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AlignFrame | 178 | 1,901 | 743 | ||
PrintThread | 6451 | 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.HashMap; | |
60 | import java.util.Hashtable; | |
61 | import java.util.List; | |
62 | import java.util.Locale; | |
63 | import java.util.Map; | |
64 | import java.util.Vector; | |
65 | ||
66 | import javax.swing.ButtonGroup; | |
67 | import javax.swing.JCheckBoxMenuItem; | |
68 | import javax.swing.JComponent; | |
69 | import javax.swing.JEditorPane; | |
70 | import javax.swing.JInternalFrame; | |
71 | import javax.swing.JLabel; | |
72 | import javax.swing.JLayeredPane; | |
73 | import javax.swing.JMenu; | |
74 | import javax.swing.JMenuItem; | |
75 | import javax.swing.JPanel; | |
76 | import javax.swing.JProgressBar; | |
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.AlignExportSettingsI; | |
89 | import jalview.api.AlignViewControllerGuiI; | |
90 | import jalview.api.AlignViewControllerI; | |
91 | import jalview.api.AlignViewportI; | |
92 | import jalview.api.AlignmentViewPanel; | |
93 | import jalview.api.FeatureSettingsControllerI; | |
94 | import jalview.api.FeatureSettingsModelI; | |
95 | import jalview.api.SplitContainerI; | |
96 | import jalview.api.ViewStyleI; | |
97 | import jalview.api.analysis.SimilarityParamsI; | |
98 | import jalview.bin.Cache; | |
99 | import jalview.bin.Console; | |
100 | import jalview.bin.Jalview; | |
101 | import jalview.bin.groovy.JalviewObjectI; | |
102 | import jalview.commands.CommandI; | |
103 | import jalview.commands.EditCommand; | |
104 | import jalview.commands.EditCommand.Action; | |
105 | import jalview.commands.OrderCommand; | |
106 | import jalview.commands.RemoveGapColCommand; | |
107 | import jalview.commands.RemoveGapsCommand; | |
108 | import jalview.commands.SlideSequencesCommand; | |
109 | import jalview.commands.TrimRegionCommand; | |
110 | import jalview.datamodel.AlignExportSettingsAdapter; | |
111 | import jalview.datamodel.AlignedCodonFrame; | |
112 | import jalview.datamodel.Alignment; | |
113 | import jalview.datamodel.AlignmentAnnotation; | |
114 | import jalview.datamodel.AlignmentExportData; | |
115 | import jalview.datamodel.AlignmentI; | |
116 | import jalview.datamodel.AlignmentOrder; | |
117 | import jalview.datamodel.AlignmentView; | |
118 | import jalview.datamodel.ColumnSelection; | |
119 | import jalview.datamodel.ContactMatrixI; | |
120 | import jalview.datamodel.HiddenColumns; | |
121 | import jalview.datamodel.PDBEntry; | |
122 | import jalview.datamodel.SeqCigar; | |
123 | import jalview.datamodel.Sequence; | |
124 | import jalview.datamodel.SequenceGroup; | |
125 | import jalview.datamodel.SequenceI; | |
126 | import jalview.gui.ColourMenuHelper.ColourChangeListener; | |
127 | import jalview.gui.ViewSelectionMenu.ViewSetProvider; | |
128 | import jalview.io.AlignmentProperties; | |
129 | import jalview.io.AnnotationFile; | |
130 | import jalview.io.BackupFiles; | |
131 | import jalview.io.BioJsHTMLOutput; | |
132 | import jalview.io.DataSourceType; | |
133 | import jalview.io.FileFormat; | |
134 | import jalview.io.FileFormatI; | |
135 | import jalview.io.FileFormats; | |
136 | import jalview.io.FileLoader; | |
137 | import jalview.io.FileParse; | |
138 | import jalview.io.FormatAdapter; | |
139 | import jalview.io.HtmlSvgOutput; | |
140 | import jalview.io.IdentifyFile; | |
141 | import jalview.io.JPredFile; | |
142 | import jalview.io.JalviewFileChooser; | |
143 | import jalview.io.JalviewFileView; | |
144 | import jalview.io.JnetAnnotationMaker; | |
145 | import jalview.io.NewickFile; | |
146 | import jalview.io.ScoreMatrixFile; | |
147 | import jalview.io.TCoffeeScoreFile; | |
148 | import jalview.io.exceptions.ImageOutputException; | |
149 | import jalview.io.vcf.VCFLoader; | |
150 | import jalview.jbgui.GAlignFrame; | |
151 | import jalview.project.Jalview2XML; | |
152 | import jalview.schemes.ColourSchemeI; | |
153 | import jalview.schemes.ColourSchemes; | |
154 | import jalview.schemes.ResidueColourScheme; | |
155 | import jalview.schemes.TCoffeeColourScheme; | |
156 | import jalview.util.Constants; | |
157 | import jalview.util.HttpUtils; | |
158 | import jalview.util.ImageMaker.TYPE; | |
159 | import jalview.util.MessageManager; | |
160 | import jalview.util.Platform; | |
161 | import jalview.util.imagemaker.BitmapImageSizing; | |
162 | import jalview.viewmodel.AlignmentViewport; | |
163 | import jalview.viewmodel.ViewportRanges; | |
164 | import jalview.ws.DBRefFetcher; | |
165 | import jalview.ws.DBRefFetcher.FetchFinishedListenerI; | |
166 | import jalview.ws.jws1.Discoverer; | |
167 | import jalview.ws.jws2.Jws2Discoverer; | |
168 | import jalview.ws.jws2.jabaws2.Jws2Instance; | |
169 | import jalview.ws.seqfetcher.DbSourceProxy; | |
170 | ||
171 | /** | |
172 | * DOCUMENT ME! | |
173 | * | |
174 | * @author $author$ | |
175 | * @version $Revision$ | |
176 | */ | |
177 | @SuppressWarnings("serial") | |
178 | public class AlignFrame extends GAlignFrame implements DropTargetListener, | |
179 | IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener | |
180 | { | |
181 | ||
182 | public static final int DEFAULT_WIDTH = 700; | |
183 | ||
184 | public static final int DEFAULT_HEIGHT = 500; | |
185 | ||
186 | /* | |
187 | * The currently displayed panel (selected tabbed view if more than one) | |
188 | */ | |
189 | public AlignmentPanel alignPanel; | |
190 | ||
191 | AlignViewport viewport; | |
192 | ||
193 | public AlignViewControllerI avc; | |
194 | ||
195 | List<AlignmentPanel> alignPanels = new ArrayList<>(); | |
196 | ||
197 | /** | |
198 | * Last format used to load or save alignments in this window | |
199 | */ | |
200 | FileFormatI currentFileFormat = null; | |
201 | ||
202 | /** | |
203 | * Current filename for this alignment | |
204 | */ | |
205 | String fileName = null; | |
206 | ||
207 | File fileObject; | |
208 | ||
209 | /** | |
210 | * Creates a new AlignFrame object with specific width and height. | |
211 | * | |
212 | * @param al | |
213 | * @param width | |
214 | * @param height | |
215 | */ | |
216 | 357 | public AlignFrame(AlignmentI al, int width, int height) |
217 | { | |
218 | 357 | this(al, null, width, height); |
219 | } | |
220 | ||
221 | /** | |
222 | * Creates a new AlignFrame object with specific width, height and | |
223 | * sequenceSetId | |
224 | * | |
225 | * @param al | |
226 | * @param width | |
227 | * @param height | |
228 | * @param sequenceSetId | |
229 | */ | |
230 | 0 | public AlignFrame(AlignmentI al, int width, int height, |
231 | String sequenceSetId) | |
232 | { | |
233 | 0 | this(al, null, width, height, sequenceSetId); |
234 | } | |
235 | ||
236 | /** | |
237 | * Creates a new AlignFrame object with specific width, height and | |
238 | * sequenceSetId | |
239 | * | |
240 | * @param al | |
241 | * @param width | |
242 | * @param height | |
243 | * @param sequenceSetId | |
244 | * @param viewId | |
245 | */ | |
246 | 85 | public AlignFrame(AlignmentI al, int width, int height, |
247 | String sequenceSetId, String viewId) | |
248 | { | |
249 | 85 | this(al, null, width, height, sequenceSetId, viewId); |
250 | } | |
251 | ||
252 | /** | |
253 | * new alignment window with hidden columns | |
254 | * | |
255 | * @param al | |
256 | * AlignmentI | |
