItem.isSelected()); |
3464 | 0 | alignPanel.paintAlignment(false, false); |
3465 | } | |
3466 | ||
3467 | /** | |
3468 | * DOCUMENT ME! | |
3469 | * | |
3470 | * @param e | |
3471 | * DOCUMENT ME! | |
3472 | */ | |
3473 | 0 | @Override |
3474 | protected void renderGapsMenuItem_actionPerformed(ActionEvent e) | |
3475 | { | |
3476 | 0 | viewport.setRenderGaps(renderGapsMenuItem.isSelected()); |
3477 | 0 | alignPanel.paintAlignment(false, false); |
3478 | } | |
3479 | ||
3480 | public FeatureSettings featureSettings; | |
3481 | ||
3482 | 4 | @Override |
3483 | public FeatureSettingsControllerI getFeatureSettingsUI() | |
3484 | { | |
3485 | 4 | return featureSettings; |
3486 | } | |
3487 | ||
3488 | 0 | @Override |
3489 | public void featureSettings_actionPerformed(ActionEvent e) | |
3490 | { | |
3491 | 0 | showFeatureSettingsUI(); |
3492 | } | |
3493 | ||
3494 | 0 | @Override |
3495 | public FeatureSettingsControllerI showFeatureSettingsUI() | |
3496 | { | |
3497 | 0 | if (featureSettings != null) |
3498 | { | |
3499 | 0 | featureSettings.closeOldSettings(); |
3500 | 0 | featureSettings = null; |
3501 | } | |
3502 | 0 | if (!showSeqFeatures.isSelected()) |
3503 | { | |
3504 | // make sure features are actually displayed | |
3505 | 0 | showSeqFeatures.setSelected(true); |
3506 | 0 | showSeqFeatures_actionPerformed(null); |
3507 | } | |
3508 | 0 | featureSettings = new FeatureSettings(this); |
3509 | 0 | return featureSettings; |
3510 | } | |
3511 | ||
3512 | /** | |
3513 | * Set or clear 'Show Sequence Features' | |
3514 | * | |
3515 | * @param evt | |
3516 | * DOCUMENT ME! | |
3517 | */ | |
3518 | 0 | @Override |
3519 | public void showSeqFeatures_actionPerformed(ActionEvent evt) | |
3520 | { | |
3521 | 0 | viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); |
3522 | 0 | alignPanel.paintAlignment(true, true); |
3523 | } | |
3524 | ||
3525 | /** | |
3526 | * Action on toggle of the 'Show annotations' menu item. This shows or hides | |
3527 | * the annotations panel as a whole. | |
3528 | * | |
3529 | * The options to show/hide all annotations should be enabled when the panel | |
3530 | * is shown, and disabled when the panel is hidden. | |
3531 | * | |
3532 | * @param e | |
3533 | */ | |
3534 | 0 | @Override |
3535 | public void annotationPanelMenuItem_actionPerformed(ActionEvent e) | |
3536 | { | |
3537 | 0 | final boolean setVisible = annotationPanelMenuItem.isSelected(); |
3538 | 0 | viewport.setShowAnnotation(setVisible); |
3539 | 0 | this.showAllSeqAnnotations.setEnabled(setVisible); |
3540 | 0 | this.hideAllSeqAnnotations.setEnabled(setVisible); |
3541 | 0 | this.showAllAlAnnotations.setEnabled(setVisible); |
3542 | 0 | this.hideAllAlAnnotations.setEnabled(setVisible); |
3543 | 0 | alignPanel.updateLayout(); |
3544 | } | |
3545 | ||
3546 | 0 | @Override |
3547 | public void alignmentProperties() | |
3548 | { | |
3549 | 0 | JComponent pane; |
3550 | 0 | StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) |
3551 | ||
3552 | .formatAsHtml(); | |
3553 | 0 | String content = MessageManager.formatMessage("label.html_content", |
3554 | new Object[] | |
3555 | { contents.toString() }); | |
3556 | 0 | contents = null; |
3557 | ||
3558 | 0 | if (Platform.isJS()) |
3559 | { | |
3560 | 0 | JLabel textLabel = new JLabel(); |
3561 | 0 | textLabel.setText(content); |
3562 | 0 | textLabel.setBackground(Color.WHITE); |
3563 | ||
3564 | 0 | pane = new JPanel(new BorderLayout()); |
3565 | 0 | ((JPanel) pane).setOpaque(true); |
3566 | 0 | pane.setBackground(Color.WHITE); |
3567 | 0 | ((JPanel) pane).add(textLabel, BorderLayout.NORTH); |
3568 | } | |
3569 | else | |
3570 | /** | |
3571 | * Java only | |
3572 | * | |
3573 | * @j2sIgnore | |
3574 | */ | |
3575 | { | |
3576 | 0 | JEditorPane editPane = new JEditorPane("text/html", ""); |
3577 | 0 | editPane.setEditable(false); |
3578 | 0 | editPane.setText(content); |
3579 | 0 | pane = editPane; |
3580 | } | |
3581 | ||
3582 | 0 | JInternalFrame frame = new JInternalFrame(); |
3583 | 0 | frame.setFrameIcon(null); |
3584 | 0 | frame.getContentPane().add(new JScrollPane(pane)); |
3585 | ||
3586 | 0 | Desktop.addInternalFrame(frame, MessageManager |
3587 | .formatMessage("label.alignment_properties", new Object[] | |
3588 | { getTitle() }), 500, 400); | |
3589 | } | |
3590 | ||
3591 | /** | |
3592 | * Opens an Overview panel for the alignment, unless one is open already | |
3593 | * | |
3594 | * @param e | |
3595 | */ | |
3596 | 30 | @Override |
3597 | public void overviewMenuItem_actionPerformed(ActionEvent e) | |
3598 | { | |
3599 | 30 | boolean showHiddenRegions = Cache |
3600 | .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false); | |
3601 | 30 | openOverviewPanel(showHiddenRegions); |
3602 | } | |
3603 | ||
3604 | 43 | public OverviewPanel openOverviewPanel(boolean showHidden) |
3605 | { | |
3606 | 43 | if (alignPanel.overviewPanel != null) |
3607 | { | |
3608 | 0 | return alignPanel.overviewPanel; |
3609 | } | |
3610 | 43 | JInternalFrame frame = new JInternalFrame(); |
3611 | 43 | frame.setFrameIcon(null); |
3612 | 43 | final OverviewPanel overview = new OverviewPanel(alignPanel, frame, |
3613 | showHidden); | |
3614 | 43 | frame.setContentPane(overview); |
3615 | ||
3616 | 43 | alignPanel.setOverviewPanel(overview); |
3617 | 43 | alignPanel.setOverviewTitle(this); |
3618 | ||
3619 | 43 | Desktop.addInternalFrame(frame, overview.getTitle(), true, |
3620 | frame.getWidth(), frame.getHeight(), true, true); | |
3621 | 43 | frame.pack(); |
3622 | 43 | frame.setLayer(JLayeredPane.PALETTE_LAYER); |
3623 | 43 | final AlignmentPanel thePanel = this.alignPanel; |
3624 | 43 | frame.addInternalFrameListener( |
3625 | new javax.swing.event.InternalFrameAdapter() | |
3626 | { | |
3627 | 39 | @Override |
3628 | public void internalFrameClosed( | |
3629 | javax.swing.event.InternalFrameEvent evt) | |
3630 | { | |
3631 | 39 | overview.dispose(); |
3632 | 39 | thePanel.setOverviewPanel(null); |
3633 | } | |
3634 | }); | |
3635 | 43 | if (getKeyListeners().length > 0) |
3636 | { | |
3637 | 15 | frame.addKeyListener(getKeyListeners()[0]); |
3638 | } | |
3639 | ||
3640 | 43 | return overview; |
3641 | } | |
3642 | ||
3643 | 0 | @Override |
3644 | public void textColour_actionPerformed() | |
3645 | { | |
3646 | 0 | new TextColourChooser().chooseColour(alignPanel, null); |
3647 | } | |
3648 | ||
3649 | /* | |
3650 | * public void covariationColour_actionPerformed() { | |
3651 | * changeColour(new | |
3652 | * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation | |
3653 | * ()[0])); } | |
3654 | */ | |
3655 | 0 | @Override |
3656 | public void annotationColour_actionPerformed() | |
3657 | { | |
3658 | 0 | new AnnotationColourChooser(viewport, alignPanel); |
3659 | } | |
3660 | ||
3661 | 0 | @Override |
3662 | public void annotationColumn_actionPerformed(ActionEvent e) | |
3663 | { | |
3664 | 0 | new AnnotationColumnChooser(viewport, alignPanel); |
3665 | } | |
3666 | ||
3667 | /** | |
3668 | * Action on the user checking or unchecking the option to apply the selected | |
3669 | * colour scheme to all groups. If unchecked, groups may have their own | |
3670 | * independent colour schemes. | |
3671 | * | |
3672 | * @param selected | |
3673 | */ | |
3674 | 3 | @Override |
3675 | public void applyToAllGroups_actionPerformed(boolean selected) | |
3676 | { | |
3677 | 3 | viewport.setColourAppliesToAllGroups(selected); |
3678 | } | |
3679 | ||
3680 | /** | |
3681 | * Action on user selecting a colour from the colour menu | |
3682 | * | |
3683 | * @param name | |
3684 | * the name (not the menu item label!) of the colour scheme | |
3685 | */ | |
3686 | 15 | @Override |
3687 | public void changeColour_actionPerformed(String name) | |
3688 | { | |
3689 | /* | |
3690 | * 'User Defined' opens a panel to configure or load a | |
3691 | * user-defined colour scheme | |
3692 | */ | |
3693 | 15 | if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) |
3694 | { | |
3695 | 0 | new UserDefinedColours(alignPanel); |
3696 | 0 | return; |
3697 | } | |
3698 | ||
3699 | /* | |
3700 | * otherwise set the chosen colour scheme (or null for 'None') | |
3701 | */ | |
3702 | 15 | ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, |
3703 | viewport, viewport.getAlignment(), | |
3704 | viewport.getHiddenRepSequences()); | |
3705 | 15 | changeColour(cs); |
3706 | } | |
3707 | ||
3708 | /** | |
3709 | * Actions on setting or changing the alignment colour scheme | |
3710 | * | |
3711 | * @param cs | |
3712 | */ | |
3713 | 179 | @Override |
3714 | public void changeColour(ColourSchemeI cs) | |
3715 | { | |
3716 | // TODO: pull up to controller method | |
3717 | 179 | ColourMenuHelper.setColourSelected(colourMenu, cs); |
3718 | ||
3719 | 179 | viewport.setGlobalColourScheme(cs); |
3720 | ||
3721 | 179 | alignPanel.paintAlignment(true, true); |
3722 | } | |
3723 | ||
3724 | /** | |
3725 | * Show the PID threshold slider panel | |
3726 | */ | |
3727 | 6 | @Override |
3728 | protected void modifyPID_actionPerformed() | |
3729 | { | |
3730 | 6 | SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), |
3731 | alignPanel.getViewName()); | |
3732 | 6 | SliderPanel.showPIDSlider(); |
3733 | } | |
3734 | ||
3735 | /** | |
3736 | * Show the Conservation slider panel | |
3737 | */ | |
3738 | 6 | @Override |
3739 | protected void modifyConservation_actionPerformed() | |
3740 | { | |
3741 | 6 | SliderPanel.setConservationSlider(alignPanel, |
3742 | viewport.getResidueShading(), alignPanel.getViewName()); | |
3743 | 6 | SliderPanel.showConservationSlider(); |
3744 | } | |
3745 | ||
3746 | /** | |
3747 | * Action on selecting or deselecting (Colour) By Conservation | |
3748 | */ | |
3749 | 8 | @Override |
3750 | public void conservationMenuItem_actionPerformed(boolean selected) | |
3751 | { | |
3752 | 8 | modifyConservation.setEnabled(selected); |
3753 | 8 | viewport.setConservationSelected(selected); |
3754 | 8 | viewport.getResidueShading().setConservationApplied(selected); |
3755 | ||
3756 | 8 | changeColour(viewport.getGlobalColourScheme()); |
3757 | 8 | if (selected) |
3758 | { | |
3759 | 6 | modifyConservation_actionPerformed(); |
3760 | } | |
3761 | else | |
3762 | { | |
3763 | 2 | SliderPanel.hideConservationSlider(); |
3764 | } | |
3765 | } | |
3766 | ||
3767 | /** | |
3768 | * Action on selecting or deselecting (Colour) Above PID Threshold | |
3769 | */ | |
3770 | 9 | @Override |
3771 | public void abovePIDThreshold_actionPerformed(boolean selected) | |
3772 | { | |
3773 | 9 | modifyPID.setEnabled(selected); |
3774 | 9 | viewport.setAbovePIDThreshold(selected); |
3775 | 9 | if (!selected) |
3776 | { | |
3777 | 3 | viewport.getResidueShading().setThreshold(0, |
3778 | viewport.isIgnoreGapsConsensus()); | |
3779 | } | |
3780 | ||
3781 | 9 | changeColour(viewport.getGlobalColourScheme()); |
3782 | 9 | if (selected) |
3783 | { | |
3784 | 6 | modifyPID_actionPerformed(); |
3785 | } | |
3786 | else | |
3787 | { | |
3788 | 3 | SliderPanel.hidePIDSlider(); |
3789 | } | |
3790 | } | |
3791 | ||
3792 | /** | |
3793 | * DOCUMENT ME! | |
3794 | * | |
3795 | * @param e | |
3796 | * DOCUMENT ME! | |
3797 | */ | |
3798 | 0 | @Override |
3799 | public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) | |
3800 | { | |
3801 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3802 | 0 | AlignmentSorter.sortByPID(viewport.getAlignment(), |
3803 | viewport.getAlignment().getSequenceAt(0)); | |
3804 | 0 | addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, |
3805 | viewport.getAlignment())); | |
3806 | 0 | alignPanel.paintAlignment(true, false); |
3807 | } | |
3808 | ||
3809 | /** | |
3810 | * DOCUMENT ME! | |
3811 | * | |
3812 | * @param e | |
3813 | * DOCUMENT ME! | |
3814 | */ | |
3815 | 0 | @Override |
3816 | public void sortIDMenuItem_actionPerformed(ActionEvent e) | |
3817 | { | |
3818 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3819 | 0 | AlignmentSorter.sortByID(viewport.getAlignment()); |
3820 | 0 | addHistoryItem( |
3821 | new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); | |
3822 | 0 | alignPanel.paintAlignment(true, false); |
3823 | } | |
3824 | ||
3825 | /** | |
3826 | * DOCUMENT ME! | |
3827 | * | |
3828 | * @param e | |
3829 | * DOCUMENT ME! | |
3830 | */ | |
3831 | 0 | @Override |
3832 | public void sortLengthMenuItem_actionPerformed(ActionEvent e) | |
3833 | { | |
3834 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3835 | 0 | AlignmentSorter.sortByLength(viewport.getAlignment()); |
3836 | 0 | addHistoryItem(new OrderCommand("Length Sort", oldOrder, |
3837 | viewport.getAlignment())); | |
3838 | 0 | alignPanel.paintAlignment(true, false); |
3839 | } | |
3840 | ||
3841 | /** | |
3842 | * DOCUMENT ME! | |
3843 | * | |
3844 | * @param e | |
3845 | * DOCUMENT ME! | |
3846 | */ | |
3847 | 0 | @Override |
3848 | public void sortGroupMenuItem_actionPerformed(ActionEvent e) | |
3849 | { | |
3850 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3851 | 0 | AlignmentSorter.sortByGroup(viewport.getAlignment()); |
3852 | 0 | addHistoryItem(new OrderCommand("Group Sort", oldOrder, |
3853 | viewport.getAlignment())); | |
3854 | ||
3855 | 0 | alignPanel.paintAlignment(true, false); |
3856 | } | |
3857 | ||
3858 | /** | |
3859 | * DOCUMENT ME! | |
3860 | * | |
3861 | * @param e | |
3862 | * DOCUMENT ME! | |
3863 | */ | |
3864 | 0 | @Override |
3865 | public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) | |
3866 | { | |
3867 | 0 | new RedundancyPanel(alignPanel, this); |
3868 | } | |
3869 | ||
3870 | /** | |
3871 | * DOCUMENT ME! | |
3872 | * | |
3873 | * @param e | |
3874 | * DOCUMENT ME! | |
3875 | */ | |
3876 | 0 | @Override |
3877 | public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) | |
3878 | { | |
3879 | 0 | if ((viewport.getSelectionGroup() == null) |
3880 | || (viewport.getSelectionGroup().getSize() < 2)) | |
3881 | { | |
3882 | 0 | JvOptionPane.showInternalMessageDialog(this, |
3883 | MessageManager.getString( | |
3884 | "label.you_must_select_least_two_sequences"), | |
3885 | MessageManager.getString("label.invalid_selection"), | |
3886 | JvOptionPane.WARNING_MESSAGE); | |
3887 | } | |
3888 | else | |
3889 | { | |
3890 | 0 | new Thread(new Runnable() |
3891 | { | |
3892 | 0 | @Override |
3893 | public void run() | |
3894 | { | |
3895 | 0 | JInternalFrame frame = new JInternalFrame(); |
3896 | 0 | frame.setFrameIcon(null); |
3897 | 0 | frame.setContentPane(new PairwiseAlignPanel(viewport)); |
3898 | 0 | Desktop.addInternalFrame(frame, |
3899 | MessageManager.getString("action.pairwise_alignment"), | |
3900 | 600, 500); | |
3901 | } | |
3902 | }).start(); | |
3903 | ||
3904 | } | |
3905 | } | |
3906 | ||
3907 | 0 | @Override |
3908 | public void autoCalculate_actionPerformed(ActionEvent e) | |
3909 | { | |
3910 | 0 | viewport.autoCalculateConsensus = autoCalculate.isSelected(); |
3911 | 0 | if (viewport.autoCalculateConsensus) |
3912 | { | |
3913 | 0 | viewport.firePropertyChange("alignment", null, |
3914 | viewport.getAlignment().getSequences()); | |
3915 | } | |
3916 | } | |
3917 | ||
3918 | 0 | @Override |
3919 | public void sortByTreeOption_actionPerformed(ActionEvent e) | |
3920 | { | |
3921 | 0 | viewport.sortByTree = sortByTree.isSelected(); |
3922 | } | |
3923 | ||
3924 | 0 | @Override |
3925 | protected void listenToViewSelections_actionPerformed(ActionEvent e) | |
3926 | { | |
3927 | 0 | viewport.followSelection = listenToViewSelections.isSelected(); |
3928 | } | |
3929 | ||
3930 | /** | |
3931 | * Constructs a tree panel and adds it to the desktop | |
3932 | * | |
3933 | * @param type | |
3934 | * tree type (NJ or AV) | |
3935 | * @param modelName | |
3936 | * name of score model used to compute the tree | |
3937 | * @param options | |
3938 | * parameters for the distance or similarity calculation | |
3939 | */ | |
3940 | 0 | void newTreePanel(String type, String modelName, |
3941 | SimilarityParamsI options) | |
3942 | { | |
3943 | 0 | String frameTitle = ""; |
3944 | 0 | TreePanel tp; |
3945 | ||
3946 | 0 | boolean onSelection = false; |
3947 | 0 | if (viewport.getSelectionGroup() != null |
3948 | && viewport.getSelectionGroup().getSize() > 0) | |
3949 | { | |
3950 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
3951 | ||
3952 | /* Decide if the selection is a column region */ | |
3953 | 0 | for (SequenceI _s : sg.getSequences()) |
3954 | { | |
3955 | 0 | if (_s.getLength() < sg.getEndRes()) |
3956 | { | |
3957 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
3958 | MessageManager.getString( | |
3959 | "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), | |
3960 | MessageManager.getString( | |
3961 | "label.sequences_selection_not_aligned"), | |
3962 | JvOptionPane.WARNING_MESSAGE); | |
3963 | ||
3964 | 0 | return; |
3965 | } | |
3966 | } | |
3967 | 0 | onSelection = true; |
3968 | } | |
3969 | else | |
3970 | { | |
3971 | 0 | if (viewport.getAlignment().getHeight() < 2) |
3972 | { | |
3973 | 0 | return; |
3974 | } | |
3975 | } | |
3976 | ||
3977 | 0 | tp = new TreePanel(alignPanel, type, modelName, options); |
3978 | ||
3979 | 0 | frameTitle = formCalculationTitle(tp.getPanelTitle(), onSelection, |
3980 | this.title); | |
3981 | ||
3982 | 0 | Desktop.addInternalFrame(tp, frameTitle, 600, 500); |
3983 | } | |
3984 | ||
3985 | /** | |
3986 | * | |
3987 | * @param panelTitle | |
3988 | * - calculation name | |
3989 | * @param onSelection | |
3990 | * - true if a selection was analysed | |
3991 | * @param viewName | |
3992 | * - null or current view name | |
3993 | * @param title | |
3994 | * - alignment frame title | |
3995 | * @return <calculation Name> (?on region) from (?viewName of) alignment name | |
3996 | */ | |
3997 | 2 | public String formCalculationTitle(String panelTitle, boolean onSelection, |
3998 | String title) | |
3999 | { | |
4000 | 2 | String frameTitle = panelTitle; |
4001 | ||
4002 | 2 | frameTitle += (onSelection ? " on region" : ""); |
4003 | ||
4004 | 2 | frameTitle += " from "; |
4005 | ||
4006 | 2 | if (viewport.getViewName() != null) |
4007 | { | |
4008 | 2 | frameTitle += viewport.getViewName() + " of "; |
4009 | } | |
4010 | ||
4011 | 2 | frameTitle += title; |
4012 | 2 | return frameTitle; |
4013 | } | |
4014 | ||
4015 | /** | |
4016 | * DOCUMENT ME! | |
4017 | * | |
4018 | * @param title | |
4019 | * DOCUMENT ME! | |
4020 | * @param order | |
4021 | * DOCUMENT ME! | |
4022 | */ | |
4023 | 0 | public void addSortByOrderMenuItem(String title, |
4024 | final AlignmentOrder order) | |
4025 | { | |
4026 | 0 | final JMenuItem item = new JMenuItem(MessageManager |
4027 | .formatMessage("action.by_title_param", new Object[] | |
4028 | { title })); | |
4029 | 0 | sort.add(item); |
4030 | 0 | item.addActionListener(new java.awt.event.ActionListener() |
4031 | { | |
4032 | 0 | @Override |
4033 | public void actionPerformed(ActionEvent e) | |
4034 | { | |
4035 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
4036 | ||
4037 | // TODO: JBPNote - have to map order entries to curent SequenceI | |
4038 | // pointers | |
4039 | 0 | AlignmentSorter.sortBy(viewport.getAlignment(), order); |
4040 | ||
4041 | 0 | addHistoryItem(new OrderCommand(order.getName(), oldOrder, |
4042 | viewport.getAlignment())); | |
4043 | ||
4044 | 0 | alignPanel.paintAlignment(true, false); |
4045 | } | |
4046 | }); | |
4047 | } | |
4048 | ||
4049 | /** | |
4050 | * Add a new sort by annotation score menu item | |
4051 | * | |
4052 | * @param sort | |
4053 | * the menu to add the option to | |
4054 | * @param scoreLabel | |
4055 | * the label used to retrieve scores for each sequence on the | |
4056 | * alignment | |
4057 | */ | |
4058 | 4 | public void addSortByAnnotScoreMenuItem(JMenu sort, |
4059 | final String scoreLabel) | |
4060 | { | |
4061 | 4 | final JMenuItem item = new JMenuItem(scoreLabel); |
4062 | 4 | sort.add(item); |
4063 | 4 | item.addActionListener(new java.awt.event.ActionListener() |
4064 | { | |
4065 | 0 | @Override |
4066 | public void actionPerformed(ActionEvent e) | |
4067 | { | |
4068 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
4069 | 0 | AlignmentSorter.sortByAnnotationScore(scoreLabel, |
4070 | viewport.getAlignment());// ,viewport.getSelectionGroup()); | |
4071 | 0 | addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, |
4072 | viewport.getAlignment())); | |
4073 | 0 | alignPanel.paintAlignment(true, false); |
4074 | } | |
4075 | }); | |
4076 | } | |
4077 | ||
4078 | /** | |
4079 | * last hash for alignment's annotation array - used to minimise cost of | |
4080 | * rebuild. | |
4081 | */ | |
4082 | protected int _annotationScoreVectorHash; | |
4083 | ||
4084 | /** | |
4085 | * search the alignment and rebuild the sort by annotation score submenu the | |
4086 | * last alignment annotation vector hash is stored to minimize cost of | |
4087 | * rebuilding in subsequence calls. | |
4088 | * | |
4089 | */ | |
4090 | 457 | @Override |
4091 | public void buildSortByAnnotationScoresMenu() | |
4092 | { | |
4093 | 457 | if (viewport.getAlignment().getAlignmentAnnotation() == null) |
4094 | { | |
4095 | 0 | return; |
4096 | } | |
4097 | ||
4098 | 457 | if (viewport.getAlignment().getAlignmentAnnotation() |
4099 | .hashCode() != _annotationScoreVectorHash) | |
4100 | { | |
4101 | 456 | sortByAnnotScore.removeAll(); |
4102 | // almost certainly a quicker way to do this - but we keep it simple | |
4103 | 456 | Hashtable<String, String> scoreSorts = new Hashtable<>(); |
4104 | 456 | AlignmentAnnotation aann[]; |
4105 | 456 | for (SequenceI sqa : viewport.getAlignment().getSequences()) |
4106 | { | |
4107 | 4095 | aann = sqa.getAnnotation(); |
4108 | 4399 | for (int i = 0; aann != null && i < aann.length; i++) |
4109 | { | |
4110 | 304 | if (aann[i].hasScore() && aann[i].sequenceRef != null) |
4111 | { | |
4112 | 152 | scoreSorts.put(aann[i].label, aann[i].label); |
4113 | } | |
4114 | } | |
4115 | } | |
4116 | 456 | Enumeration<String> labels = scoreSorts.keys(); |
4117 | 460 | while (labels.hasMoreElements()) |
4118 | { | |
4119 | 4 | addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement()); |
4120 | } | |
4121 | 456 | sortByAnnotScore.setVisible(scoreSorts.size() > 0); |
4122 | 456 | scoreSorts.clear(); |
4123 | ||
4124 | 456 | _annotationScoreVectorHash = viewport.getAlignment() |
4125 | .getAlignmentAnnotation().hashCode(); | |
4126 | } | |
4127 | } | |
4128 | ||
4129 | /** | |
4130 | * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a | |
4131 | * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code> | |
4132 | * call. Listeners are added to remove the menu item when the treePanel is | |
4133 | * closed, and adjust the tree leaf to sequence mapping when the alignment is | |
4134 | * modified. | |
4135 | */ | |
4136 | 0 | @Override |
4137 | public void buildTreeSortMenu() | |
4138 | { | |
4139 | 0 | sortByTreeMenu.removeAll(); |
4140 | ||
4141 | 0 | List<Component> comps = PaintRefresher.components |
4142 | .get(viewport.getSequenceSetId()); | |
4143 | 0 | List<TreePanel> treePanels = new ArrayList<>(); |
4144 | 0 | for (Component comp : comps) |
4145 | { | |
4146 | 0 | if (comp instanceof TreePanel) |
4147 | { | |
4148 | 0 | treePanels.add((TreePanel) comp); |
4149 | } | |
4150 | } | |
4151 | ||
4152 | 0 | if (treePanels.size() < 1) |
4153 | { | |
4154 | 0 | sortByTreeMenu.setVisible(false); |
4155 | 0 | return; |
4156 | } | |
4157 | ||
4158 | 0 | sortByTreeMenu.setVisible(true); |
4159 | ||
4160 | 0 | for (final TreePanel tp : treePanels) |
4161 | { | |
4162 | 0 | final JMenuItem item = new JMenuItem(tp.getTitle()); |
4163 | 0 | item.addActionListener(new java.awt.event.ActionListener() |
4164 | { | |
4165 | 0 | @Override |
4166 | public void actionPerformed(ActionEvent e) | |
4167 | { | |
4168 | 0 | tp.sortByTree_actionPerformed(); |
4169 | 0 | addHistoryItem(tp.sortAlignmentIn(alignPanel)); |
4170 | ||
4171 | } | |
4172 | }); | |
4173 | ||
4174 | 0 | sortByTreeMenu.add(item); |
4175 | } | |
4176 | } | |
4177 | ||
4178 | 0 | public boolean sortBy(AlignmentOrder alorder, String undoname) |
4179 | { | |
4180 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
4181 | 0 | AlignmentSorter.sortBy(viewport.getAlignment(), alorder); |
4182 | 0 | if (undoname != null) |
4183 | { | |
4184 | 0 | addHistoryItem(new OrderCommand(undoname, oldOrder, |
4185 | viewport.getAlignment())); | |
4186 | } | |
4187 | 0 | alignPanel.paintAlignment(true, false); |
4188 | 0 | return true; |
4189 | } | |
4190 | ||
4191 | /** | |
4192 | * Work out whether the whole set of sequences or just the selected set will | |
4193 | * be submitted for multiple alignment. | |
4194 | * | |
4195 | */ | |
4196 | 0 | public jalview.datamodel.AlignmentView gatherSequencesForAlignment() |
4197 | { | |
4198 | // Now, check we have enough sequences | |
4199 | 0 | AlignmentView msa = null; |
4200 | ||
4201 | 0 | if ((viewport.getSelectionGroup() != null) |
4202 | && (viewport.getSelectionGroup().getSize() > 1)) | |
4203 | { | |
4204 | // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to | |
4205 | // some common interface! | |
4206 | /* | |
4207 | * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new | |