257 | * @param hiddenColumns | |
258 | * ColumnSelection or null | |
259 | * @param width | |
260 | * Width of alignment frame | |
261 | * @param height | |
262 | * height of frame. | |
263 | */ | |
264 | 357 | public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, |
265 | int height) | |
266 | { | |
267 | 357 | this(al, hiddenColumns, width, height, null); |
268 | } | |
269 | ||
270 | /** | |
271 | * Create alignment frame for al with hiddenColumns, a specific width and | |
272 | * height, and specific sequenceId | |
273 | * | |
274 | * @param al | |
275 | * @param hiddenColumns | |
276 | * @param width | |
277 | * @param height | |
278 | * @param sequenceSetId | |
279 | * (may be null) | |
280 | */ | |
281 | 357 | public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, |
282 | int height, String sequenceSetId) | |
283 | { | |
284 | 357 | this(al, hiddenColumns, width, height, sequenceSetId, null); |
285 | } | |
286 | ||
287 | /** | |
288 | * Create alignment frame for al with hiddenColumns, a specific width and | |
289 | * height, and specific sequenceId | |
290 | * | |
291 | * @param al | |
292 | * @param hiddenColumns | |
293 | * @param width | |
294 | * @param height | |
295 | * @param sequenceSetId | |
296 | * (may be null) | |
297 | * @param viewId | |
298 | * (may be null) | |
299 | */ | |
300 | 442 | public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, |
301 | int height, String sequenceSetId, String viewId) | |
302 | { | |
303 | 442 | setSize(width, height); |
304 | ||
305 | 442 | if (al.getDataset() == null) |
306 | { | |
307 | 342 | al.setDataset(null); |
308 | } | |
309 | ||
310 | 442 | viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); |
311 | ||
312 | 442 | alignPanel = new AlignmentPanel(this, viewport); |
313 | ||
314 | 442 | addAlignmentPanel(alignPanel, true); |
315 | 442 | init(); |
316 | } | |
317 | ||
318 | 5 | public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, |
319 | HiddenColumns hiddenColumns, int width, int height) | |
320 | { | |
321 | 5 | setSize(width, height); |
322 | ||
323 | 5 | if (al.getDataset() == null) |
324 | { | |
325 | 5 | al.setDataset(null); |
326 | } | |
327 | ||
328 | 5 | viewport = new AlignViewport(al, hiddenColumns); |
329 | ||
330 | 5 | if (hiddenSeqs != null && hiddenSeqs.length > 0) |
331 | { | |
332 | 5 | viewport.hideSequence(hiddenSeqs); |
333 | } | |
334 | 5 | alignPanel = new AlignmentPanel(this, viewport); |
335 | 5 | addAlignmentPanel(alignPanel, true); |
336 | 5 | init(); |
337 | } | |
338 | ||
339 | /** | |
340 | * Make a new AlignFrame from existing alignmentPanels | |
341 | * | |
342 | * @param ap | |
343 | * AlignmentPanel | |
344 | * @param av | |
345 | * AlignViewport | |
346 | */ | |
347 | 5 | public AlignFrame(AlignmentPanel ap) |
348 | { | |
349 | 5 | viewport = ap.av; |
350 | 5 | alignPanel = ap; |
351 | 5 | addAlignmentPanel(ap, false); |
352 | 5 | init(); |
353 | } | |
354 | ||
355 | /** | |
356 | * initalise the alignframe from the underlying viewport data and the | |
357 | * configurations | |
358 | */ | |
359 | 452 | void init() |
360 | { | |
361 | 452 | setFrameIcon(null); |
362 | ||
363 | // setBackground(Color.white); // BH 2019 | |
364 | ||
365 | 452 | if (!Jalview.isHeadlessMode()) |
366 | { | |
367 | 389 | progressBar = new ProgressBar(this.statusPanel, this.statusBar); |
368 | } | |
369 | ||
370 | 452 | avc = new jalview.controller.AlignViewController(this, viewport, |
371 | alignPanel); | |
372 | 452 | if (viewport.getAlignmentConservationAnnotation() == null) |
373 | { | |
374 | // BLOSUM62Colour.setEnabled(false); | |
375 | 82 | conservationMenuItem.setEnabled(false); |
376 | 82 | modifyConservation.setEnabled(false); |
377 | // PIDColour.setEnabled(false); | |
378 | // abovePIDThreshold.setEnabled(false); | |
379 | // modifyPID.setEnabled(false); | |
380 | } | |
381 | ||
382 | 452 | String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort"); |
383 | ||
384 | 452 | if (sortby.equals("Id")) |
385 | { | |
386 | 0 | sortIDMenuItem_actionPerformed(null); |
387 | } | |
388 | 452 | else if (sortby.equals("Pairwise Identity")) |
389 | { | |
390 | 0 | sortPairwiseMenuItem_actionPerformed(null); |
391 | } | |
392 | ||
393 | 452 | this.alignPanel.av |
394 | .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); | |
395 | ||
396 | 452 | setMenusFromViewport(viewport); |
397 | 452 | buildSortByAnnotationScoresMenu(); |
398 | 452 | calculateTree.addActionListener(new ActionListener() |
399 | { | |
400 | ||
401 | 0 | @Override |
402 | public void actionPerformed(ActionEvent e) | |
403 | { | |
404 | 0 | openTreePcaDialog(); |
405 | } | |
406 | }); | |
407 | 452 | buildColourMenu(); |
408 | ||
409 | 452 | if (Desktop.desktop != null) |
410 | { | |
411 | 397 | this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); |
412 | 397 | if (!Platform.isJS()) |
413 | { | |
414 | 397 | addServiceListeners(); |
415 | } | |
416 | 397 | setGUINucleotide(); |
417 | } | |
418 | ||
419 | 452 | if (viewport.getWrapAlignment()) |
420 | { | |
421 | 7 | wrapMenuItem_actionPerformed(null); |
422 | } | |
423 | ||
424 | 452 | if (Cache.getDefault("SHOW_OVERVIEW", false)) |
425 | { | |
426 | 28 | this.overviewMenuItem_actionPerformed(null); |
427 | } | |
428 | ||
429 | 452 | addKeyListener(); |
430 | ||
431 | 452 | final List<AlignmentViewPanel> selviews = new ArrayList<>(); |
432 | 452 | final List<AlignmentPanel> origview = new ArrayList<>(); |
433 | 452 | final String menuLabel = MessageManager |
434 | .getString("label.copy_format_from"); | |
435 | 452 | ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, |
436 | new ViewSetProvider() | |
437 | { | |
438 | ||
439 | 0 | @Override |
440 | public AlignmentPanel[] getAllAlignmentPanels() | |
441 | { | |
442 | 0 | origview.clear(); |
443 | 0 | origview.add(alignPanel); |
444 | // make an array of all alignment panels except for this one | |
445 | 0 | List<AlignmentPanel> aps = new ArrayList<>( |
446 | Arrays.asList(Desktop.getAlignmentPanels(null))); | |
447 | 0 | aps.remove(AlignFrame.this.alignPanel); |
448 | 0 | return aps.toArray(new AlignmentPanel[aps.size()]); |
449 | } | |
450 | }, selviews, new ItemListener() | |
451 | { | |
452 | ||
453 | 0 | @Override |
454 | public void itemStateChanged(ItemEvent e) | |
455 | { | |
456 | 0 | if (origview.size() > 0) |
457 | { | |
458 | 0 | final AlignmentPanel ap = origview.get(0); |
459 | ||
460 | /* | |
461 | * Copy the ViewStyle of the selected panel to 'this one'. | |
462 | * Don't change value of 'scaleProteinAsCdna' unless copying | |
463 | * from a SplitFrame. | |
464 | */ | |
465 | 0 | ViewStyleI vs = selviews.get(0).getAlignViewport() |
466 | .getViewStyle(); | |
467 | 0 | boolean fromSplitFrame = selviews.get(0) |
468 | .getAlignViewport().getCodingComplement() != null; | |
469 | 0 | if (!fromSplitFrame) |
470 | { | |
471 | 0 | vs.setScaleProteinAsCdna(ap.getAlignViewport() |
472 | .getViewStyle().isScaleProteinAsCdna()); | |
473 | } | |
474 | 0 | ap.getAlignViewport().setViewStyle(vs); |
475 | ||
476 | /* | |
477 | * Also rescale ViewStyle of SplitFrame complement if there is | |
478 | * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy | |
479 | * the whole ViewStyle (allow cDNA protein to have different | |
480 | * fonts) | |
481 | */ | |
482 | 0 | AlignViewportI complement = ap.getAlignViewport() |
483 | .getCodingComplement(); | |
484 | 0 | if (complement != null && vs.isScaleProteinAsCdna()) |
485 | { | |
486 | 0 | AlignFrame af = Desktop.getAlignFrameFor(complement); |
487 | 0 | ((SplitFrame) af.getSplitViewContainer()) |
488 | .adjustLayout(); | |
489 | 0 | af.setMenusForViewport(); |
490 | } | |
491 | ||
492 | 0 | ap.updateLayout(); |
493 | 0 | ap.setSelected(true); |
494 | 0 | ap.alignFrame.setMenusForViewport(); |
495 | ||
496 | } | |
497 | } | |
498 | }); | |
499 | 452 | if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) |
500 | .indexOf("devel") > -1 | |
501 | || Cache.getDefault("VERSION", "DEVELOPMENT") | |
502 | .toLowerCase(Locale.ROOT).indexOf("test") > -1) | |
503 | { | |
504 | 452 | formatMenu.add(vsel); |
505 | } | |
506 | 452 | addFocusListener(new FocusAdapter() |
507 | { | |
508 | 365 | @Override |
509 | public void focusGained(FocusEvent e) | |
510 | { | |
511 | 365 | Jalview.getInstance().setCurrentAlignFrame(AlignFrame.this); |
512 | } | |
513 | }); | |
514 | ||
515 | } | |
516 | ||
517 | /** | |
518 | * Change the filename and format for the alignment, and enable the 'reload' | |
519 | * button functionality. | |
520 | * | |
521 | * @param file | |
522 | * valid filename | |
523 | * @param format | |
524 | * format of file | |
525 | */ | |
526 | 326 | public void setFileName(String file, FileFormatI format) |
527 | { | |
528 | 326 | fileName = file; |
529 | 326 | setFileFormat(format); |
530 | 326 | reload.setEnabled(true); |
531 | } | |
532 | ||
533 | /** | |
534 | * JavaScript will have this, maybe others. More dependable than a file name | |
535 | * and maintains a reference to the actual bytes loaded. | |
536 | * | |
537 | * @param file | |
538 | */ | |
539 | 241 | public void setFileObject(File file) |
540 | { | |
541 | 241 | this.fileObject = file; |
542 | } | |
543 | ||
544 | /** | |
545 | * Add a KeyListener with handlers for various KeyPressed and KeyReleased | |
546 | * events | |
547 | */ | |
548 | 452 | void addKeyListener() |
549 | { | |
550 | 452 | addKeyListener(new KeyAdapter() |
551 | { | |
552 | 0 | @Override |
553 | public void keyPressed(KeyEvent evt) | |
554 | { | |
555 | 0 | if (viewport.cursorMode |
556 | && ((evt.getKeyCode() >= KeyEvent.VK_0 | |
557 | && evt.getKeyCode() <= KeyEvent.VK_9) | |
558 | || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 | |
559 | && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)) | |
560 | && Character.isDigit(evt.getKeyChar())) | |
561 | { | |
562 | 0 | alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); |
563 | } | |
564 | ||
565 | 0 | switch (evt.getKeyCode()) |
566 | { | |
567 | ||
568 | 0 | case 27: // escape key |
569 | 0 | deselectAllSequenceMenuItem_actionPerformed(null); |
570 | ||
571 | 0 | break; |
572 | ||
573 | 0 | case KeyEvent.VK_DOWN: |
574 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
575 | { | |
576 | 0 | moveSelectedSequences(false); |
577 | } | |
578 | 0 | if (viewport.cursorMode) |
579 | { | |
580 | 0 | alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); |
581 | } | |
582 | 0 | break; |
583 | ||
584 | 0 | case KeyEvent.VK_UP: |
585 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
586 | { | |
587 | 0 | moveSelectedSequences(true); |
588 | } | |
589 | 0 | if (viewport.cursorMode) |
590 | { | |
591 | 0 | alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown()); |
592 | } | |
593 | ||
594 | 0 | break; |
595 | ||
596 | 0 | case KeyEvent.VK_LEFT: |
597 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
598 | { | |
599 | 0 | slideSequences(false, |
600 | alignPanel.getSeqPanel().getKeyboardNo1()); | |
601 | } | |
602 | else | |
603 | { | |
604 | 0 | alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); |
605 | } | |
606 | ||
607 | 0 | break; |
608 | ||
609 | 0 | case KeyEvent.VK_RIGHT: |
610 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
611 | { | |
612 | 0 | slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); |
613 | } | |
614 | else | |
615 | { | |
616 | 0 | alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); |
617 | } | |
618 | 0 | break; |
619 | ||
620 | 0 | case KeyEvent.VK_SPACE: |
621 | 0 | if (viewport.cursorMode) |
622 | { | |
623 | 0 | alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() |
624 | || evt.isShiftDown() || evt.isAltDown()); | |
625 | } | |
626 | 0 | break; |
627 | ||
628 | // case KeyEvent.VK_A: | |
629 | // if (viewport.cursorMode) | |
630 | // { | |
631 | // alignPanel.seqPanel.insertNucAtCursor(false,"A"); | |
632 | // //jalview.bin.Console.outPrintln("A"); | |
633 | // } | |
634 | // break; | |
635 | /* | |
636 | * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { | |
637 | * jalview.bin.Console.outPrintln("closing bracket"); } break; | |
638 | */ | |
639 | 0 | case KeyEvent.VK_DELETE: |
640 | 0 | case KeyEvent.VK_BACK_SPACE: |
641 | 0 | if (!viewport.cursorMode) |
642 | { | |
643 | 0 | cut_actionPerformed(); |
644 | } | |
645 | else | |
646 | { | |
647 | 0 | alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() |
648 | || evt.isShiftDown() || evt.isAltDown()); | |
649 | } | |
650 | ||
651 | 0 | break; |
652 | ||
653 | 0 | case KeyEvent.VK_S: |
654 | 0 | if (viewport.cursorMode) |
655 | { | |
656 | 0 | alignPanel.getSeqPanel().setCursorRow(); |
657 | } | |
658 | 0 | break; |
659 | 0 | case KeyEvent.VK_C: |
660 | 0 | if (viewport.cursorMode && !evt.isControlDown()) |
661 | { | |
662 | 0 | alignPanel.getSeqPanel().setCursorColumn(); |
663 | } | |
664 | 0 | break; |
665 | 0 | case KeyEvent.VK_P: |
666 | 0 | if (viewport.cursorMode) |
667 | { | |
668 | 0 | alignPanel.getSeqPanel().setCursorPosition(); |
669 | } | |
670 | 0 | break; |
671 | ||
672 | 0 | case KeyEvent.VK_ENTER: |
673 | 0 | case KeyEvent.VK_COMMA: |
674 | 0 | if (viewport.cursorMode) |
675 | { | |
676 | 0 | alignPanel.getSeqPanel().setCursorRowAndColumn(); |
677 | } | |
678 | 0 | break; |
679 | ||
680 | 0 | case KeyEvent.VK_Q: |
681 | 0 | if (viewport.cursorMode) |
682 | { | |
683 | 0 | alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); |
684 | } | |
685 | 0 | break; |
686 | 0 | case KeyEvent.VK_M: |
687 | 0 | if (viewport.cursorMode) |
688 | { | |
689 | 0 | alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); |
690 | } | |
691 | 0 | break; |
692 | ||
693 | 0 | case KeyEvent.VK_F2: |
694 | 0 | viewport.cursorMode = !viewport.cursorMode; |
695 | 0 | setStatus(MessageManager |
696 | .formatMessage("label.keyboard_editing_mode", new String[] | |
697 | 0 | { (viewport.cursorMode ? "on" : "off") })); |
698 | 0 | if (viewport.cursorMode) |
699 | { | |
700 | 0 | ViewportRanges ranges = viewport.getRanges(); |
701 | 0 | alignPanel.getSeqPanel().seqCanvas.cursorX = ranges |
702 | .getStartRes(); | |
703 | 0 | alignPanel.getSeqPanel().seqCanvas.cursorY = ranges |
704 | .getStartSeq(); | |
705 | } | |
706 | 0 | alignPanel.getSeqPanel().seqCanvas.repaint(); |
707 | 0 | break; |
708 | ||
709 | 0 | case KeyEvent.VK_F1: |
710 | 0 | try |
711 | { | |
712 | 0 | Help.showHelpWindow(); |
713 | } catch (Exception ex) | |
714 | { | |
715 | 0 | ex.printStackTrace(); |
716 | } | |
717 | 0 | break; |
718 | 0 | case KeyEvent.VK_H: |
719 | { | |
720 | 0 | boolean toggleSeqs = !evt.isControlDown(); |