4208 | * SequenceI[sz = seqs.getSize(false)]; | |
4209 | * | |
4210 | * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) | |
4211 | * seqs.getSequenceAt(i); } | |
4212 | */ | |
4213 | 0 | msa = viewport.getAlignmentView(true); |
4214 | } | |
4215 | 0 | else if (viewport.getSelectionGroup() != null |
4216 | && viewport.getSelectionGroup().getSize() == 1) | |
4217 | { | |
4218 | 0 | int option = JvOptionPane.showConfirmDialog(this, |
4219 | MessageManager.getString("warn.oneseq_msainput_selection"), | |
4220 | MessageManager.getString("label.invalid_selection"), | |
4221 | JvOptionPane.OK_CANCEL_OPTION); | |
4222 | 0 | if (option == JvOptionPane.OK_OPTION) |
4223 | { | |
4224 | 0 | msa = viewport.getAlignmentView(false); |
4225 | } | |
4226 | } | |
4227 | else | |
4228 | { | |
4229 | 0 | msa = viewport.getAlignmentView(false); |
4230 | } | |
4231 | 0 | return msa; |
4232 | } | |
4233 | ||
4234 | /** | |
4235 | * Decides what is submitted to a secondary structure prediction service: the | |
4236 | * first sequence in the alignment, or in the current selection, or, if the | |
4237 | * alignment is 'aligned' (ie padded with gaps), then the currently selected | |
4238 | * region or the whole alignment. (where the first sequence in the set is the | |
4239 | * one that the prediction will be for). | |
4240 | */ | |
4241 | 0 | public AlignmentView gatherSeqOrMsaForSecStrPrediction() |
4242 | { | |
4243 | 0 | AlignmentView seqs = null; |
4244 | ||
4245 | 0 | if ((viewport.getSelectionGroup() != null) |
4246 | && (viewport.getSelectionGroup().getSize() > 0)) | |
4247 | { | |
4248 | 0 | seqs = viewport.getAlignmentView(true); |
4249 | } | |
4250 | else | |
4251 | { | |
4252 | 0 | seqs = viewport.getAlignmentView(false); |
4253 | } | |
4254 | // limit sequences - JBPNote in future - could spawn multiple prediction | |
4255 | // jobs | |
4256 | // TODO: viewport.getAlignment().isAligned is a global state - the local | |
4257 | // selection may well be aligned - we preserve 2.0.8 behaviour for moment. | |
4258 | 0 | if (!viewport.getAlignment().isAligned(false)) |
4259 | { | |
4260 | 0 | seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); |
4261 | // TODO: if seqs.getSequences().length>1 then should really have warned | |
4262 | // user! | |
4263 | ||
4264 | } | |
4265 | 0 | return seqs; |
4266 | } | |
4267 | ||
4268 | /** | |
4269 | * DOCUMENT ME! | |
4270 | * | |
4271 | * @param e | |
4272 | * DOCUMENT ME! | |
4273 | */ | |
4274 | 0 | @Override |
4275 | protected void loadTreeMenuItem_actionPerformed(ActionEvent e) | |
4276 | { | |
4277 | // Pick the tree file | |
4278 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
4279 | Cache.getProperty("LAST_DIRECTORY")); | |
4280 | 0 | chooser.setFileView(new JalviewFileView()); |
4281 | 0 | chooser.setDialogTitle( |
4282 | MessageManager.getString("label.select_newick_like_tree_file")); | |
4283 | 0 | chooser.setToolTipText( |
4284 | MessageManager.getString("label.load_tree_file")); | |
4285 | ||
4286 | 0 | chooser.setResponseHandler(0, () -> { |
4287 | 0 | String filePath = chooser.getSelectedFile().getPath(); |
4288 | 0 | Cache.setProperty("LAST_DIRECTORY", filePath); |
4289 | 0 | NewickFile fin = null; |
4290 | 0 | try |
4291 | { | |
4292 | 0 | fin = new NewickFile(new FileParse(chooser.getSelectedFile(), |
4293 | DataSourceType.FILE)); | |
4294 | 0 | viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); |
4295 | } catch (Exception ex) | |
4296 | { | |
4297 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), |
4298 | MessageManager.getString("label.problem_reading_tree_file"), | |
4299 | JvOptionPane.WARNING_MESSAGE); | |
4300 | 0 | ex.printStackTrace(); |
4301 | } | |
4302 | 0 | if (fin != null && fin.hasWarningMessage()) |
4303 | { | |
4304 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
4305 | fin.getWarningMessage(), | |
4306 | MessageManager | |
4307 | .getString("label.possible_problem_with_tree_file"), | |
4308 | JvOptionPane.WARNING_MESSAGE); | |
4309 | } | |
4310 | }); | |
4311 | 0 | chooser.showOpenDialog(this); |
4312 | } | |
4313 | ||
4314 | 2 | public TreePanel showNewickTree(NewickFile nf, String treeTitle) |
4315 | { | |
4316 | 2 | return showNewickTree(nf, treeTitle, 600, 500, 4, 5); |
4317 | } | |
4318 | ||
4319 | 14 | public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w, |
4320 | int h, int x, int y) | |
4321 | { | |
4322 | 14 | return showNewickTree(nf, treeTitle, null, w, h, x, y); |
4323 | } | |
4324 | ||
4325 | /** | |
4326 | * Add a treeviewer for the tree extracted from a Newick file object to the | |
4327 | * current alignment view | |
4328 | * | |
4329 | * @param nf | |
4330 | * the tree | |
4331 | * @param title | |
4332 | * tree viewer title | |
4333 | * @param input | |
4334 | * Associated alignment input data (or null) | |
4335 | * @param w | |
4336 | * width | |
4337 | * @param h | |
4338 | * height | |
4339 | * @param x | |
4340 | * position | |
4341 | * @param y | |
4342 | * position | |
4343 | * @return TreePanel handle | |
4344 | */ | |
4345 | 14 | public TreePanel showNewickTree(NewickFile nf, String treeTitle, |
4346 | AlignmentView input, int w, int h, int x, int y) | |
4347 | { | |
4348 | 14 | TreePanel tp = null; |
4349 | ||
4350 | 14 | try |
4351 | { | |
4352 | 14 | nf.parse(); |
4353 | ||
4354 | 14 | if (nf.getTree() != null) |
4355 | { | |
4356 | 14 | tp = new TreePanel(alignPanel, nf, treeTitle, input); |
4357 | ||
4358 | 14 | tp.setSize(w, h); |
4359 | ||
4360 | 14 | if (x > 0 && y > 0) |
4361 | { | |
4362 | 14 | tp.setLocation(x, y); |
4363 | } | |
4364 | ||
4365 | 14 | Desktop.addInternalFrame(tp, treeTitle, w, h); |
4366 | } | |
4367 | } catch (Exception ex) | |
4368 | { | |
4369 | 0 | ex.printStackTrace(); |
4370 | } | |
4371 | ||
4372 | 14 | return tp; |
4373 | } | |
4374 | ||
4375 | 0 | public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm) |
4376 | { | |
4377 | 0 | int x = 4, y = 5; |
4378 | 0 | int w = 400, h = 500; |
4379 | ||
4380 | 0 | try |
4381 | { | |
4382 | 0 | NewickFile fin = new NewickFile( |
4383 | new FileParse(cm.getNewick(), DataSourceType.PASTE)); | |
4384 | 0 | String title = aa.label + " " + cm.getTreeMethod() + " tree" |
4385 | 0 | + (aa.sequenceRef != null |
4386 | ? (" for " + aa.sequenceRef.getDisplayId(false)) | |
4387 | : ""); | |
4388 | ||
4389 | 0 | showColumnWiseTree(fin, aa, title, w, h, x, y); |
4390 | } catch (Throwable xx) | |
4391 | { | |
4392 | 0 | Console.error("Unexpected exception showing tree for contact matrix", |
4393 | xx); | |
4394 | } | |
4395 | } | |
4396 | ||
4397 | 0 | public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, |
4398 | String treeTitle, int w, int h, int x, int y) | |
4399 | { | |
4400 | 0 | try |
4401 | { | |
4402 | 0 | nf.parse(); |
4403 | 0 | if (nf.getTree() == null) |
4404 | { | |
4405 | 0 | return null; |
4406 | } | |
4407 | 0 | TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle); |
4408 | ||
4409 | 0 | tp.setSize(w, h); |
4410 | ||
4411 | 0 | if (x > 0 && y > 0) |
4412 | { | |
4413 | 0 | tp.setLocation(x, y); |
4414 | } | |
4415 | ||
4416 | 0 | Desktop.addInternalFrame(tp, treeTitle, w, h); |
4417 | 0 | return tp; |
4418 | } catch (Throwable xx) | |
4419 | { | |
4420 | 0 | Console.error("Unexpected exception showing tree for contact matrix", |
4421 | xx); | |
4422 | } | |
4423 | 0 | return null; |
4424 | } | |
4425 | ||
4426 | private boolean buildingMenu = false; | |
4427 | ||
4428 | /** | |
4429 | * Generates menu items and listener event actions for web service clients | |
4430 | * | |
4431 | */ | |
4432 | 3372 | public void BuildWebServiceMenu() |
4433 | { | |
4434 | 3375 | while (buildingMenu) |
4435 | { | |
4436 | 3 | try |
4437 | { | |
4438 | 3 | jalview.bin.Console |
4439 | .errPrintln("Waiting for building menu to finish."); | |
4440 | 3 | Thread.sleep(10); |
4441 | } catch (Exception e) | |
4442 | { | |
4443 | } | |
4444 | } | |
4445 | 3372 | final AlignFrame me = this; |
4446 | 3372 | buildingMenu = true; |
4447 | 3372 | new Thread(new Runnable() |
4448 | { | |
4449 | 3372 | @Override |
4450 | public void run() | |
4451 | { | |
4452 | 3372 | final List<JMenuItem> legacyItems = new ArrayList<>(); |
4453 | 3372 | try |
4454 | { | |
4455 | // jalview.bin.Console.errPrintln("Building ws menu again " | |
4456 | // + Thread.currentThread()); | |
4457 | // TODO: add support for context dependent disabling of services based | |
4458 | // on | |
4459 | // alignment and current selection | |
4460 | // TODO: add additional serviceHandle parameter to specify abstract | |
4461 | // handler | |
4462 | // class independently of AbstractName | |
4463 | // TODO: add in rediscovery GUI function to restart discoverer | |
4464 | // TODO: group services by location as well as function and/or | |
4465 | // introduce | |
4466 | // object broker mechanism. | |
4467 | 3372 | final Vector<JMenu> wsmenu = new Vector<>(); |
4468 | 3372 | final IProgressIndicator af = me; |
4469 | ||
4470 | /* | |
4471 | * do not i18n these strings - they are hard-coded in class | |
4472 | * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and | |
4473 | * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() | |
4474 | */ | |
4475 | 3372 | final JMenu msawsmenu = new JMenu("Alignment"); |
4476 | 3372 | final JMenu secstrmenu = new JMenu( |
4477 | "Secondary Structure Prediction"); | |
4478 | 3372 | final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); |
4479 | 3372 | final JMenu analymenu = new JMenu("Analysis"); |
4480 | 3372 | final JMenu dismenu = new JMenu("Protein Disorder"); |
4481 | // JAL-940 - only show secondary structure prediction services from | |
4482 | // the legacy server | |
4483 | 3372 | if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) |
4484 | // && | |
4485 | 3372 | Discoverer.services != null && (Discoverer.services.size() > 0)) |
4486 | { | |
4487 | // TODO: refactor to allow list of AbstractName/Handler bindings to | |
4488 | // be | |
4489 | // stored or retrieved from elsewhere | |
4490 | // No MSAWS used any more: | |
4491 | // Vector msaws = null; // (Vector) | |
4492 | // Discoverer.services.get("MsaWS"); | |
4493 | 3372 | Vector<ServiceHandle> secstrpr = Discoverer.services |
4494 | .get("SecStrPred"); | |
4495 | 3372 | if (secstrpr != null) |
4496 | { | |
4497 | // Add any secondary structure prediction services | |
4498 | 6744 | for (int i = 0, j = secstrpr.size(); i < j; i++) |
4499 | { | |
4500 | 3372 | final ext.vamsas.ServiceHandle sh = secstrpr.get(i); |
4501 | 3372 | jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer |
4502 | .getServiceClient(sh); | |
4503 | 3372 | int p = secstrmenu.getItemCount(); |
4504 | 3372 | impl.attachWSMenuEntry(secstrmenu, me); |
4505 | 3372 | int q = secstrmenu.getItemCount(); |
4506 | 6744 | for (int litm = p; litm < q; litm++) |
4507 | { | |
4508 | 3372 | legacyItems.add(secstrmenu.getItem(litm)); |
4509 | } | |
4510 | } | |
4511 | } | |
4512 | } | |
4513 | ||
4514 | // Add all submenus in the order they should appear on the web | |
4515 | // services menu | |
4516 | 3372 | wsmenu.add(msawsmenu); |
4517 | 3372 | wsmenu.add(secstrmenu); |
4518 | 3372 | wsmenu.add(dismenu); |
4519 | 3372 | wsmenu.add(analymenu); |
4520 | // No search services yet | |
4521 | // wsmenu.add(seqsrchmenu); | |
4522 | ||
4523 | 3372 | javax.swing.SwingUtilities.invokeLater(new Runnable() |
4524 | { | |
4525 | 3372 | @Override |
4526 | public void run() | |
4527 | { | |
4528 | 3372 | try |
4529 | { | |
4530 | 3372 | webService.removeAll(); |
4531 | // first, add discovered services onto the webservices menu | |
4532 | 3372 | if (wsmenu.size() > 0) |
4533 | { | |
4534 | 16860 | for (int i = 0, j = wsmenu.size(); i < j; i++) |
4535 | { | |
4536 | 13488 | webService.add(wsmenu.get(i)); |
4537 | } | |
4538 | } | |
4539 | else | |
4540 | { | |
4541 | 0 | webService.add(me.webServiceNoServices); |
4542 | } | |
4543 | // TODO: move into separate menu builder class. | |
4544 | { | |
4545 | // logic for 2.11.1.4 is | |
4546 | // always look to see if there is a discover. if there isn't | |
4547 | // we can't show any Jws2 services | |
4548 | // if there are services available, show them - regardless of | |
4549 | // the 'show JWS2 preference' | |
4550 | // if the discoverer is running then say so | |
4551 | // otherwise offer to trigger discovery if 'show JWS2' is not | |
4552 | // enabled | |
4553 | 3372 | Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); |
4554 | 3372 | if (jws2servs != null) |
4555 | { | |
4556 | 3372 | if (jws2servs.hasServices()) |