721 | 0 | boolean toggleCols = !evt.isShiftDown(); |
722 | 0 | toggleHiddenRegions(toggleSeqs, toggleCols); |
723 | 0 | break; |
724 | } | |
725 | 0 | case KeyEvent.VK_B: |
726 | { | |
727 | 0 | boolean toggleSel = evt.isControlDown() || evt.isMetaDown(); |
728 | 0 | boolean modifyExisting = true; // always modify, don't clear |
729 | // evt.isShiftDown(); | |
730 | 0 | boolean invertHighlighted = evt.isAltDown(); |
731 | 0 | avc.markHighlightedColumns(invertHighlighted, modifyExisting, |
732 | toggleSel); | |
733 | 0 | break; |
734 | } | |
735 | 0 | case KeyEvent.VK_PAGE_UP: |
736 | 0 | viewport.getRanges().pageUp(); |
737 | 0 | break; |
738 | 0 | case KeyEvent.VK_PAGE_DOWN: |
739 | 0 | viewport.getRanges().pageDown(); |
740 | 0 | break; |
741 | } | |
742 | } | |
743 | ||
744 | 0 | @Override |
745 | public void keyReleased(KeyEvent evt) | |
746 | { | |
747 | 0 | switch (evt.getKeyCode()) |
748 | { | |
749 | 0 | case KeyEvent.VK_LEFT: |
750 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
751 | { | |
752 | 0 | viewport.firePropertyChange("alignment", null, |
753 | viewport.getAlignment().getSequences()); | |
754 | } | |
755 | 0 | break; |
756 | ||
757 | 0 | case KeyEvent.VK_RIGHT: |
758 | 0 | if (evt.isAltDown() || !viewport.cursorMode) |
759 | { | |
760 | 0 | viewport.firePropertyChange("alignment", null, |
761 | viewport.getAlignment().getSequences()); | |
762 | } | |
763 | 0 | break; |
764 | } | |
765 | } | |
766 | }); | |
767 | } | |
768 | ||
769 | 501 | public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) |
770 | { | |
771 | 501 | ap.alignFrame = this; |
772 | 501 | avc = new jalview.controller.AlignViewController(this, viewport, |
773 | alignPanel); | |
774 | ||
775 | 501 | alignPanels.add(ap); |
776 | ||
777 | 501 | PaintRefresher.Register(ap, ap.av.getSequenceSetId()); |
778 | ||
779 | 501 | int aSize = alignPanels.size(); |
780 | ||
781 | 501 | tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null); |
782 | ||
783 | 501 | if (aSize == 1 && ap.av.getViewName() == null) |
784 | { | |
785 | 447 | this.getContentPane().add(ap, BorderLayout.CENTER); |
786 | } | |
787 | else | |
788 | { | |
789 | 54 | if (aSize == 2) |
790 | { | |
791 | 23 | setInitialTabVisible(); |
792 | } | |
793 | ||
794 | 54 | expandViews.setEnabled(true); |
795 | 54 | gatherViews.setEnabled(true); |
796 | 54 | tabbedPane.addTab(ap.av.getViewName(), ap); |
797 | ||
798 | 54 | ap.setVisible(false); |
799 | } | |
800 | ||
801 | 501 | if (newPanel) |
802 | { | |
803 | 457 | if (ap.av.isPadGaps()) |
804 | { | |
805 | 188 | ap.av.getAlignment().padGaps(); |
806 | } | |
807 | 457 | ap.av.updateConservation(ap); |
808 | 457 | ap.av.updateConsensus(ap); |
809 | 457 | ap.av.updateSecondaryStructureConsensus(ap); |
810 | 457 | ap.av.updateStrucConsensus(ap); |
811 | } | |
812 | } | |
813 | ||
814 | 82 | public void setInitialTabVisible() |
815 | { | |
816 | 82 | expandViews.setEnabled(true); |
817 | 82 | gatherViews.setEnabled(true); |
818 | 82 | tabbedPane.setVisible(true); |
819 | 82 | AlignmentPanel first = alignPanels.get(0); |
820 | 82 | tabbedPane.addTab(first.av.getViewName(), first); |
821 | 82 | this.getContentPane().add(tabbedPane, BorderLayout.CENTER); |
822 | } | |
823 | ||
824 | 2647 | public AlignViewport getViewport() |
825 | { | |
826 | 2647 | return viewport; |
827 | } | |
828 | ||
829 | /* Set up intrinsic listeners for dynamically generated GUI bits. */ | |
830 | 397 | private void addServiceListeners() |
831 | { | |
832 | 397 | final java.beans.PropertyChangeListener thisListener; |
833 | 397 | Desktop.instance.addJalviewPropertyChangeListener("services", |
834 | thisListener = new java.beans.PropertyChangeListener() | |
835 | { | |
836 | 2303 | @Override |
837 | public void propertyChange(PropertyChangeEvent evt) | |
838 | { | |
839 | // // jalview.bin.Console.outPrintln("Discoverer property | |
840 | // change."); | |
841 | // if (evt.getPropertyName().equals("services")) | |
842 | { | |
843 | 2303 | SwingUtilities.invokeLater(new Runnable() |
844 | { | |
845 | ||
846 | 2303 | @Override |
847 | public void run() | |
848 | { | |
849 | 2303 | jalview.bin.Console.errPrintln( |
850 | "Rebuild WS Menu for service change"); | |
851 | 2303 | BuildWebServiceMenu(); |
852 | } | |
853 | ||
854 | }); | |
855 | } | |
856 | } | |
857 | }); | |
858 | 397 | addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() |
859 | { | |
860 | 260 | @Override |
861 | public void internalFrameClosed( | |
862 | javax.swing.event.InternalFrameEvent evt) | |
863 | { | |
864 | // jalview.bin.Console.outPrintln("deregistering discoverer listener"); | |
865 | 260 | Desktop.instance.removeJalviewPropertyChangeListener("services", |
866 | thisListener); | |
867 | 260 | closeMenuItem_actionPerformed(true); |
868 | } | |
869 | }); | |
870 | // Finally, build the menu once to get current service state | |
871 | 397 | new Thread(new Runnable() |
872 | { | |
873 | 397 | @Override |
874 | public void run() | |
875 | { | |
876 | 397 | BuildWebServiceMenu(); |
877 | } | |
878 | }).start(); | |
879 | } | |
880 | ||
881 | /** | |
882 | * Configure menu items that vary according to whether the alignment is | |
883 | * nucleotide or protein | |
884 | */ | |
885 | 397 | public void setGUINucleotide() |
886 | { | |
887 | 397 | AlignmentI al = getViewport().getAlignment(); |
888 | 397 | boolean nucleotide = al.isNucleotide(); |
889 | ||
890 | 397 | loadVcf.setVisible(nucleotide); |
891 | 397 | showTranslation.setVisible(nucleotide); |
892 | 397 | showReverse.setVisible(nucleotide); |
893 | 397 | showReverseComplement.setVisible(nucleotide); |
894 | 397 | conservationMenuItem.setEnabled(!nucleotide); |
895 | 397 | modifyConservation |
896 | .setEnabled(!nucleotide && conservationMenuItem.isSelected()); | |
897 | 397 | byConsensusSecondaryStructureMenuItem.setEnabled(!nucleotide); |
898 | 397 | modifyConsensusSecondaryStructureThreshold.setEnabled(!nucleotide |
899 | && byConsensusSecondaryStructureMenuItem.isSelected()); | |
900 | 397 | showGroupConservation.setEnabled(!nucleotide); |
901 | ||
902 | 397 | showComplementMenuItem |
903 | 397 | .setText(nucleotide ? MessageManager.getString("label.protein") |
904 | : MessageManager.getString("label.nucleotide")); | |
905 | } | |
906 | ||
907 | /** | |
908 | * set up menus for the current viewport. This may be called after any | |
909 | * operation that affects the data in the current view (selection changed, | |
910 | * etc) to update the menus to reflect the new state. | |
911 | */ | |
912 | 30 | @Override |
913 | public void setMenusForViewport() | |
914 | { | |
915 | 30 | setMenusFromViewport(viewport); |
916 | } | |
917 | ||
918 | /** | |
919 | * Need to call this method when tabs are selected for multiple views, or when | |
920 | * loading from Jalview2XML.java | |
921 | * | |
922 | * @param av | |
923 | * AlignViewport | |
924 | */ | |
925 | 672 | public void setMenusFromViewport(AlignViewport av) |
926 | { | |
927 | 672 | padGapsMenuitem.setSelected(av.isPadGaps()); |
928 | 672 | colourTextMenuItem.setSelected(av.isShowColourText()); |
929 | 672 | abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); |
930 | 672 | modifyPID.setEnabled(abovePIDThreshold.isSelected()); |
931 | 672 | conservationMenuItem.setSelected(av.getConservationSelected()); |