4557 | { | |
4558 | 1126 | jws2servs.attachWSMenuEntry(webService, me); |
4559 | 1115 | for (Jws2Instance sv : jws2servs.getServices()) |
4560 | { | |
4561 | 15065 | if (sv.description.toLowerCase(Locale.ROOT) |
4562 | .contains("jpred")) | |
4563 | { | |
4564 | 0 | for (JMenuItem jmi : legacyItems) |
4565 | { | |
4566 | 0 | jmi.setVisible(false); |
4567 | } | |
4568 | } | |
4569 | } | |
4570 | } | |
4571 | ||
4572 | 3361 | if (jws2servs.isRunning()) |
4573 | { | |
4574 | 2234 | JMenuItem tm = new JMenuItem( |
4575 | "Still discovering JABA Services"); | |
4576 | 2234 | tm.setEnabled(false); |
4577 | 2234 | webService.add(tm); |
4578 | } | |
4579 | 1127 | else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true)) |
4580 | { | |
4581 | 0 | JMenuItem enableJws2 = new JMenuItem( |
4582 | "Discover Web Services"); | |
4583 | 0 | enableJws2.setToolTipText( |
4584 | "Select to start JABA Web Service discovery (or enable option in Web Service preferences)"); | |
4585 | 0 | enableJws2.setEnabled(true); |
4586 | 0 | enableJws2.addActionListener(new ActionListener() |
4587 | { | |
4588 | ||
4589 | 0 | @Override |
4590 | public void actionPerformed(ActionEvent e) | |
4591 | { | |
4592 | // start service discoverer, but ignore preference | |
4593 | 0 | Desktop.instance.startServiceDiscovery(false, |
4594 | true); | |
4595 | } | |
4596 | }); | |
4597 | 0 | webService.add(enableJws2); |
4598 | } | |
4599 | } | |
4600 | } | |
4601 | 3361 | build_urlServiceMenu(me.webService); |
4602 | 3361 | build_fetchdbmenu(webService); |
4603 | 3361 | for (JMenu item : wsmenu) |
4604 | { | |
4605 | 13444 | if (item.getItemCount() == 0) |
4606 | { | |
4607 | 4599 | item.setEnabled(false); |
4608 | } | |
4609 | else | |
4610 | { | |
4611 | 8845 | item.setEnabled(true); |
4612 | } | |
4613 | } | |
4614 | } catch (Exception e) | |
4615 | { | |
4616 | 11 | Console.debug( |
4617 | "Exception during web service menu building process.", | |
4618 | e); | |
4619 | } | |
4620 | } | |
4621 | }); | |
4622 | } catch (Exception e) | |
4623 | { | |
4624 | } | |
4625 | 3372 | buildingMenu = false; |
4626 | } | |
4627 | }).start(); | |
4628 | ||
4629 | } | |
4630 | ||
4631 | /** | |
4632 | * construct any groupURL type service menu entries. | |
4633 | * | |
4634 | * @param webService | |
4635 | */ | |
4636 | 3361 | protected void build_urlServiceMenu(JMenu webService) |
4637 | { | |
4638 | // TODO: remove this code when 2.7 is released | |
4639 | // DEBUG - alignmentView | |
4640 | /* | |
4641 | * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final | |
4642 | * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { | |
4643 | * | |
4644 | * @Override public void actionPerformed(ActionEvent e) { | |
4645 | * jalview.datamodel.AlignmentView | |
4646 | * .testSelectionViews(af.viewport.getAlignment(), | |
4647 | * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } | |
4648 | * | |
4649 | * }); webService.add(testAlView); | |
4650 | */ | |
4651 | // TODO: refactor to RestClient discoverer and merge menu entries for | |
4652 | // rest-style services with other types of analysis/calculation service | |
4653 | // SHmmr test client - still being implemented. | |
4654 | // DEBUG - alignmentView | |
4655 | ||
4656 | 3361 | for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient |
4657 | .getRestClients()) | |
4658 | { | |
4659 | 3361 | client.attachWSMenuEntry( |
4660 | JvSwingUtils.findOrCreateMenu(webService, client.getAction()), | |
4661 | this); | |
4662 | } | |
4663 | } | |
4664 | ||
4665 | /** | |
4666 | * Searches the alignment sequences for xRefs and builds the Show | |
4667 | * Cross-References menu (formerly called Show Products), with database | |
4668 | * sources for which cross-references are found (protein sources for a | |
4669 | * nucleotide alignment and vice versa) | |
4670 | * | |
4671 | * @return true if Show Cross-references menu should be enabled | |
4672 | */ | |
4673 | 672 | public boolean canShowProducts() |
4674 | { | |
4675 | 672 | SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); |
4676 | 672 | AlignmentI dataset = viewport.getAlignment().getDataset(); |
4677 | ||
4678 | 672 | showProducts.removeAll(); |
4679 | 672 | final boolean dna = viewport.getAlignment().isNucleotide(); |
4680 | ||
4681 | 672 | if (seqs == null || seqs.length == 0) |
4682 | { | |
4683 | // nothing to see here. | |
4684 | 0 | return false; |
4685 | } | |
4686 | ||
4687 | 672 | boolean showp = false; |
4688 | 672 | try |
4689 | { | |
4690 | 672 | List<String> ptypes = new CrossRef(seqs, dataset) |
4691 | .findXrefSourcesForSequences(dna); | |
4692 | ||
4693 | 672 | for (final String source : ptypes) |
4694 | { | |
4695 | 6 | showp = true; |
4696 | 6 | final AlignFrame af = this; |
4697 | 6 | JMenuItem xtype = new JMenuItem(source); |
4698 | 6 | xtype.addActionListener(new ActionListener() |
4699 | { | |
4700 | 0 | @Override |
4701 | public void actionPerformed(ActionEvent e) | |
4702 | { | |
4703 | 0 | showProductsFor(af.viewport.getSequenceSelection(), dna, |
4704 | source); | |
4705 | } | |
4706 | }); | |
4707 | 6 | showProducts.add(xtype); |
4708 | } | |
4709 | 672 | showProducts.setVisible(showp); |
4710 | 672 | showProducts.setEnabled(showp); |
4711 | } catch (Exception e) | |
4712 | { | |
4713 | 0 | Console.warn( |
4714 | "canShowProducts threw an exception - please report to help@jalview.org", | |
4715 | e); | |
4716 | 0 | return false; |
4717 | } | |
4718 | 672 | return showp; |
4719 | } | |
4720 | ||
4721 | /** | |
4722 | * Finds and displays cross-references for the selected sequences (protein | |
4723 | * products for nucleotide sequences, dna coding sequences for peptides). | |
4724 | * | |
4725 | * @param sel | |
4726 | * the sequences to show cross-references for | |
4727 | * @param dna | |
4728 | * true if from a nucleotide alignment (so showing proteins) | |
4729 | * @param source | |
4730 | * the database to show cross-references for | |
4731 | */ | |
4732 | 0 | protected void showProductsFor(final SequenceI[] sel, final boolean _odna, |
4733 | final String source) | |
4734 | { | |
4735 | 0 | new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this)) |
4736 | .start(); | |
4737 | } | |
4738 | ||
4739 | /** | |
4740 | * Construct and display a new frame containing the translation of this | |
4741 | * frame's DNA sequences to their aligned protein (amino acid) equivalents. | |
4742 | */ | |
4743 | 1 | @Override |
4744 | public void showTranslation_actionPerformed(GeneticCodeI codeTable) | |
4745 | { | |
4746 | 1 | AlignmentI al = null; |
4747 | 1 | try |
4748 | { | |
4749 | 1 | Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); |
4750 | ||
4751 | 1 | al = dna.translateCdna(codeTable); |
4752 | } catch (Exception ex) | |
4753 | { | |
4754 | 0 | Console.error("Exception during translation. Please report this !", |
4755 | ex); | |
4756 | 0 | final String msg = MessageManager.getString( |
4757 | "label.error_when_translating_sequences_submit_bug_report"); | |
4758 | 0 | final String errorTitle = MessageManager |
4759 | .getString("label.implementation_error") | |
4760 | + MessageManager.getString("label.translation_failed"); | |
4761 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, |
4762 | JvOptionPane.ERROR_MESSAGE); | |
4763 | 0 | return; |
4764 | } | |
4765 | 1 | if (al == null || al.getHeight() == 0) |
4766 | { | |
4767 | 0 | final String msg = MessageManager.getString( |
4768 | "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); | |
4769 | 0 | final String errorTitle = MessageManager |
4770 | .getString("label.translation_failed"); | |
4771 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, |
4772 | JvOptionPane.WARNING_MESSAGE); | |
4773 | } | |
4774 | else | |
4775 | { | |
4776 | 1 | AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); |
4777 | 1 | af.setFileFormat(this.currentFileFormat); |
4778 | 1 | final String newTitle = MessageManager |
4779 | .formatMessage("label.translation_of_params", new Object[] | |
4780 | { this.getTitle(), codeTable.getId() }); | |
4781 | 1 | af.setTitle(newTitle); |
4782 | 1 | if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) |
4783 | { | |
4784 | 1 | final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); |
4785 | 1 | viewport.openSplitFrame(af, new Alignment(seqs)); |
4786 | } | |
4787 | else | |
4788 | { | |
4789 | 0 | Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, |
4790 | DEFAULT_HEIGHT); | |
4791 | } | |
4792 | } | |
4793 | } | |
4794 | ||
4795 | /** | |
4796 | * Set the file format | |
4797 | * | |
4798 | * @param format | |
4799 | */ | |
4800 | 327 | public void setFileFormat(FileFormatI format) |
4801 | { | |
4802 | 327 | this.currentFileFormat = format; |
4803 | } | |
4804 | ||
4805 | /** | |
4806 | * Try to load a features file onto the alignment. | |
4807 | * | |
4808 | * @param file | |
4809 | * contents or path to retrieve file or a File object | |
4810 | * @param sourceType | |
4811 | * access mode of file (see jalview.io.AlignFile) | |
4812 | * @return true if features file was parsed correctly. | |
4813 | */ | |
4814 | 4 | public boolean parseFeaturesFile(Object file, DataSourceType sourceType) |
4815 | { | |
4816 | // BH 2018 | |
4817 | 4 | return avc.parseFeaturesFile(file, sourceType, |
4818 | Cache.getDefault("RELAXEDSEQIDMATCHING", false)); | |
4819 | ||
4820 | } | |
4821 | ||
4822 | 5 | @Override |
4823 | public void refreshFeatureUI(boolean enableIfNecessary) | |
4824 | { | |
4825 | // note - currently this is only still here rather than in the controller | |
4826 | // because of the featureSettings hard reference that is yet to be | |
4827 | // abstracted | |
4828 | 5 | if (enableIfNecessary) |
4829 | { | |
4830 | 5 | viewport.setShowSequenceFeatures(true); |
4831 | 5 | showSeqFeatures.setSelected(true); |
4832 | } | |
4833 | ||
4834 | } | |
4835 | ||
4836 | 0 | @Override |
4837 | public void dragEnter(DropTargetDragEvent evt) | |
4838 | { | |
4839 | } | |
4840 | ||
4841 | 0 | @Override |
4842 | public void dragExit(DropTargetEvent evt) | |
4843 | { | |
4844 | } | |
4845 | ||
4846 | 0 | @Override |
4847 | public void dragOver(DropTargetDragEvent evt) | |
4848 | { | |
4849 | } | |
4850 | ||
4851 | 0 | @Override |
4852 | public void dropActionChanged(DropTargetDragEvent evt) | |
4853 | { | |
4854 | } | |
4855 | ||
4856 | 0 | @Override |
4857 | public void drop(DropTargetDropEvent evt) | |
4858 | { | |
4859 | // JAL-1552 - acceptDrop required before getTransferable call for | |
4860 | // Java's Transferable for native dnd | |
4861 | 0 | evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); |
4862 | 0 | Transferable t = evt.getTransferable(); |
4863 | ||
4864 | 0 | final AlignFrame thisaf = this; |
4865 | 0 | final List<Object> files = new ArrayList<>(); |
4866 | 0 | List<DataSourceType> protocols = new ArrayList<>(); |
4867 | ||
4868 | 0 | try |
4869 | { | |
4870 | 0 | Desktop.transferFromDropTarget(files, protocols, evt, t); |
4871 | } catch (Exception e) | |
4872 | { | |
4873 | 0 | e.printStackTrace(); |
4874 | } | |
4875 | 0 | if (files != null) |
4876 | { | |
4877 | 0 | new Thread(new Runnable() |
4878 | { | |
4879 | 0 | @Override |
4880 | public void run() | |
4881 | { | |
4882 | 0 | try |
4883 | { | |
4884 | // check to see if any of these files have names matching sequences | |
4885 | // in | |
4886 | // the alignment | |
4887 | 0 | SequenceIdMatcher idm = new SequenceIdMatcher( |
4888 | viewport.getAlignment().getSequencesArray()); | |
4889 | /** | |
4890 | * Object[] { String,SequenceI} | |
4891 | */ | |
4892 | 0 | ArrayList<Object[]> filesmatched = new ArrayList<>(); |
4893 | 0 | ArrayList<Object[]> filesnotmatched = new ArrayList<>(); |
4894 | 0 | for (int i = 0; i < files.size(); i++) |
4895 | { | |
4896 | // BH 2018 | |
4897 | 0 | Object file = files.get(i); |
4898 | 0 | String fileName = file.toString(); |
4899 | 0 | String pdbfn = ""; |
4900 | 0 | DataSourceType protocol = (file instanceof File |
4901 | ? DataSourceType.FILE | |
4902 | : FormatAdapter.checkProtocol(fileName)); | |
4903 | 0 | if (protocol == DataSourceType.FILE) |
4904 | { | |
4905 | 0 | File fl; |
4906 | 0 | if (file instanceof File) |
4907 | { | |
4908 | 0 | fl = (File) file; |
4909 | 0 | Platform.cacheFileData(fl); |
4910 | } | |
4911 | else | |
4912 | { | |
4913 | 0 | fl = new File(fileName); |
4914 | } | |
4915 | 0 | pdbfn = fl.getName(); |
4916 | } | |
4917 | 0 | else if (protocol == DataSourceType.URL) |
4918 | { | |
4919 | 0 | URL url = new URL(fileName); |
4920 | 0 | pdbfn = url.getFile(); |
4921 | } | |