932 | 672 | modifyConservation.setEnabled(conservationMenuItem.isSelected()); |
933 | 672 | byConsensusSecondaryStructureMenuItem |
934 | .setSelected(av.getByConsensusSecondaryStructureSelected()); | |
935 | 672 | modifyConsensusSecondaryStructureThreshold |
936 | .setEnabled(byConsensusSecondaryStructureMenuItem.isSelected()); | |
937 | 672 | seqLimits.setSelected(av.getShowJVSuffix()); |
938 | 672 | idRightAlign.setSelected(av.isRightAlignIds()); |
939 | 672 | centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); |
940 | 672 | renderGapsMenuItem.setSelected(av.isRenderGaps()); |
941 | 672 | wrapMenuItem.setSelected(av.getWrapAlignment()); |
942 | 672 | scaleAbove.setVisible(av.getWrapAlignment()); |
943 | 672 | scaleLeft.setVisible(av.getWrapAlignment()); |
944 | 672 | scaleRight.setVisible(av.getWrapAlignment()); |
945 | 672 | annotationPanelMenuItem.setState(av.isShowAnnotation()); |
946 | /* | |
947 | * Show/hide annotations only enabled if annotation panel is shown | |
948 | */ | |
949 | 672 | showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
950 | 672 | hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
951 | 672 | showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
952 | 672 | hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
953 | 672 | viewBoxesMenuItem.setSelected(av.getShowBoxes()); |
954 | 672 | viewTextMenuItem.setSelected(av.getShowText()); |
955 | 672 | showNonconservedMenuItem.setSelected(av.getShowUnconserved()); |
956 | 672 | showGroupConsensus.setSelected(av.isShowGroupConsensus()); |
957 | 672 | showGroupSSConsensus.setSelected(av.isShowGroupSSConsensus()); |
958 | 672 | showStrucProvider.setSelected(av.isShowStructureProvider()); |
959 | 672 | showGroupConservation.setSelected(av.isShowGroupConservation()); |
960 | 672 | showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); |
961 | 672 | showSequenceLogo.setSelected(av.isShowSequenceLogo()); |
962 | 672 | normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); |
963 | ||
964 | 672 | ColourMenuHelper.setColourSelected(colourMenu, |
965 | av.getGlobalColourScheme()); | |
966 | ||
967 | 672 | showSeqFeatures.setSelected(av.isShowSequenceFeatures()); |
968 | 672 | hiddenMarkers.setState(av.getShowHiddenMarkers()); |
969 | 672 | applyToAllGroups.setState(av.getColourAppliesToAllGroups()); |
970 | 672 | showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); |
971 | 672 | showDbRefsMenuitem.setSelected(av.isShowDBRefs()); |
972 | 672 | autoCalculate.setSelected(av.autoCalculateConsensus); |
973 | 672 | sortByTree.setSelected(av.sortByTree); |
974 | 672 | listenToViewSelections.setSelected(av.followSelection); |
975 | ||
976 | 672 | showProducts.setEnabled(canShowProducts()); |
977 | 672 | setGroovyEnabled(Desktop.getGroovyConsole() != null); |
978 | ||
979 | 672 | updateEditMenuBar(); |
980 | } | |
981 | ||
982 | /** | |
983 | * Set the enabled state of the 'Run Groovy' option in the Calculate menu | |
984 | * | |
985 | * @param b | |
986 | */ | |
987 | 672 | public void setGroovyEnabled(boolean b) |
988 | { | |
989 | 672 | runGroovy.setEnabled(b); |
990 | } | |
991 | ||
992 | private IProgressIndicator progressBar; | |
993 | ||
994 | /* | |
995 | * (non-Javadoc) | |
996 | * | |
997 | * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) | |
998 | */ | |
999 | 661 | @Override |
1000 | public void setProgressBar(String message, long id) | |
1001 | { | |
1002 | 661 | if (!Platform.isHeadless() && progressBar != null) |
1003 | 279 | progressBar.setProgressBar(message, id); |
1004 | } | |
1005 | ||
1006 | 0 | @Override |
1007 | public JProgressBar getProgressBar(long id) | |
1008 | { | |
1009 | 0 | if (progressBar != null) |
1010 | 0 | return progressBar.getProgressBar(id); |
1011 | 0 | return null; |
1012 | } | |
1013 | ||
1014 | 0 | public String getMessage(long id) |
1015 | { | |
1016 | 0 | return progressBar.getMessage(id); |
1017 | } | |
1018 | ||
1019 | 0 | public void setProgressBarMessage(long id, String message) |
1020 | { | |
1021 | 0 | progressBar.setProgressBarMessage(id, message); |
1022 | } | |
1023 | ||
1024 | 0 | @Override |
1025 | public void registerHandler(final long id, | |
1026 | final IProgressIndicatorHandler handler) | |
1027 | { | |
1028 | 0 | if (progressBar != null) |
1029 | 0 | progressBar.registerHandler(id, handler); |
1030 | } | |
1031 | ||
1032 | /** | |
1033 | * | |
1034 | * @return true if any progress bars are still active | |
1035 | */ | |
1036 | 19 | @Override |
1037 | public boolean operationInProgress() | |
1038 | { | |
1039 | 19 | return progressBar == null ? false : progressBar.operationInProgress(); |
1040 | } | |
1041 | ||
1042 | /** | |
1043 | * Sets the text of the status bar. Note that setting a null or empty value | |
1044 | * will cause the status bar to be hidden, with possibly undesirable flicker | |
1045 | * of the screen layout. | |
1046 | */ | |
1047 | 398 | @Override |
1048 | public void setStatus(String text) | |
1049 | { | |
1050 | 398 | statusBar.setText(text == null || text.isEmpty() ? " " : text); |
1051 | } | |
1052 | ||
1053 | /* | |
1054 | * Added so Castor Mapping file can obtain Jalview Version | |
1055 | */ | |
1056 | 0 | public String getVersion() |
1057 | { | |
1058 | 0 | return Cache.getProperty("VERSION"); |
1059 | } | |
1060 | ||
1061 | 49 | public FeatureRenderer getFeatureRenderer() |
1062 | { | |
1063 | 49 | return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); |
1064 | } | |
1065 | ||
1066 | 0 | @Override |
1067 | public void fetchSequence_actionPerformed() | |
1068 | { | |
1069 | 0 | new SequenceFetcher(this); |
1070 | } | |
1071 | ||
1072 | 0 | @Override |
1073 | public void addFromFile_actionPerformed(ActionEvent e) | |
1074 | { | |
1075 | 0 | Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); |
1076 | } | |
1077 | ||
1078 | 0 | @Override |
1079 | public void reload_actionPerformed(ActionEvent e) | |
1080 | { | |
1081 | 0 | if (fileName != null) |
1082 | { | |
1083 | // TODO: JAL-1108 - ensure all associated frames are closed regardless of | |
1084 | // originating file's format | |
1085 | // TODO: work out how to recover feature settings for correct view(s) when | |
1086 | // file is reloaded. | |
1087 | 0 | if (FileFormat.Jalview.equals(currentFileFormat)) |
1088 | { | |
1089 | 0 | JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
1090 | 0 | for (int i = 0; i < frames.length; i++) |
1091 | { | |
1092 | 0 | if (frames[i] instanceof AlignFrame && frames[i] != this |
1093 | && ((AlignFrame) frames[i]).fileName != null | |
1094 | && ((AlignFrame) frames[i]).fileName.equals(fileName)) | |
1095 | { | |
1096 | 0 | try |
1097 | { | |
1098 | 0 | frames[i].setSelected(true); |
1099 | 0 | Desktop.instance.closeAssociatedWindows(); |
1100 | } catch (java.beans.PropertyVetoException ex) | |
1101 | { | |
1102 | } | |
1103 | } | |
1104 | ||
1105 | } | |
1106 | 0 | Desktop.instance.closeAssociatedWindows(); |
1107 | ||
1108 | 0 | FileLoader loader = new FileLoader(); |
1109 | 0 | DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName) |
1110 | ? DataSourceType.URL | |
1111 | : DataSourceType.FILE; | |
1112 | 0 | loader.LoadFile(viewport, fileName, protocol, currentFileFormat); |
1113 | } | |
1114 | else | |
1115 | { | |
1116 | 0 | Rectangle bounds = this.getBounds(); |