4922 | 0 | if (pdbfn.length() > 0) |
4923 | { | |
4924 | // attempt to find a match in the alignment | |
4925 | 0 | SequenceI[] mtch = idm.findAllIdMatches(pdbfn); |
4926 | 0 | int l = 0, c = pdbfn.indexOf("."); |
4927 | 0 | while (mtch == null && c != -1) |
4928 | { | |
4929 | 0 | do |
4930 | { | |
4931 | 0 | l = c; |
4932 | ? | } while ((c = pdbfn.indexOf(".", l)) > l); |
4933 | 0 | if (l > -1) |
4934 | { | |
4935 | 0 | pdbfn = pdbfn.substring(0, l); |
4936 | } | |
4937 | 0 | mtch = idm.findAllIdMatches(pdbfn); |
4938 | } | |
4939 | 0 | FileFormatI type = null; |
4940 | 0 | if (mtch != null) |
4941 | { | |
4942 | 0 | try |
4943 | { | |
4944 | 0 | type = new IdentifyFile().identify(file, protocol); |
4945 | } catch (Exception ex) | |
4946 | { | |
4947 | 0 | type = null; |
4948 | } | |
4949 | 0 | if (type != null && type.isStructureFile()) |
4950 | { | |
4951 | 0 | filesmatched.add(new Object[] { file, protocol, mtch }); |
4952 | 0 | continue; |
4953 | } | |
4954 | } | |
4955 | // File wasn't named like one of the sequences or wasn't a PDB | |
4956 | // file. | |
4957 | 0 | filesnotmatched.add(new Object[] { file, protocol, type }); |
4958 | } | |
4959 | } | |
4960 | 0 | int assocfiles = 0; |
4961 | 0 | if (filesmatched.size() > 0) |
4962 | { | |
4963 | 0 | boolean autoAssociate = Cache |
4964 | .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); | |
4965 | 0 | if (!autoAssociate) |
4966 | { | |
4967 | 0 | String msg = MessageManager.formatMessage( |
4968 | "label.automatically_associate_structure_files_with_sequences_same_name", | |
4969 | new Object[] | |
4970 | { Integer.valueOf(filesmatched.size()) | |
4971 | .toString() }); | |
4972 | 0 | String ttl = MessageManager.getString( |
4973 | "label.automatically_associate_structure_files_by_name"); | |
4974 | 0 | int choice = JvOptionPane.showConfirmDialog(thisaf, msg, |
4975 | ttl, JvOptionPane.YES_NO_OPTION); | |
4976 | 0 | autoAssociate = choice == JvOptionPane.YES_OPTION; |
4977 | } | |
4978 | 0 | if (autoAssociate) |
4979 | { | |
4980 | 0 | for (Object[] fm : filesmatched) |
4981 | { | |
4982 | // try and associate | |
4983 | // TODO: may want to set a standard ID naming formalism for | |
4984 | // associating PDB files which have no IDs. | |
4985 | 0 | for (SequenceI toassoc : (SequenceI[]) fm[2]) |
4986 | { | |
4987 | 0 | PDBEntry pe = new AssociatePdbFileWithSeq() |
4988 | .associatePdbWithSeq(fm[0].toString(), | |
4989 | (DataSourceType) fm[1], toassoc, false, | |
4990 | Desktop.instance); | |
4991 | 0 | if (pe != null) |
4992 | { | |
4993 | 0 | jalview.bin.Console.errPrintln("Associated file : " |
4994 | + (fm[0].toString()) + " with " | |
4995 | + toassoc.getDisplayId(true)); | |
4996 | 0 | assocfiles++; |
4997 | } | |
4998 | } | |
4999 | // TODO: do we need to update overview ? only if features are | |
5000 | // shown I guess | |
5001 | 0 | alignPanel.paintAlignment(true, false); |
5002 | } | |
5003 | } | |
5004 | else | |
5005 | { | |
5006 | /* | |
5007 | * add declined structures as sequences | |
5008 | */ | |
5009 | 0 | for (Object[] o : filesmatched) |
5010 | { | |
5011 | 0 | filesnotmatched.add(new Object[] { o[0], o[1] }); |
5012 | } | |
5013 | } | |
5014 | } | |
5015 | 0 | if (filesnotmatched.size() > 0) |
5016 | { | |
5017 | 0 | if (assocfiles > 0 && (Cache.getDefault( |
5018 | "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) | |
5019 | || JvOptionPane.showConfirmDialog(thisaf, | |
5020 | "<html>" + MessageManager.formatMessage( | |
5021 | "label.ignore_unmatched_dropped_files_info", | |
5022 | new Object[] | |
5023 | { Integer.valueOf( | |
5024 | filesnotmatched.size()) | |
5025 | .toString() }) | |
5026 | + "</html>", | |
5027 | MessageManager.getString( | |
5028 | "label.ignore_unmatched_dropped_files"), | |
5029 | JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) | |
5030 | { | |
5031 | 0 | return; |
5032 | } | |
5033 | 0 | for (Object[] fn : filesnotmatched) |
5034 | { | |
5035 | 0 | loadJalviewDataFile(fn[0], (DataSourceType) fn[1], |
5036 | (FileFormatI) fn[2], null); | |
5037 | } | |
5038 | ||
5039 | } | |
5040 | } catch (Exception ex) | |
5041 | { | |
5042 | 0 | ex.printStackTrace(); |
5043 | } | |
5044 | } | |
5045 | }).start(); | |
5046 | } | |
5047 | } | |
5048 | ||
5049 | /** | |
5050 | * Attempt to load a "dropped" file or URL string, by testing in turn for | |
5051 | * <ul> | |
5052 | * <li>an Annotation file</li> | |
5053 | * <li>a JNet file</li> | |
5054 | * <li>a features file</li> | |
5055 | * <li>else try to interpret as an alignment file</li> | |
5056 | * </ul> | |
5057 | * | |
5058 | * @param file | |
5059 | * either a filename or a URL string. | |
5060 | */ | |
5061 | 7 | public void loadJalviewDataFile(Object file, DataSourceType sourceType, |
5062 | FileFormatI format, SequenceI assocSeq) | |
5063 | { | |
5064 | // BH 2018 was String file | |
5065 | 7 | try |
5066 | { | |
5067 | 7 | if (sourceType == null) |
5068 | { | |
5069 | 2 | sourceType = FormatAdapter.checkProtocol(file); |
5070 | } | |
5071 | // if the file isn't identified, or not positively identified as some | |
5072 | // other filetype (PFAM is default unidentified alignment file type) then | |
5073 | // try to parse as annotation. | |
5074 | 7 | boolean isAnnotation = (format == null |
5075 | || FileFormat.Pfam.equals(format)) | |
5076 | ? new AnnotationFile().annotateAlignmentView(viewport, | |
5077 | file, sourceType) | |
5078 | : false; | |
5079 | ||
5080 | 7 | if (!isAnnotation) |
5081 | { | |
5082 | // first see if its a T-COFFEE score file | |
5083 | 3 | TCoffeeScoreFile tcf = null; |
5084 | 3 | try |
5085 | { | |
5086 | 3 | tcf = new TCoffeeScoreFile(file, sourceType); |
5087 | 3 | if (tcf.isValid()) |
5088 | { | |
5089 | 1 | if (tcf.annotateAlignment(viewport.getAlignment(), true)) |
5090 | { | |
5091 | 1 | buildColourMenu(); |
5092 | 1 | changeColour( |
5093 | new TCoffeeColourScheme(viewport.getAlignment())); | |
5094 | 1 | isAnnotation = true; |
5095 | 1 | setStatus(MessageManager.getString( |
5096 | "label.successfully_pasted_tcoffee_scores_to_alignment")); | |
5097 | } | |
5098 | else | |
5099 | { | |
5100 | // some problem - if no warning its probable that the ID matching | |
5101 | // process didn't work | |
5102 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
5103 | 0 | tcf.getWarningMessage() == null |
5104 | ? MessageManager.getString( | |
5105 | "label.check_file_matches_sequence_ids_alignment") | |
5106 | : tcf.getWarningMessage(), | |
5107 | MessageManager.getString( | |
5108 | "label.problem_reading_tcoffee_score_file"), | |
5109 | JvOptionPane.WARNING_MESSAGE); | |
5110 | } | |
5111 | } | |
5112 | else | |
5113 | { | |
5114 | 2 | tcf = null; |
5115 | } | |
5116 | } catch (Exception x) | |
5117 | { | |
5118 | 0 | Console.debug( |
5119 | "Exception when processing data source as T-COFFEE score file", | |
5120 | x); | |
5121 | 0 | tcf = null; |
5122 | } | |
5123 | 3 | if (tcf == null) |
5124 | { | |
5125 | // try to see if its a JNet 'concise' style annotation file *before* | |
5126 | // we | |
5127 | // try to parse it as a features file | |
5128 | 2 | if (format == null) |
5129 | { | |
5130 | 2 | format = new IdentifyFile().identify(file, sourceType); |
5131 | } | |
5132 | 2 | if (FileFormat.FeatureSettings == format) |
5133 | { | |
5134 | 0 | if (featureSettings != null) |
5135 | { | |
5136 | 0 | featureSettings.load(file, sourceType); |
5137 | } | |
5138 | else | |
5139 | { | |
5140 | 0 | FeatureSettings.loadFeatureSettingsFile(getFeatureRenderer(), |
5141 | fileObject, sourceType); | |
5142 | } | |
5143 | } | |
5144 | 2 | else if (FileFormat.ScoreMatrix == format) |
5145 | { | |
5146 | 0 | ScoreMatrixFile sm = new ScoreMatrixFile( |
5147 | new FileParse(file, sourceType)); | |
5148 | 0 | sm.parse(); |
5149 | // todo: i18n this message | |
5150 | 0 | setStatus(MessageManager.formatMessage( |
5151 | "label.successfully_loaded_matrix", | |
5152 | sm.getMatrixName())); | |
5153 | } | |
5154 | 2 | else if (FileFormat.Jnet.equals(format)) |
5155 | { | |
5156 | 0 | JPredFile predictions = new JPredFile(file, sourceType); |
5157 | 0 | new JnetAnnotationMaker(); |
5158 | 0 | JnetAnnotationMaker.add_annotation(predictions, |
5159 | viewport.getAlignment(), 0, false); | |
5160 | 0 | viewport.getAlignment().setupJPredAlignment(); |
5161 | 0 | isAnnotation = true; |
5162 | } | |
5163 | // else if (IdentifyFile.FeaturesFile.equals(format)) | |
5164 | 2 | else if (FileFormat.Features.equals(format)) |
5165 | { | |
5166 | 2 | if (parseFeaturesFile(file, sourceType)) |
5167 | { | |
5168 | 2 | SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); |
5169 | 2 | if (splitFrame != null) |
5170 | { | |
5171 | 0 | splitFrame.repaint(); |
5172 | } | |
5173 | else | |
5174 | { | |
5175 | 2 | alignPanel.paintAlignment(true, true); |
5176 | } | |
5177 | } | |
5178 | } | |
5179 | else | |
5180 | { | |
5181 | 0 | new FileLoader().LoadFile(viewport, file, sourceType, format); |
5182 | } | |
5183 | } | |
5184 | } | |
5185 | 7 | if (isAnnotation) |
5186 | { | |
5187 | ||
5188 | 5 | alignPanel.adjustAnnotationHeight(); |
5189 | 5 | viewport.updateSequenceIdColours(); |
5190 | 5 | buildSortByAnnotationScoresMenu(); |
5191 | 5 | alignPanel.paintAlignment(true, true); |
5192 | } | |
5193 | } catch (Exception ex) | |
5194 | { | |
5195 | 0 | ex.printStackTrace(); |
5196 | } catch (OutOfMemoryError oom) | |
5197 | { | |
5198 | 0 | try |
5199 | { | |
5200 | 0 | System.gc(); |
5201 | } catch (Exception x) | |
5202 | { | |
5203 | } | |
5204 | 0 | new OOMWarning( |
5205 | "loading data " | |
5206 | 0 | + (sourceType != null |
5207 | 0 | ? (sourceType == DataSourceType.PASTE |
5208 | ? "from clipboard." | |
5209 | : "using " + sourceType + " from " | |
5210 | + file) | |
5211 | : ".") | |
5212 | 0 | + (format != null |
5213 | ? "(parsing as '" + format + "' file)" | |
5214 | : ""), | |
5215 | oom, Desktop.desktop); | |
5216 | } | |
5217 | } | |
5218 | ||
5219 | /** | |
5220 | * Method invoked by the ChangeListener on the tabbed pane, in other words | |
5221 | * when a different tabbed pane is selected by the user or programmatically. | |
5222 | */ | |
5223 | 160 | @Override |
5224 | public void tabSelectionChanged(int index) | |
5225 | { | |
5226 | 160 | if (index > -1) |
5227 | { | |
5228 | /* | |
5229 | * update current Overview window title (if there is one) | |
5230 | * to add view name "Original" if necessary | |
5231 | */ | |
5232 | 105 | alignPanel.setOverviewTitle(this); |
5233 | ||
5234 | /* | |
5235 | * switch panels and set Overview title (if there is one | |
5236 | * because it was opened automatically) | |
5237 | */ | |
5238 | 105 | alignPanel = alignPanels.get(index); |
5239 | 105 | alignPanel.setOverviewTitle(this); |
5240 | ||
5241 | 105 | viewport = alignPanel.av; |
5242 | 105 | avc.setViewportAndAlignmentPanel(viewport, alignPanel); |
5243 | 105 | setMenusFromViewport(viewport); |
5244 | 105 | if (featureSettings != null && featureSettings.isOpen() |
5245 | && featureSettings.fr.getViewport() != viewport) | |
5246 | { | |
5247 | 0 | if (viewport.isShowSequenceFeatures()) |
5248 | { | |
5249 | // refresh the featureSettings to reflect UI change | |
5250 | 0 | showFeatureSettingsUI(); |
5251 | } | |
5252 | else | |
5253 | { | |
5254 | // close feature settings for this view. | |
5255 | 0 | featureSettings.close(); |
5256 | } | |
5257 | } | |
5258 | ||
5259 | } | |
5260 | ||
5261 | /* | |
5262 | * 'focus' any colour slider that is open to the selected viewport | |
5263 | */ | |
5264 | 160 | if (viewport.getConservationSelected()) |
5265 | { | |
5266 | 2 | SliderPanel.setConservationSlider(alignPanel, |
5267 | viewport.getResidueShading(), alignPanel.getViewName()); | |
5268 | } | |
5269 | else | |
5270 | { | |
5271 | 158 | SliderPanel.hideConservationSlider(); |
5272 | } | |
5273 | 160 | if (viewport.getAbovePIDThreshold()) |
5274 | { | |
5275 | 2 | SliderPanel.setPIDSliderSource(alignPanel, |
5276 | viewport.getResidueShading(), alignPanel.getViewName()); | |
5277 | } | |
5278 | else | |
5279 | { | |
5280 | 158 | SliderPanel.hidePIDSlider(); |
5281 | } | |
5282 | ||
5283 | /* | |
5284 | * If there is a frame linked to this one in a SplitPane, switch it to the | |
5285 | * same view tab index. No infinite recursion of calls should happen, since | |
5286 | * tabSelectionChanged() should not get invoked on setting the selected | |
5287 | * index to an unchanged value. Guard against setting an invalid index | |
5288 | * before the new view peer tab has been created. | |
5289 | */ | |
5290 | 160 | final AlignViewportI peer = viewport.getCodingComplement(); |