1117 | ||
1118 | 0 | FileLoader loader = new FileLoader(); |
1119 | ||
1120 | 0 | AlignFrame newframe = null; |
1121 | ||
1122 | 0 | if (fileObject == null) |
1123 | { | |
1124 | ||
1125 | 0 | DataSourceType protocol = HttpUtils.startsWithHttpOrHttps( |
1126 | fileName) ? DataSourceType.URL : DataSourceType.FILE; | |
1127 | 0 | newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, |
1128 | currentFileFormat); | |
1129 | } | |
1130 | else | |
1131 | { | |
1132 | 0 | newframe = loader.LoadFileWaitTillLoaded(fileObject, |
1133 | DataSourceType.FILE, currentFileFormat); | |
1134 | } | |
1135 | ||
1136 | 0 | newframe.setBounds(bounds); |
1137 | 0 | if (featureSettings != null && featureSettings.isShowing()) |
1138 | { | |
1139 | 0 | final Rectangle fspos = featureSettings.frame.getBounds(); |
1140 | // TODO: need a 'show feature settings' function that takes bounds - | |
1141 | // need to refactor Desktop.addFrame | |
1142 | 0 | newframe.featureSettings_actionPerformed(null); |
1143 | 0 | final FeatureSettings nfs = newframe.featureSettings; |
1144 | 0 | SwingUtilities.invokeLater(new Runnable() |
1145 | { | |
1146 | 0 | @Override |
1147 | public void run() | |
1148 | { | |
1149 | 0 | nfs.frame.setBounds(fspos); |
1150 | } | |
1151 | }); | |
1152 | 0 | this.featureSettings.close(); |
1153 | 0 | this.featureSettings = null; |
1154 | } | |
1155 | 0 | this.closeMenuItem_actionPerformed(true); |
1156 | } | |
1157 | } | |
1158 | } | |
1159 | ||
1160 | 0 | @Override |
1161 | public void addFromText_actionPerformed(ActionEvent e) | |
1162 | { | |
1163 | 0 | Desktop.instance |
1164 | .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); | |
1165 | } | |
1166 | ||
1167 | 0 | @Override |
1168 | public void addFromURL_actionPerformed(ActionEvent e) | |
1169 | { | |
1170 | 0 | Desktop.instance.inputURLMenuItem_actionPerformed(viewport); |
1171 | } | |
1172 | ||
1173 | 0 | @Override |
1174 | public void save_actionPerformed(ActionEvent e) | |
1175 | { | |
1176 | 0 | if (fileName == null || (currentFileFormat == null) |
1177 | || HttpUtils.startsWithHttpOrHttps(fileName)) | |
1178 | { | |
1179 | 0 | saveAs_actionPerformed(); |
1180 | } | |
1181 | else | |
1182 | { | |
1183 | 0 | saveAlignment(fileName, currentFileFormat); |
1184 | } | |
1185 | } | |
1186 | ||
1187 | /** | |
1188 | * Saves the alignment to a file with a name chosen by the user, if necessary | |
1189 | * warning if a file would be overwritten | |
1190 | */ | |
1191 | 0 | @Override |
1192 | public void saveAs_actionPerformed() | |
1193 | { | |
1194 | 0 | String format = currentFileFormat == null ? null |
1195 | : currentFileFormat.getName(); | |
1196 | 0 | JalviewFileChooser chooser = JalviewFileChooser |
1197 | .forWrite(Cache.getProperty("LAST_DIRECTORY"), format); | |
1198 | ||
1199 | 0 | chooser.setFileView(new JalviewFileView()); |
1200 | 0 | chooser.setDialogTitle( |
1201 | MessageManager.getString("label.save_alignment_to_file")); | |
1202 | 0 | chooser.setToolTipText(MessageManager.getString("action.save")); |
1203 | ||
1204 | 0 | int value = chooser.showSaveDialog(this); |
1205 | ||
1206 | 0 | if (value != JalviewFileChooser.APPROVE_OPTION) |
1207 | { | |
1208 | 0 | return; |
1209 | } | |
1210 | 0 | currentFileFormat = chooser.getSelectedFormat(); |
1211 | // todo is this (2005) test now obsolete - value is never null? | |
1212 | 0 | while (currentFileFormat == null) |
1213 | { | |
1214 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
1215 | MessageManager | |
1216 | .getString("label.select_file_format_before_saving"), | |
1217 | MessageManager.getString("label.file_format_not_specified"), | |
1218 | JvOptionPane.WARNING_MESSAGE); | |
1219 | 0 | value = chooser.showSaveDialog(this); |
1220 | 0 | if (value != JalviewFileChooser.APPROVE_OPTION) |
1221 | { | |
1222 | 0 | return; |
1223 | } | |
1224 | 0 | currentFileFormat = chooser.getSelectedFormat(); |
1225 | } | |
1226 | ||
1227 | 0 | fileName = chooser.getSelectedFile().getPath(); |
1228 | ||
1229 | 0 | Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); |
1230 | 0 | Cache.setProperty("LAST_DIRECTORY", fileName); |
1231 | 0 | saveAlignment(fileName, currentFileFormat); |
1232 | } | |
1233 | ||
1234 | boolean lastSaveSuccessful = false; | |
1235 | ||
1236 | FileFormatI lastFormatSaved; | |
1237 | ||
1238 | String lastFilenameSaved; | |
1239 | ||
1240 | /** | |
1241 | * Raise a dialog or status message for the last call to saveAlignment. | |
1242 | * | |
1243 | * @return true if last call to saveAlignment(file, format) was successful. | |
1244 | */ | |
1245 | 88 | public boolean isSaveAlignmentSuccessful() |
1246 | { | |
1247 | ||
1248 | 88 | if (!lastSaveSuccessful) |
1249 | { | |
1250 | 0 | if (!Platform.isHeadless()) |
1251 | { | |
1252 | 0 | JvOptionPane.showInternalMessageDialog(this, MessageManager |
1253 | .formatMessage("label.couldnt_save_file", new Object[] | |
1254 | { lastFilenameSaved }), | |
1255 | MessageManager.getString("label.error_saving_file"), | |
1256 | JvOptionPane.WARNING_MESSAGE); | |
1257 | } | |
1258 | else | |
1259 | { | |
1260 | 0 | Console.error(MessageManager |
1261 | .formatMessage("label.couldnt_save_file", new Object[] | |
1262 | { lastFilenameSaved })); | |
1263 | } | |
1264 | } | |
1265 | else | |
1266 | { | |
1267 | ||
1268 | 88 | setStatus(MessageManager.formatMessage( |
1269 | "label.successfully_saved_to_file_in_format", new Object[] | |
1270 | { lastFilenameSaved, lastFormatSaved })); | |
1271 | ||
1272 | } | |
1273 | 88 | return lastSaveSuccessful; |
1274 | } | |
1275 | ||
1276 | /** | |
1277 | * Saves the alignment to the specified file path, in the specified format, | |
1278 | * which may be an alignment format, or Jalview project format. If the | |
1279 | * alignment has hidden regions, or the format is one capable of including | |
1280 | * non-sequence data (features, annotations, groups), then the user may be | |
1281 | * prompted to specify what to include in the output. | |
1282 | * | |
1283 | * @param file | |
1284 | * @param format | |
1285 | */ | |
1286 | 54 | public void saveAlignment(String file, FileFormatI format) |
1287 | { | |
1288 | 54 | saveAlignment(file, format, false, false); |
1289 | } | |
1290 | ||
1291 | 128 | public void saveAlignment(String file, FileFormatI format, boolean stdout, |
1292 | boolean forceBackup) | |
1293 | { | |
1294 | 128 | lastSaveSuccessful = true; |
1295 | 128 | if (!stdout) |
1296 | { | |
1297 | 116 | lastFilenameSaved = file; |
1298 | } | |
1299 | 128 | lastFormatSaved = format; |
1300 | ||
1301 | 128 | if (FileFormat.Jalview.equals(format)) |
1302 | { | |
1303 | 8 | String shortName = title; |
1304 | 8 | if (shortName.indexOf(File.separatorChar) > -1) |
1305 | { | |
1306 | 5 | shortName = shortName |
1307 | .substring(shortName.lastIndexOf(File.separatorChar) + 1); | |
1308 | } | |
1309 | // TODO deal with stdout=true | |
1310 | 8 | lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, |
1311 | shortName); | |
1312 | ||
1313 | 8 | Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); |
1314 | 8 | if (lastSaveSuccessful) |
1315 | { | |
1316 | 8 | this.getViewport().setSavedUpToDate(true); |
1317 | } | |
1318 | ||
1319 | 8 | statusBar.setText(MessageManager.formatMessage( |
1320 | "label.successfully_saved_to_file_in_format", new Object[] | |
1321 | { file, format })); | |
1322 | ||
1323 | 8 | return; |
1324 | } | |
1325 | ||
1326 | 120 | AlignExportSettingsI options = new AlignExportSettingsAdapter(false); |
1327 | 120 | Runnable cancelAction = () -> { |
1328 | 0 | lastSaveSuccessful = false; |
1329 | }; | |
1330 | 120 | Runnable outputAction = () -> { |
1331 | // todo defer this to inside formatSequences (or later) | |
1332 | 120 | AlignmentExportData exportData = viewport.getAlignExportData(options); |
1333 | 120 | String output = new FormatAdapter(alignPanel, options) |
1334 | .formatSequences(format, exportData.getAlignment(), | |
1335 | exportData.getOmitHidden(), | |
1336 | exportData.getStartEndPostions(), | |
1337 | viewport.getAlignment().getHiddenColumns()); | |
1338 | 120 | if (output == null) |
1339 | { | |
1340 | 0 | lastSaveSuccessful = false; |
1341 | } | |
1342 | else | |
1343 | { | |
1344 | // create backupfiles object and get new temp filename destination | |
1345 | 120 | boolean doBackup = forceBackup |
1346 | || (BackupFiles.getEnabled() && !stdout); | |
1347 | 120 | BackupFiles backupfiles = null; |
1348 | 120 | if (doBackup) |
1349 | { | |
1350 | 92 | Console.trace("ALIGNFRAME making backupfiles object for " + file); |
1351 | 92 | backupfiles = new BackupFiles(file); |
1352 | } | |
1353 | 120 | try |
1354 | { | |
1355 | 120 | String tempFilePath = doBackup ? backupfiles.getTempFilePath() |
1356 | : file; | |
1357 | 120 | Console.trace("ALIGNFRAME setting PrintWriter"); |
1358 | 120 | PrintWriter out = stdout |
1359 | ? new PrintWriter(new OutputStreamWriter(System.out)) | |
1360 | : new PrintWriter(new FileWriter(tempFilePath)); | |
1361 | ||
1362 | 120 | if (backupfiles != null) |
1363 | { | |
1364 | 92 | Console.trace("ALIGNFRAME about to write to temp file " |
1365 | + backupfiles.getTempFilePath()); | |
1366 | } | |
1367 | ||
1368 | 120 | out.print(output); |
1369 | 120 | out.flush(); |
1370 | 120 | if (!stdout) |
1371 | { | |
1372 | 108 | Console.trace("ALIGNFRAME about to close file"); |
1373 | 108 | out.close(); |
1374 | 108 | Console.trace("ALIGNFRAME closed file"); |
1375 | } | |
1376 | 120 | AlignFrame.this.setTitle(stdout ? "STDOUT" : file); |
1377 | 120 | if (stdout) |
1378 | { | |
1379 | 12 | statusBar.setText(MessageManager.formatMessage( |
1380 | "label.successfully_printed_to_stdout_in_format", | |
1381 | new Object[] | |
1382 | { format.getName() })); | |
1383 | } | |
1384 | else | |
1385 | { | |
1386 | 108 | statusBar.setText(MessageManager.formatMessage( |
1387 | "label.successfully_saved_to_file_in_format", | |
1388 | new Object[] | |
1389 | { fileName, format.getName() })); | |
1390 | } | |
1391 | 120 | lastSaveSuccessful = true; |
1392 | } catch (IOException e) | |
1393 | { | |
1394 | 0 | lastSaveSuccessful = false; |
1395 | 0 | Console.error( |
1396 | "ALIGNFRAME Something happened writing the temp file"); | |
1397 | 0 | Console.error(e.getMessage()); |
1398 | 0 | Console.debug(Cache.getStackTraceString(e)); |
1399 | } catch (Exception ex) | |
1400 | { | |
1401 | 0 | lastSaveSuccessful = false; |
1402 | 0 | Console.error( |
1403 | "ALIGNFRAME Something unexpected happened writing the temp file"); | |
1404 | 0 | Console.error(ex.getMessage()); |
1405 | 0 | Console.debug(Cache.getStackTraceString(ex)); |
1406 | } | |
1407 | ||
1408 | 120 | if (doBackup) |
1409 | { | |
1410 | 92 | backupfiles.setWriteSuccess(lastSaveSuccessful); |
1411 | 92 | Console.debug("ALIGNFRAME writing temp file was " |
1412 | 92 | + (lastSaveSuccessful ? "" : "NOT ") + "successful"); |
1413 | // do the backup file roll and rename the temp file to actual file | |
1414 | 92 | Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile"); |
1415 | 92 | lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); |
1416 | 92 | Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile " |
1417 | 92 | + (lastSaveSuccessful ? "" : "un") + "successfully"); |
1418 | } | |
1419 | ||
1420 | 120 | Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); |
1421 | 120 | if (lastSaveSuccessful) |
1422 | { | |
1423 | 120 | AlignFrame.this.getViewport().setSavedUpToDate(true); |
1424 | } | |
1425 | } | |
1426 | }; | |
1427 | ||
1428 | /* | |
1429 | * show dialog with export options if applicable; else just do it | |
1430 | */ | |
1431 | 120 | if (AlignExportOptions.isNeeded(viewport, format)) |
1432 | { | |
1433 | 0 | AlignExportOptions choices = new AlignExportOptions( |
1434 | alignPanel.getAlignViewport(), format, options); | |
1435 | 0 | choices.setResponseAction(0, outputAction); |
1436 | 0 | choices.setResponseAction(1, cancelAction); |
1437 | 0 | choices.showDialog(); |
1438 | } | |
1439 | else | |
1440 | { | |
1441 | 120 | try |
1442 | { | |
1443 | 120 | outputAction.run(); |
1444 | } catch (Exception e) | |
1445 | { | |
1446 | // TODO Auto-generated catch block | |
1447 | 0 | e.printStackTrace(); |
1448 | } | |
1449 | } | |
1450 | } | |
1451 | ||
1452 | /** | |
1453 | * Outputs the alignment to textbox in the requested format, if necessary | |
1454 | * first prompting the user for whether to include hidden regions or | |
1455 | * non-sequence data | |
1456 | * | |
1457 | * @param fileFormatName | |
1458 | */ | |
1459 | 0 | @Override |
1460 | protected void outputText_actionPerformed(String fileFormatName) | |
1461 | { | |
1462 | 0 | FileFormatI fileFormat = FileFormats.getInstance() |
1463 | .forName(fileFormatName); | |
1464 | 0 | AlignExportSettingsI options = new AlignExportSettingsAdapter(false); |
1465 | 0 | Runnable outputAction = () -> { |
1466 | // todo defer this to inside formatSequences (or later) | |
1467 | 0 | AlignmentExportData exportData = viewport.getAlignExportData(options); |
1468 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
1469 | 0 | cap.setForInput(null); |
1470 | 0 | try |
1471 | { | |
1472 | 0 | FileFormatI format = fileFormat; |
1473 | 0 | cap.setText(new FormatAdapter(alignPanel, options).formatSequences( |
1474 | format, exportData.getAlignment(), | |
1475 | exportData.getOmitHidden(), | |
1476 | exportData.getStartEndPostions(), | |
1477 | viewport.getAlignment().getHiddenColumns())); | |
1478 | 0 | Desktop.addInternalFrame(cap, MessageManager.formatMessage( |
1479 | "label.alignment_output_command", new Object[] | |
1480 | { fileFormat.getName() }), 600, 500); | |
1481 | } catch (OutOfMemoryError oom) | |
1482 | { | |
1483 | 0 | new OOMWarning("Outputting alignment as " + fileFormat.getName(), |
1484 | oom); | |
1485 | 0 | cap.dispose(); |
1486 | } | |
1487 | }; | |
1488 | ||
1489 | /* | |
1490 | * show dialog with export options if applicable; else just do it | |
1491 | */ | |
1492 | 0 | if (AlignExportOptions.isNeeded(viewport, fileFormat)) |
1493 | { | |
1494 | 0 | AlignExportOptions choices = new AlignExportOptions( |
1495 | alignPanel.getAlignViewport(), fileFormat, options); | |
1496 | 0 | choices.setResponseAction(0, outputAction); |
1497 | 0 | choices.showDialog(); |
1498 | } | |
1499 | else | |
1500 | { | |
1501 | 0 | try |
1502 | { | |
1503 | 0 | outputAction.run(); |
1504 | } catch (Exception e) | |
1505 | { | |
1506 | 0 | e.printStackTrace(); |
1507 | } | |
1508 | } | |
1509 | } | |
1510 | ||
1511 | /** | |
1512 | * DOCUMENT ME! | |
1513 | * | |
1514 | * @param e | |
1515 | * DOCUMENT ME! | |
1516 | */ | |