5291 | 160 | if (peer != null) |
5292 | { | |
5293 | 0 | AlignFrame linkedAlignFrame = ((AlignViewport) peer) |
5294 | .getAlignPanel().alignFrame; | |
5295 | 0 | if (linkedAlignFrame.tabbedPane.getTabCount() > index) |
5296 | { | |
5297 | 0 | linkedAlignFrame.tabbedPane.setSelectedIndex(index); |
5298 | } | |
5299 | } | |
5300 | } | |
5301 | ||
5302 | /** | |
5303 | * On right mouse click on view tab, prompt for and set new view name. | |
5304 | */ | |
5305 | 0 | @Override |
5306 | public void tabbedPane_mousePressed(MouseEvent e) | |
5307 | { | |
5308 | 0 | if (e.isPopupTrigger()) |
5309 | { | |
5310 | 0 | String msg = MessageManager.getString("label.enter_view_name"); |
5311 | 0 | String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex()); |
5312 | 0 | String reply = JvOptionPane.showInputDialog(msg, ttl); |
5313 | ||
5314 | 0 | if (reply != null) |
5315 | { | |
5316 | 0 | viewport.setViewName(reply); |
5317 | // TODO warn if reply is in getExistingViewNames()? | |
5318 | 0 | tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); |
5319 | } | |
5320 | } | |
5321 | } | |
5322 | ||
5323 | 185 | public AlignViewport getCurrentView() |
5324 | { | |
5325 | 185 | return viewport; |
5326 | } | |
5327 | ||
5328 | /** | |
5329 | * Open the dialog for regex description parsing. | |
5330 | */ | |
5331 | 0 | @Override |
5332 | protected void extractScores_actionPerformed(ActionEvent e) | |
5333 | { | |
5334 | 0 | ParseProperties pp = new jalview.analysis.ParseProperties( |
5335 | viewport.getAlignment()); | |
5336 | // TODO: verify regex and introduce GUI dialog for version 2.5 | |
5337 | // if (pp.getScoresFromDescription("col", "score column ", | |
5338 | // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", | |
5339 | // true)>0) | |
5340 | 0 | if (pp.getScoresFromDescription("description column", |
5341 | "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0) | |
5342 | { | |
5343 | 0 | buildSortByAnnotationScoresMenu(); |
5344 | } | |
5345 | } | |
5346 | ||
5347 | /* | |
5348 | * (non-Javadoc) | |
5349 | * | |
5350 | * @see | |
5351 | * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent | |
5352 | * ) | |
5353 | */ | |
5354 | 0 | @Override |
5355 | protected void showDbRefs_actionPerformed(ActionEvent e) | |
5356 | { | |
5357 | 0 | viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); |
5358 | } | |
5359 | ||
5360 | /* | |
5361 | * (non-Javadoc) | |
5362 | * | |
5363 | * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. | |
5364 | * ActionEvent) | |
5365 | */ | |
5366 | 0 | @Override |
5367 | protected void showNpFeats_actionPerformed(ActionEvent e) | |
5368 | { | |
5369 | 0 | viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); |
5370 | } | |
5371 | ||
5372 | /** | |
5373 | * find the viewport amongst the tabs in this alignment frame and close that | |
5374 | * tab | |
5375 | * | |
5376 | * @param av | |
5377 | */ | |
5378 | 0 | public boolean closeView(AlignViewportI av) |
5379 | { | |
5380 | 0 | if (viewport == av) |
5381 | { | |
5382 | 0 | this.closeMenuItem_actionPerformed(false); |
5383 | 0 | return true; |
5384 | } | |
5385 | 0 | Component[] comp = tabbedPane.getComponents(); |
5386 | 0 | for (int i = 0; comp != null && i < comp.length; i++) |
5387 | { | |
5388 | 0 | if (comp[i] instanceof AlignmentPanel) |
5389 | { | |
5390 | 0 | if (((AlignmentPanel) comp[i]).av == av) |
5391 | { | |
5392 | // close the view. | |
5393 | 0 | closeView((AlignmentPanel) comp[i]); |
5394 | 0 | return true; |
5395 | } | |
5396 | } | |
5397 | } | |
5398 | 0 | return false; |
5399 | } | |
5400 | ||
5401 | 3361 | protected void build_fetchdbmenu(JMenu webService) |
5402 | { | |
5403 | // Temporary hack - DBRef Fetcher always top level ws entry. | |
5404 | // TODO We probably want to store a sequence database checklist in | |
5405 | // preferences and have checkboxes.. rather than individual sources selected | |
5406 | // here | |
5407 | 3361 | final JMenu rfetch = new JMenu( |
5408 | MessageManager.getString("action.fetch_db_references")); | |
5409 | 3361 | rfetch.setToolTipText(MessageManager.getString( |
5410 | "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); | |
5411 | 3361 | webService.add(rfetch); |
5412 | ||
5413 | 3361 | final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem( |
5414 | MessageManager.getString("option.trim_retrieved_seqs")); | |
5415 | 3361 | trimrs.setToolTipText( |
5416 | MessageManager.getString("label.trim_retrieved_sequences")); | |
5417 | 3361 | trimrs.setSelected( |
5418 | Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); | |
5419 | 3361 | trimrs.addActionListener(new ActionListener() |
5420 | { | |
5421 | 0 | @Override |
5422 | public void actionPerformed(ActionEvent e) | |
5423 | { | |
5424 | 0 | trimrs.setSelected(trimrs.isSelected()); |
5425 | 0 | Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, |
5426 | Boolean.valueOf(trimrs.isSelected()).toString()); | |
5427 | } | |
5428 | }); | |
5429 | 3361 | rfetch.add(trimrs); |
5430 | 3361 | JMenuItem fetchr = new JMenuItem( |
5431 | MessageManager.getString("label.standard_databases")); | |
5432 | 3361 | fetchr.setToolTipText( |
5433 | MessageManager.getString("label.fetch_embl_uniprot")); | |
5434 | 3361 | fetchr.addActionListener(new ActionListener() |
5435 | { | |
5436 | ||
5437 | 0 | @Override |
5438 | public void actionPerformed(ActionEvent e) | |
5439 | { | |
5440 | 0 | new Thread(new Runnable() |
5441 | { | |
5442 | 0 | @Override |
5443 | public void run() | |
5444 | { | |
5445 | 0 | boolean isNucleotide = alignPanel.alignFrame.getViewport() |
5446 | .getAlignment().isNucleotide(); | |
5447 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher( |
5448 | alignPanel.av.getSequenceSelection(), | |
5449 | alignPanel.alignFrame, null, | |
5450 | alignPanel.alignFrame.featureSettings, isNucleotide); | |
5451 | 0 | dbRefFetcher.addListener(new FetchFinishedListenerI() |
5452 | { | |
5453 | 0 | @Override |
5454 | public void finished() | |
5455 | { | |
5456 | ||
5457 | 0 | for (FeatureSettingsModelI srcSettings : dbRefFetcher |
5458 | .getFeatureSettingsModels()) | |
5459 | { | |
5460 | ||
5461 | 0 | alignPanel.av.mergeFeaturesStyle(srcSettings); |
5462 | } | |
5463 | 0 | AlignFrame.this.setMenusForViewport(); |
5464 | } | |
5465 | }); | |
5466 | 0 | dbRefFetcher.fetchDBRefs(false); |
5467 | } | |
5468 | }).start(); | |
5469 | ||
5470 | } | |
5471 | ||
5472 | }); | |
5473 | 3361 | rfetch.add(fetchr); |
5474 | 3361 | new Thread(new Runnable() |
5475 | { | |
5476 | 3361 | @Override |
5477 | public void run() | |
5478 | { | |
5479 | 3361 | final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher |
5480 | .getSequenceFetcherSingleton(); | |
5481 | 3361 | javax.swing.SwingUtilities.invokeLater(new Runnable() |
5482 | { | |
5483 | 3361 | @Override |
5484 | public void run() | |
5485 | { | |
5486 | 3361 | String[] dbclasses = sf.getNonAlignmentSources(); |
5487 | 3361 | List<DbSourceProxy> otherdb; |
5488 | 3361 | JMenu dfetch = new JMenu(); |
5489 | 3361 | JMenu ifetch = new JMenu(); |
5490 | 3361 | JMenuItem fetchr = null; |
5491 | 3361 | int comp = 0, icomp = 0, mcomp = 15; |
5492 | 3361 | String mname = null; |
5493 | 3361 | int dbi = 0; |
5494 | 3361 | for (String dbclass : dbclasses) |
5495 | { | |
5496 | 16805 | otherdb = sf.getSourceProxy(dbclass); |
5497 | // add a single entry for this class, or submenu allowing 'fetch | |
5498 | // all' or pick one | |
5499 | 16805 | if (otherdb == null || otherdb.size() < 1) |
5500 | { | |
5501 | 0 | continue; |
5502 | } | |
5503 | 16805 | if (mname == null) |
5504 | { | |
5505 | 3361 | mname = "From " + dbclass; |
5506 | } | |
5507 | 16805 | if (otherdb.size() == 1) |
5508 | { | |
5509 | 16805 | final DbSourceProxy[] dassource = otherdb |
5510 | .toArray(new DbSourceProxy[0]); | |
5511 | 16805 | DbSourceProxy src = otherdb.get(0); |
5512 | 16805 | fetchr = new JMenuItem(src.getDbSource()); |
5513 | 16805 | fetchr.addActionListener(new ActionListener() |
5514 | { | |
5515 | ||
5516 | 0 | @Override |
5517 | public void actionPerformed(ActionEvent e) | |
5518 | { | |
5519 | 0 | new Thread(new Runnable() |
5520 | { | |
5521 | ||
5522 | 0 | @Override |
5523 | public void run() | |
5524 | { | |
5525 | 0 | boolean isNucleotide = alignPanel.alignFrame |
5526 | .getViewport().getAlignment() | |
5527 | .isNucleotide(); | |
5528 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher( |
5529 | alignPanel.av.getSequenceSelection(), | |
5530 | alignPanel.alignFrame, dassource, | |
5531 | alignPanel.alignFrame.featureSettings, | |
5532 | isNucleotide); | |
5533 | 0 | dbRefFetcher |
5534 | .addListener(new FetchFinishedListenerI() | |
5535 | { | |
5536 | 0 | @Override |
5537 | public void finished() | |
5538 | { | |
5539 | 0 | FeatureSettingsModelI srcSettings = dassource[0] |
5540 | .getFeatureColourScheme(); | |
5541 | 0 | alignPanel.av.mergeFeaturesStyle( |
5542 | srcSettings); | |
5543 | 0 | AlignFrame.this.setMenusForViewport(); |
5544 | } | |
5545 | }); | |
5546 | 0 | dbRefFetcher.fetchDBRefs(false); |
5547 | } | |
5548 | }).start(); | |
5549 | } | |
5550 | ||
5551 | }); | |
5552 | 16805 | fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, |
5553 | MessageManager.formatMessage( | |
5554 | "label.fetch_retrieve_from", new Object[] | |
5555 | { src.getDbName() }))); | |
5556 | 16805 | dfetch.add(fetchr); |
5557 | 16805 | comp++; |
5558 | } | |
5559 | else | |
5560 | { | |
5561 | 0 | final DbSourceProxy[] dassource = otherdb |
5562 | .toArray(new DbSourceProxy[0]); | |
5563 | // fetch all entry | |
5564 | 0 | DbSourceProxy src = otherdb.get(0); |
5565 | 0 | fetchr = new JMenuItem(MessageManager |
5566 | .formatMessage("label.fetch_all_param", new Object[] | |
5567 | { src.getDbSource() })); | |
5568 | 0 | fetchr.addActionListener(new ActionListener() |
5569 | { | |
5570 | 0 | @Override |
5571 | public void actionPerformed(ActionEvent e) | |
5572 | { | |
5573 | 0 | new Thread(new Runnable() |
5574 | { | |
5575 | ||
5576 | 0 | @Override |
5577 | public void run() | |
5578 | { | |
5579 | 0 | boolean isNucleotide = alignPanel.alignFrame |
5580 | .getViewport().getAlignment() | |
5581 | .isNucleotide(); | |
5582 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher( |
5583 | alignPanel.av.getSequenceSelection(), | |
5584 | alignPanel.alignFrame, dassource, | |
5585 | alignPanel.alignFrame.featureSettings, | |
5586 | isNucleotide); | |
5587 | 0 | dbRefFetcher |
5588 | .addListener(new FetchFinishedListenerI() | |
5589 | { | |
5590 | 0 | @Override |
5591 | public void finished() | |
5592 | { | |
5593 | 0 | AlignFrame.this.setMenusForViewport(); |
5594 | } | |
5595 | }); | |
5596 | 0 | dbRefFetcher.fetchDBRefs(false); |
5597 | } | |
5598 | }).start(); | |
5599 | } | |
5600 | }); | |
5601 | ||
5602 | 0 | fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, |
5603 | MessageManager.formatMessage( | |
5604 | "label.fetch_retrieve_from_all_sources", | |
5605 | new Object[] | |
5606 | { Integer.valueOf(otherdb.size()) | |
5607 | .toString(), | |
5608 | src.getDbSource(), src.getDbName() }))); | |
5609 | 0 | dfetch.add(fetchr); |
5610 | 0 | comp++; |
5611 | // and then build the rest of the individual menus | |
5612 | 0 | ifetch = new JMenu(MessageManager.formatMessage( |
5613 | "label.source_from_db_source", new Object[] | |
5614 | { src.getDbSource() })); | |
5615 | 0 | icomp = 0; |
5616 | 0 | String imname = null; |
5617 | 0 | int i = 0; |
5618 | 0 | for (DbSourceProxy sproxy : otherdb) |
5619 | { | |
5620 | 0 | String dbname = sproxy.getDbName(); |
5621 | 0 | String sname = dbname.length() > 5 |
5622 | ? dbname.substring(0, 5) + "..." | |
5623 | : dbname; | |
5624 | 0 | String msname = dbname.length() > 10 |
5625 | ? dbname.substring(0, 10) + "..." | |
5626 | : dbname; | |
5627 | 0 | if (imname == null) |
5628 | { | |
5629 | 0 | imname = MessageManager |
5630 | .formatMessage("label.from_msname", new Object[] | |
5631 | { sname }); | |
5632 | } | |
5633 | 0 | fetchr = new JMenuItem(msname); |
5634 | 0 | final DbSourceProxy[] dassrc = { sproxy }; |
5635 | 0 | fetchr.addActionListener(new ActionListener() |
5636 | { | |
5637 | ||
5638 | 0 | @Override |
5639 | public void actionPerformed(ActionEvent e) | |
5640 | { | |
5641 | 0 | new Thread(new Runnable() |
5642 | { | |
5643 | ||
5644 | 0 | @Override |
5645 | public void run() | |
5646 | { | |
5647 | 0 | boolean isNucleotide = alignPanel.alignFrame |
5648 | .getViewport().getAlignment() | |
5649 | .isNucleotide(); | |
5650 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher( |
5651 | alignPanel.av.getSequenceSelection(), | |
5652 | alignPanel.alignFrame, dassrc, | |
5653 | alignPanel.alignFrame.featureSettings, | |
5654 | isNucleotide); | |
5655 | 0 | dbRefFetcher |
5656 | .addListener(new FetchFinishedListenerI() | |
5657 | { | |
5658 | 0 | @Override |
5659 | public void finished() | |
5660 | { | |
5661 | 0 | AlignFrame.this.setMenusForViewport(); |
5662 | } | |
5663 | }); | |
5664 | 0 | dbRefFetcher.fetchDBRefs(false); |
5665 | } | |
5666 | }).start(); | |
5667 | } | |
5668 | ||
5669 | }); | |
5670 | 0 | fetchr.setToolTipText( |
5671 | "<html>" + MessageManager.formatMessage( | |
5672 | "label.fetch_retrieve_from", new Object[] | |
5673 | { dbname })); | |
5674 | 0 | ifetch.add(fetchr); |
5675 | 0 | ++i; |
5676 | 0 | if (++icomp >= mcomp || i == (otherdb.size())) |
5677 | { | |
5678 | 0 | ifetch.setText(MessageManager.formatMessage( |
5679 | "label.source_to_target", imname, sname)); | |
5680 | 0 | dfetch.add(ifetch); |
5681 | 0 | ifetch = new JMenu(); |
5682 | 0 | imname = null; |
5683 | 0 | icomp = 0; |
5684 | 0 | comp++; |
5685 | } | |
5686 | } | |
5687 | } | |
5688 | 16805 | ++dbi; |
5689 | 16805 | if (comp >= mcomp || dbi >= (dbclasses.length)) |
5690 | { | |
5691 | 3361 | dfetch.setText(MessageManager.formatMessage( |
5692 | "label.source_to_target", mname, dbclass)); | |
5693 | 3361 | rfetch.add(dfetch); |
5694 | 3361 | dfetch = new JMenu(); |
5695 | 3361 | mname = null; |
5696 | 3361 | comp = 0; |
5697 | } | |
5698 | } | |
5699 | } | |
5700 | ||
5701 | }); | |
5702 | } | |
5703 | }).start(); | |
5704 | ||
5705 | } | |
5706 | ||
5707 | /** | |
5708 | * Left justify the whole alignment. | |
5709 | */ | |
5710 | 0 | @Override |
5711 | protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) | |
5712 | { | |
5713 | 0 | avc.justify_Region(true); |
5714 | } | |
5715 | ||
5716 | /** | |
5717 | * Right justify the whole alignment. | |
5718 | */ | |
5719 | 0 | @Override |
5720 | protected void justifyRightMenuItem_actionPerformed(ActionEvent e) | |
5721 | { | |
5722 | 0 | avc.justify_Region(false); |
5723 | } | |
5724 | ||
5725 | 12 | @Override |
5726 | public void setShowSeqFeatures(boolean b) | |
5727 | { | |
5728 | 12 | showSeqFeatures.setSelected(b); |
5729 | 12 | viewport.setShowSequenceFeatures(b); |
5730 | } | |
5731 | ||
5732 | /* | |
5733 | * (non-Javadoc) | |
5734 | * | |
5735 | * @see | |
5736 | * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. | |
5737 | * awt.event.ActionEvent) | |
5738 | */ | |
5739 | 0 | @Override |
5740 | protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) | |
5741 | { | |
5742 | 0 | viewport.setShowUnconserved(showNonconservedMenuItem.getState()); |
5743 | 0 | alignPanel.paintAlignment(false, false); |
5744 | } | |
5745 | ||
5746 | 0 | @Override |
5747 | protected void updateShowSSRadioButtons(JMenu showSS, | |
5748 | ButtonGroup ssButtonGroup) | |
5749 | { | |
5750 | ||
5751 | 0 | List<String> ssSources = new ArrayList<String>(); |
5752 | 0 | AlignmentAnnotation[] anns = alignPanel.getAlignment() |
5753 | .getAlignmentAnnotation(); | |
5754 | ||
5755 | 0 | ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(anns); |
5756 | ||
5757 | // Get the currently selected radio button | |
5758 | 0 | String selectedButtonModelName = getSelectedRadioButtonDisplayString( |
5759 | ssButtonGroup); | |
5760 | 0 | boolean selectedButtonModel = false; |
5761 | ||
5762 | // Clear existing radio buttons | |
5763 | 0 | showSS.removeAll(); |
5764 | 0 | JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem("All"); |
5765 | 0 | radioButtonAllSS.addActionListener(new ActionListener() |
5766 | { | |
5767 | 0 | @Override |
5768 | public void actionPerformed(ActionEvent e) | |
5769 | { | |
5770 | 0 | showSS_actionPerformed("All"); |
5771 | } | |
5772 | }); | |
5773 | 0 | ssButtonGroup.add(radioButtonAllSS); |
5774 | 0 | showSS.add(radioButtonAllSS); |
5775 | ||
5776 | 0 | JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem( |
5777 | "None"); | |
5778 | 0 | radioButtonNoneSS.addActionListener(new ActionListener() |
5779 | { | |
5780 | 0 | @Override |
5781 | public void actionPerformed(ActionEvent e) | |
5782 | { | |
5783 | 0 | showSS_actionPerformed("None"); |
5784 | } | |
5785 | }); | |
5786 | 0 | ssButtonGroup.add(radioButtonNoneSS); |
5787 | 0 | showSS.add(radioButtonNoneSS); |
5788 | 0 | showSS.addSeparator(); |
5789 | ||
5790 | 0 | for (String ssSource : ssSources) |
5791 | { | |
5792 | ||
5793 | 0 | JRadioButtonMenuItem radioButton = new JRadioButtonMenuItem(ssSource); |
5794 | 0 | radioButton.addActionListener(new ActionListener() |
5795 | { | |
5796 | 0 | @Override |
5797 | public void actionPerformed(ActionEvent e) | |
5798 | { | |
5799 | 0 | showSS_actionPerformed(ssSource); |
5800 | } | |
5801 | }); | |
5802 | 0 | ssButtonGroup.add(radioButton); |
5803 | 0 | showSS.add(radioButton); |
5804 | ||
5805 | // Check if this radio button's name matches the selected radio button's | |
5806 | // name | |
5807 | 0 | if (ssSource.equals(selectedButtonModelName)) |
5808 | { | |
5809 | 0 | radioButton.setSelected(true); // Select this radio button |
5810 | 0 | selectedButtonModel = true; |
5811 | } | |
5812 | ||
5813 | } | |
5814 | ||
5815 | 0 | if (selectedButtonModelName == "None") |
5816 | { | |
5817 | // If no radio button was previously selected, select "All" | |
5818 | 0 | ssButtonGroup.setSelected(radioButtonNoneSS.getModel(), true); |
5819 | 0 | selectedButtonModel = true; |
5820 | } | |
5821 | 0 | if (!selectedButtonModel) |
5822 | { | |
5823 | // If no radio button was previously selected, select "All" | |
5824 | 0 | ssButtonGroup.setSelected(radioButtonAllSS.getModel(), true); |
5825 | } | |
5826 | } | |
5827 | ||
5828 | 0 | @Override |
5829 | protected void showSS_actionPerformed(String ssSourceSelection) | |
5830 | { | |
5831 | ||
5832 | 0 | AlignmentAnnotation[] annotations = alignPanel.getAlignment() |
5833 | .getAlignmentAnnotation(); | |
5834 | ||
5835 | 0 | for (AlignmentAnnotation aa : annotations) |
5836 | { | |
5837 | ||
5838 | 0 | for (String label : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) |
5839 | { | |
5840 | ||
5841 | 0 | if (label.equals(aa.label)) |
5842 | { | |
5843 | ||
5844 | 0 | aa.visible = false; |
5845 | ||
5846 | 0 | if (ssSourceSelection == "All") |
5847 | { | |
5848 | 0 | aa.visible = true; |
5849 | } | |
5850 | ||
5851 | else | |
5852 | { | |
5853 | 0 | String ssSource = AlignmentUtils |
5854 | .extractSSSourceFromAnnotationDescription(aa); | |
5855 | 0 | if (ssSource.equals(ssSourceSelection)) |
5856 | { | |
5857 | 0 | aa.visible = true; |
5858 | } | |
5859 | ||
5860 | } | |
5861 | } | |
5862 | } | |
5863 | ||
5864 | } | |
5865 | ||
5866 | 0 | List<AlignCalcWorkerI> workers = viewport.getCalcManager() |
5867 | .getRegisteredWorkersOfClass( | |
5868 | SecondaryStructureConsensusThread.class); | |
5869 | 0 | if (!workers.isEmpty()) |
5870 | { | |
5871 | ||
5872 | 0 | viewport.getCalcManager().startWorker(workers.remove(0)); |
5873 | ||
5874 | } | |
5875 | ||
5876 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
5877 | 0 | alignPanel.updateAnnotation(); |
5878 | 0 | alignPanel.paintAlignment(true, true); |
5879 | ||
5880 | } | |
5881 | ||
5882 | 0 | protected String getSelectedRadioButtonDisplayString( |
5883 | ButtonGroup ssButtonGroup) | |
5884 | { | |
5885 | 0 | Enumeration<AbstractButton> buttons = ssButtonGroup.getElements(); |
5886 | 0 | while (buttons.hasMoreElements()) |
5887 | { | |
5888 | 0 | AbstractButton button = buttons.nextElement(); |
5889 | 0 | if (button.isSelected()) |
5890 | { | |
5891 | 0 | return button.getText(); |
5892 | } | |
5893 | } | |
5894 | 0 | return null; // No radio button is selected |
5895 | } | |
5896 | ||
5897 | 0 | protected void showSSConsensus_actionPerformed(ActionEvent e) |
5898 | { | |
5899 | 0 | viewport.setShowSSConsensus(showSSConsensus.getState()); |
5900 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5901 | } | |
5902 | ||
5903 | /* | |
5904 | * (non-Javadoc) | |
5905 | * | |
5906 | * @see | |
5907 | * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event | |
5908 | * .ActionEvent) | |
5909 | */ | |
5910 | 0 | @Override |
5911 | protected void showGroupConsensus_actionPerformed(ActionEvent e) | |
5912 | { | |
5913 | 0 | viewport.setShowGroupConsensus(showGroupConsensus.getState()); |
5914 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5915 | ||
5916 | } | |
5917 | ||
5918 | ||
5919 | 0 | @Override |
5920 | protected void showGroupSSConsensus_actionPerformed(ActionEvent e) | |
5921 | { | |
5922 | 0 | viewport.setShowGroupSSConsensus(showGroupSSConsensus.getState()); |
5923 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5924 | ||
5925 | } | |
5926 | ||
5927 | /* | |
5928 | * (non-Javadoc) | |
5929 | * | |
5930 | * @see | |
5931 | * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt | |
5932 | * .event.ActionEvent) | |
5933 | */ | |
5934 | 0 | @Override |
5935 | protected void showGroupConservation_actionPerformed(ActionEvent e) | |
5936 | { | |
5937 | 0 | viewport.setShowGroupConservation(showGroupConservation.getState()); |
5938 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5939 | } | |
5940 | ||
5941 | /* | |
5942 | * (non-Javadoc) | |
5943 | * | |
5944 | * @see | |
5945 | * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt | |
5946 | * .event.ActionEvent) | |
5947 | */ | |
5948 | 0 | @Override |
5949 | protected void showConsensusHistogram_actionPerformed(ActionEvent e) | |
5950 | { | |
5951 | 0 | viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); |
5952 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5953 | } | |
5954 | ||
5955 | 0 | @Override |
5956 | protected void showSSConsensusHistogram_actionPerformed(ActionEvent e) | |
5957 | { | |
5958 | 0 | viewport.setShowSSConsensusHistogram( |
5959 | showSSConsensusHistogram.getState()); | |
5960 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5961 | } | |
5962 | ||
5963 | /* | |
5964 | * (non-Javadoc) | |
5965 | * | |
5966 | * @see | |
5967 | * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt | |
5968 | * .event.ActionEvent) | |
5969 | */ | |
5970 | 0 | @Override |
5971 | protected void showSequenceLogo_actionPerformed(ActionEvent e) | |
5972 | { | |
5973 | 0 | viewport.setShowSequenceLogo(showSequenceLogo.getState()); |
5974 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5975 | } | |
5976 | ||
5977 | 0 | @Override |
5978 | protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) | |
5979 | { | |
5980 | 0 | showSequenceLogo.setState(true); |
5981 | 0 | viewport.setShowSequenceLogo(true); |
5982 | 0 | viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); |
5983 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5984 | } | |
5985 | ||
5986 | 0 | @Override |
5987 | protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) | |
5988 | { | |
5989 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5990 | } | |
5991 | ||
5992 | /* | |
5993 | * (non-Javadoc) | |
5994 | * | |
5995 | * @see | |
5996 | * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt | |
5997 | * .event.ActionEvent) | |
5998 | */ | |
5999 | 0 | @Override |
6000 | protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) | |
6001 | { | |
6002 | 0 | if (avc.makeGroupsFromSelection()) |
6003 | { | |
6004 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
6005 | 0 | alignPanel.updateAnnotation(); |
6006 | 0 | alignPanel.paintAlignment(true, |
6007 | viewport.needToUpdateStructureViews()); | |
6008 | } | |
6009 | } | |
6010 | ||
6011 | 0 | public void clearAlignmentSeqRep() |
6012 | { | |
6013 | // TODO refactor alignmentseqrep to controller | |
6014 | 0 | if (viewport.getAlignment().hasSeqrep()) |
6015 | { | |
6016 | 0 | viewport.getAlignment().setSeqrep(null); |
6017 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
6018 | 0 | alignPanel.updateAnnotation(); |
6019 | 0 | alignPanel.paintAlignment(true, true); |
6020 | } | |
6021 | } | |
6022 | ||
6023 | 0 | @Override |
6024 | protected void createGroup_actionPerformed(ActionEvent e) | |
6025 | { | |
6026 | 0 | if (avc.createGroup()) |
6027 | { | |
6028 | 0 | if (applyAutoAnnotationSettings.isSelected()) |
6029 | { | |
6030 | 0 | alignPanel.updateAnnotation(true, false); |
6031 | } | |
6032 | 0 | alignPanel.alignmentChanged(); |
6033 | } | |
6034 | } | |
6035 | ||
6036 | 0 | @Override |
6037 | protected void unGroup_actionPerformed(ActionEvent e) | |
6038 | { | |
6039 | 0 | if (avc.unGroup()) |
6040 | { | |
6041 | 0 | alignPanel.alignmentChanged(); |
6042 | } | |
6043 | } | |
6044 | ||
6045 | /** | |
6046 | * make the given alignmentPanel the currently selected tab | |
6047 | * | |
6048 | * @param alignmentPanel | |
6049 | */ | |
6050 | 0 | public void setDisplayedView(AlignmentPanel alignmentPanel) |
6051 | { | |
6052 | 0 | if (!viewport.getSequenceSetId() |
6053 | .equals(alignmentPanel.av.getSequenceSetId())) | |
6054 | { | |
6055 | 0 | throw new Error(MessageManager.getString( |
6056 | "error.implementation_error_cannot_show_view_alignment_frame")); | |
6057 | } | |
6058 | 0 | if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels |
6059 | .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) | |
6060 | { | |
6061 | 0 | tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); |
6062 | } | |
6063 | } | |
6064 | ||
6065 | /** | |
6066 | * Action on selection of menu options to Show or Hide annotations. | |
6067 | * | |
6068 | * @param visible | |
6069 | * @param forSequences | |
6070 | * update sequence-related annotations | |
6071 | * @param forAlignment | |
6072 | * update non-sequence-related annotations | |
6073 | */ | |
6074 | 302 | @Override |
6075 | public void setAnnotationsVisibility(boolean visible, | |
6076 | boolean forSequences, boolean forAlignment) | |
6077 | { | |
6078 | 302 | AlignmentAnnotation[] anns = alignPanel.getAlignment() |
6079 | .getAlignmentAnnotation(); | |
6080 | 302 | if (anns == null) |
6081 | { | |
6082 | 0 | return; |
6083 | } | |
6084 | 302 | for (AlignmentAnnotation aa : anns) |
6085 | { | |
6086 | /* | |
6087 | * don't display non-positional annotations on an alignment | |
6088 | */ | |
6089 | 1138 | if (aa.annotations == null) |
6090 | { | |
6091 | 0 | continue; |
6092 | } | |
6093 | 1138 | boolean apply = (aa.sequenceRef == null && forAlignment) |
6094 | || (aa.sequenceRef != null && forSequences); | |
6095 | 1138 | if (apply) |
6096 | { | |
6097 | 569 | aa.visible = visible; |
6098 | } | |
6099 | } | |
6100 | 302 | alignPanel.validateAnnotationDimensions(true); |
6101 | // TODO this triggers relayout of annotation panel - otherwise annotation | |
6102 | // label height is different to panel height | |
6103 | 302 | alignPanel.fontChanged(); |
6104 | 302 | alignPanel.alignmentChanged(); |
6105 | } | |
6106 | ||
6107 | /** | |
6108 | * Store selected annotation sort order for the view and repaint. | |
6109 | */ | |
6110 | 0 | @Override |
6111 | protected void sortAnnotations_actionPerformed() | |
6112 | { | |
6113 | 0 | this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); |
6114 | 0 | this.alignPanel.av |
6115 | .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); | |
6116 | 0 | alignPanel.paintAlignment(false, false); |
6117 | } | |
6118 | ||
6119 | /** | |
6120 | * | |
6121 | * @return alignment panels in this alignment frame | |
6122 | */ | |
6123 | 235 | public List<? extends AlignmentViewPanel> getAlignPanels() |
6124 | { | |
6125 | // alignPanels is never null | |
6126 | // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; | |
6127 | 235 | return alignPanels; |
6128 | } | |
6129 | ||
6130 | /** | |
6131 | * Open a new alignment window, with the cDNA associated with this (protein) | |
6132 | * alignment, aligned as is the protein. | |
6133 | */ | |
6134 | 0 | protected void viewAsCdna_actionPerformed() |
6135 | { | |
6136 | // TODO no longer a menu action - refactor as required | |
6137 | 0 | final AlignmentI alignment = getViewport().getAlignment(); |
6138 | 0 | List<AlignedCodonFrame> mappings = alignment.getCodonFrames(); |
6139 | 0 | if (mappings == null) |
6140 | { | |
6141 | 0 | return; |
6142 | } | |
6143 | 0 | List<SequenceI> cdnaSeqs = new ArrayList<>(); |
6144 | 0 | for (SequenceI aaSeq : alignment.getSequences()) |
6145 | { | |
6146 | 0 | for (AlignedCodonFrame acf : mappings) |
6147 | { | |
6148 | 0 | SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); |
6149 | 0 | if (dnaSeq != null) |
6150 | { | |
6151 | /* | |
6152 | * There is a cDNA mapping for this protein sequence - add to new | |
6153 | * alignment. It will share the same dataset sequence as other mapped | |
6154 | * cDNA (no new mappings need to be created). | |
6155 | */ | |
6156 | 0 | final Sequence newSeq = new Sequence(dnaSeq); |
6157 | 0 | newSeq.setDatasetSequence(dnaSeq); |
6158 | 0 | cdnaSeqs.add(newSeq); |
6159 | } | |
6160 | } | |
6161 | } | |
6162 | 0 | if (cdnaSeqs.size() == 0) |
6163 | { | |
6164 | // show a warning dialog no mapped cDNA | |
6165 | 0 | return; |
6166 | } | |
6167 | 0 | AlignmentI cdna = new Alignment( |
6168 | cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()])); | |
6169 | 0 | GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, |
6170 | AlignFrame.DEFAULT_HEIGHT); | |
6171 | 0 | cdna.alignAs(alignment); |
6172 | 0 | String newtitle = "cDNA " + MessageManager.getString("label.for") + " " |
6173 | + this.title; | |
6174 | 0 | Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH, |
6175 | AlignFrame.DEFAULT_HEIGHT); | |
6176 | } | |
6177 | ||
6178 | /** | |
6179 | * Set visibility of dna/protein complement view (available when shown in a | |
6180 | * split frame). | |
6181 | * | |
6182 | * @param show | |
6183 | */ | |
6184 | 0 | @Override |
6185 | protected void showComplement_actionPerformed(boolean show) | |
6186 | { | |
6187 | 0 | SplitContainerI sf = getSplitViewContainer(); |
6188 | 0 | if (sf != null) |
6189 | { | |
6190 | 0 | sf.setComplementVisible(this, show); |
6191 | } | |
6192 | } | |
6193 | ||
6194 | /** | |
6195 | * Generate the reverse (optionally complemented) of the selected sequences, | |
6196 | * and add them to the alignment | |
6197 | */ | |
6198 | 0 | @Override |
6199 | protected void showReverse_actionPerformed(boolean complement) | |
6200 | { | |
6201 | 0 | AlignmentI al = null; |
6202 | 0 | try |
6203 | { | |
6204 | 0 | Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); |
6205 | 0 | al = dna.reverseCdna(complement); |
6206 | 0 | viewport.addAlignment(al, ""); |
6207 | 0 | addHistoryItem(new EditCommand( |
6208 | MessageManager.getString("label.add_sequences"), Action.PASTE, | |
6209 | al.getSequencesArray(), 0, al.getWidth(), | |
6210 | viewport.getAlignment())); | |
6211 | } catch (Exception ex) | |
6212 | { | |
6213 | 0 | jalview.bin.Console.errPrintln(ex.getMessage()); |
6214 | 0 | return; |
6215 | } | |
6216 | } | |
6217 | ||
6218 | /** | |
6219 | * Try to run a script in the Groovy console, having first ensured that this | |
6220 | * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to | |
6221 | * be targeted at this alignment. | |
6222 | */ | |
6223 | 0 | @Override |
6224 | protected void runGroovy_actionPerformed() | |
6225 | { | |
6226 | 0 | Jalview.getInstance().setCurrentAlignFrame(this); |
6227 | 0 | groovy.console.ui.Console console = Desktop.getGroovyConsole(); |
6228 | 0 | if (console != null) |
6229 | { | |
6230 | 0 | try |
6231 | { | |
6232 | 0 | console.setVariable(JalviewObjectI.currentAlFrameName, this); |
6233 | 0 | console.runScript(); |
6234 | } catch (Exception ex) | |
6235 | { | |
6236 | 0 | jalview.bin.Console.errPrintln((ex.toString())); |
6237 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
6238 | MessageManager.getString("label.couldnt_run_groovy_script"), | |
6239 | MessageManager.getString("label.groovy_support_failed"), | |
6240 | JvOptionPane.ERROR_MESSAGE); | |
6241 | } | |
6242 | } | |
6243 | else | |
6244 | { | |
6245 | 0 | jalview.bin.Console |
6246 | .errPrintln("Can't run Groovy script as console not found"); | |
6247 | } | |
6248 | } | |
6249 | ||
6250 | /** | |
6251 | * Hides columns containing (or not containing) a specified feature, provided | |
6252 | * that would not leave all columns hidden | |
6253 | * | |
6254 | * @param featureType | |
6255 | * @param columnsContaining | |
6256 | * @return | |
6257 | */ | |
6258 | 7 | public boolean hideFeatureColumns(String featureType, |
6259 | boolean columnsContaining) | |
6260 | { | |
6261 | 7 | boolean notForHiding = avc.markColumnsContainingFeatures( |
6262 | columnsContaining, false, false, featureType); | |
6263 | 7 | if (notForHiding) |
6264 | { | |
6265 | 5 | if (avc.markColumnsContainingFeatures(!columnsContaining, false, |
6266 | false, featureType)) | |
6267 | { | |
6268 | 4 | getViewport().hideSelectedColumns(); |
6269 | 4 | return true; |
6270 | } | |
6271 | } | |
6272 | 3 | return false; |
6273 | } | |
6274 | ||
6275 | 0 | @Override |
6276 | protected void selectHighlightedColumns_actionPerformed( | |
6277 | ActionEvent actionEvent) | |
6278 | { | |
6279 | // include key modifier check in case user selects from menu | |
6280 | 0 | avc.markHighlightedColumns( |
6281 | (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true, | |
6282 | (actionEvent.getModifiers() & (ActionEvent.META_MASK | |
6283 | | ActionEvent.CTRL_MASK)) != 0); | |
6284 | } | |
6285 | ||
6286 | 0 | @Override |
6287 | protected void copyHighlightedColumns_actionPerformed( | |
6288 | ActionEvent actionEvent) | |
6289 | { | |
6290 | 0 | avc.copyHighlightedRegionsToClipboard(); |
6291 | } | |
6292 | ||
6293 | /** | |
6294 | * Rebuilds the Colour menu, including any user-defined colours which have | |
6295 | * been loaded either on startup or during the session | |
6296 | */ | |
6297 | 453 | public void buildColourMenu() |
6298 | { | |
6299 | 453 | colourMenu.removeAll(); |
6300 | ||
6301 | 453 | colourMenu.add(applyToAllGroups); |
6302 | 453 | colourMenu.add(textColour); |
6303 | 453 | colourMenu.addSeparator(); |
6304 | ||
6305 | 453 | ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, |
6306 | viewport.getAlignment(), false); | |
6307 | ||
6308 | 453 | colourMenu.add(annotationColour); |
6309 | 453 | bg.add(annotationColour); |
6310 | 453 | colourMenu.addSeparator(); |
6311 | 453 | colourMenu.add(conservationMenuItem); |
6312 | 453 | colourMenu.add(modifyConservation); |
6313 | 453 | colourMenu.add(abovePIDThreshold); |
6314 | 453 | colourMenu.add(modifyPID); |
6315 | ||
6316 | 453 | ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); |
6317 | 453 | ColourMenuHelper.setColourSelected(colourMenu, colourScheme); |
6318 | } | |
6319 | ||
6320 | /** | |
6321 | * Open a dialog (if not already open) that allows the user to select and | |
6322 | * calculate PCA or Tree analysis | |
6323 | */ | |
6324 | 0 | protected void openTreePcaDialog() |
6325 | { | |
6326 | 0 | if (alignPanel.getCalculationDialog() == null) |
6327 | { | |
6328 | 0 | new CalculationChooser(AlignFrame.this); |
6329 | } | |
6330 | } | |
6331 | ||
6332 | 0 | @Override |
6333 | protected void loadVcf_actionPerformed() | |
6334 | { | |
6335 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
6336 | Cache.getProperty("LAST_DIRECTORY")); | |
6337 | 0 | chooser.setFileView(new JalviewFileView()); |
6338 | 0 | chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); |
6339 | 0 | chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); |
6340 | 0 | final AlignFrame us = this; |
6341 | 0 | chooser.setResponseHandler(0, () -> { |
6342 | 0 | String choice = chooser.getSelectedFile().getPath(); |
6343 | 0 | Cache.setProperty("LAST_DIRECTORY", choice); |
6344 | 0 | SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); |
6345 | 0 | new VCFLoader(choice).loadVCF(seqs, us); |
6346 | }); | |
6347 | 0 | chooser.showOpenDialog(null); |
6348 | ||
6349 | } | |
6350 | ||
6351 | private Rectangle lastFeatureSettingsBounds = null; | |
6352 | ||
6353 | 1 | @Override |
6354 | public void setFeatureSettingsGeometry(Rectangle bounds) | |
6355 | { | |
6356 | 1 | lastFeatureSettingsBounds = bounds; |
6357 | } | |
6358 | ||
6359 | 2 | @Override |
6360 | public Rectangle getFeatureSettingsGeometry() | |
6361 | { | |
6362 | 2 | return lastFeatureSettingsBounds; |
6363 | } | |
6364 | ||
6365 | } | |
6366 | ||
6367 | class PrintThread extends Thread | |
6368 | { | |
6369 | AlignmentPanel ap; | |
6370 | ||
6371 | 0 | public PrintThread(AlignmentPanel ap) |
6372 | { | |
6373 | 0 | this.ap = ap; |
6374 | } | |
6375 | ||
6376 | static PageFormat pf; | |
6377 | ||
6378 | 0 | @Override |
6379 | public void run() | |
6380 | { | |
6381 | 0 | PrinterJob printJob = PrinterJob.getPrinterJob(); |
6382 | ||
6383 | 0 | if (pf != null) |
6384 | { | |
6385 | 0 | printJob.setPrintable(ap, pf); |
6386 | } | |
6387 | else | |
6388 | { | |
6389 | 0 | printJob.setPrintable(ap); |
6390 | } | |
6391 | ||
6392 | 0 | if (printJob.printDialog()) |
6393 | { | |
6394 | 0 | try |
6395 | { | |
6396 | 0 | printJob.print(); |
6397 | } catch (Exception PrintException) | |
6398 | { | |
6399 | 0 | PrintException.printStackTrace(); |
6400 | } | |
6401 | } | |
6402 | } | |
6403 | } |