1517 | 0 | @Override |
1518 | protected void htmlMenuItem_actionPerformed(ActionEvent e) | |
1519 | { | |
1520 | 0 | HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel); |
1521 | 0 | try |
1522 | { | |
1523 | 0 | htmlSVG.exportHTML(null); |
1524 | } catch (ImageOutputException x) | |
1525 | { | |
1526 | // report problem to console and raise dialog | |
1527 | } | |
1528 | } | |
1529 | ||
1530 | 0 | @Override |
1531 | public void bioJSMenuItem_actionPerformed(ActionEvent e) | |
1532 | { | |
1533 | 0 | BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); |
1534 | 0 | try |
1535 | { | |
1536 | 0 | bjs.exportHTML(null); |
1537 | } catch (ImageOutputException x) | |
1538 | { | |
1539 | // report problem to console and raise dialog | |
1540 | } | |
1541 | } | |
1542 | ||
1543 | 0 | public void createImageMap(File file, String image) |
1544 | { | |
1545 | 0 | try |
1546 | { | |
1547 | 0 | alignPanel.makePNGImageMap(file, image); |
1548 | } catch (ImageOutputException x) | |
1549 | { | |
1550 | // report problem to console and raise dialog | |
1551 | } | |
1552 | } | |
1553 | ||
1554 | 0 | @Override |
1555 | public void createPNG_actionPerformed(ActionEvent e) | |
1556 | { | |
1557 | 0 | try |
1558 | { | |
1559 | 0 | createPNG(null); |
1560 | } catch (ImageOutputException ioex) | |
1561 | { | |
1562 | // raise dialog, and report via console | |
1563 | } | |
1564 | } | |
1565 | ||
1566 | 0 | @Override |
1567 | public void createEPS_actionPerformed(ActionEvent e) | |
1568 | { | |
1569 | 0 | try |
1570 | { | |
1571 | 0 | createEPS(null); |
1572 | } catch (ImageOutputException ioex) | |
1573 | { | |
1574 | // raise dialog, and report via console | |
1575 | } | |
1576 | ||
1577 | } | |
1578 | ||
1579 | 0 | @Override |
1580 | public void createSVG_actionPerformed(ActionEvent e) | |
1581 | { | |
1582 | 0 | try |
1583 | { | |
1584 | 0 | createSVG(null); |
1585 | } catch (ImageOutputException ioex) | |
1586 | { | |
1587 | // raise dialog, and report via console | |
1588 | } | |
1589 | ||
1590 | } | |
1591 | ||
1592 | /** | |
1593 | * Creates a PNG image of the alignment and writes it to the given file. If | |
1594 | * the file is null, the user is prompted to choose a file. | |
1595 | * | |
1596 | * @param f | |
1597 | */ | |
1598 | 1 | public void createPNG(File f) throws ImageOutputException |
1599 | { | |
1600 | 1 | createPNG(f, null, BitmapImageSizing.defaultBitmapImageSizing()); |
1601 | } | |
1602 | ||
1603 | 24 | public void createPNG(File f, String renderer, BitmapImageSizing userBis) |
1604 | throws ImageOutputException | |
1605 | { | |
1606 | 24 | alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis); |
1607 | } | |
1608 | ||
1609 | /** | |
1610 | * Creates an EPS image of the alignment and writes it to the given file. If | |
1611 | * the file is null, the user is prompted to choose a file. | |
1612 | * | |
1613 | * @param f | |
1614 | */ | |
1615 | 5 | public void createEPS(File f) throws ImageOutputException |
1616 | { | |
1617 | 5 | createEPS(f, null); |
1618 | } | |
1619 | ||
1620 | 10 | public void createEPS(File f, String renderer) throws ImageOutputException |
1621 | { | |
1622 | 10 | alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer); |
1623 | } | |
1624 | ||
1625 | /** | |
1626 | * Creates an SVG image of the alignment and writes it to the given file. If | |
1627 | * the file is null, the user is prompted to choose a file. | |
1628 | * | |
1629 | * @param f | |
1630 | */ | |
1631 | 1 | public void createSVG(File f) throws ImageOutputException |
1632 | { | |
1633 | 1 | createSVG(f, null); |
1634 | } | |
1635 | ||
1636 | 2 | public void createSVG(File f, String renderer) throws ImageOutputException |
1637 | { | |
1638 | 2 | alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer); |
1639 | } | |
1640 | ||
1641 | 0 | @Override |
1642 | public void pageSetup_actionPerformed(ActionEvent e) | |
1643 | { | |
1644 | 0 | PrinterJob printJob = PrinterJob.getPrinterJob(); |
1645 | 0 | PrintThread.pf = printJob.pageDialog(printJob.defaultPage()); |
1646 | } | |
1647 | ||
1648 | /** | |
1649 | * DOCUMENT ME! | |
1650 | * | |
1651 | * @param e | |
1652 | * DOCUMENT ME! | |
1653 | */ | |
1654 | 0 | @Override |
1655 | public void printMenuItem_actionPerformed(ActionEvent e) | |
1656 | { | |
1657 | // Putting in a thread avoids Swing painting problems | |
1658 | 0 | PrintThread thread = new PrintThread(alignPanel); |
1659 | 0 | thread.start(); |
1660 | } | |
1661 | ||
1662 | 0 | @Override |
1663 | public void exportFeatures_actionPerformed(ActionEvent e) | |
1664 | { | |
1665 | 0 | new AnnotationExporter(alignPanel).exportFeatures(); |
1666 | } | |
1667 | ||
1668 | 0 | @Override |
1669 | public void exportAnnotations_actionPerformed(ActionEvent e) | |
1670 | { | |
1671 | 0 | new AnnotationExporter(alignPanel).exportAnnotations(); |
1672 | } | |
1673 | ||
1674 | 0 | @Override |
1675 | public void associatedData_actionPerformed(ActionEvent e) | |
1676 | { | |
1677 | 0 | final JalviewFileChooser chooser = new JalviewFileChooser( |
1678 | Cache.getProperty("LAST_DIRECTORY")); | |
1679 | 0 | chooser.setFileView(new JalviewFileView()); |
1680 | 0 | String tooltip = MessageManager |
1681 | .getString("label.load_jalview_annotations"); | |
1682 | 0 | chooser.setDialogTitle(tooltip); |
1683 | 0 | chooser.setToolTipText(tooltip); |
1684 | 0 | chooser.setResponseHandler(0, () -> { |
1685 | 0 | String choice = chooser.getSelectedFile().getPath(); |
1686 | 0 | Cache.setProperty("LAST_DIRECTORY", choice); |
1687 | 0 | loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); |
1688 | }); | |
1689 | ||
1690 | 0 | chooser.showOpenDialog(this); |
1691 | } | |
1692 | ||
1693 | /** | |
1694 | * Close the current view or all views in the alignment frame. If the frame | |
1695 | * only contains one view then the alignment will be removed from memory. | |
1696 | * | |
1697 | * @param closeAllTabs | |
1698 | */ | |
1699 | 386 | @Override |
1700 | public void closeMenuItem_actionPerformed(boolean closeAllTabs) | |
1701 | { | |
1702 | 386 | if (alignPanels != null && alignPanels.size() < 2) |
1703 | { | |
1704 | 366 | closeAllTabs = true; |
1705 | } | |
1706 | ||
1707 | 386 | Desktop.closeModal(this); |
1708 | ||
1709 | 386 | try |
1710 | { | |
1711 | 386 | if (alignPanels != null) |
1712 | { | |
1713 | 386 | if (closeAllTabs) |
1714 | { | |
1715 | 385 | if (this.isClosed()) |
1716 | { | |
1717 | // really close all the windows - otherwise wait till | |
1718 | // setClosed(true) is called | |
1719 | 512 | for (int i = 0; i < alignPanels.size(); i++) |
1720 | { | |
1721 | 252 | AlignmentPanel ap = alignPanels.get(i); |
1722 | 252 | ap.closePanel(); |
1723 | } | |
1724 | } | |
1725 | } | |
1726 | else | |
1727 | { | |
1728 | 1 | closeView(alignPanel); |
1729 | } | |
1730 | } | |
1731 | 386 | if (closeAllTabs) |
1732 | { | |
1733 | 385 | if (featureSettings != null && featureSettings.isOpen()) |
1734 | { | |
1735 | 0 | featureSettings.close(); |
1736 | 0 | featureSettings = null; |
1737 | } | |
1738 | ||
1739 | /* | |
1740 | * this will raise an INTERNAL_FRAME_CLOSED event and this method will | |
1741 | * be called recursively, with the frame now in 'closed' state | |
1742 | */ | |
1743 | 385 | this.setClosed(true); |
1744 | } | |
1745 | } catch (Exception ex) | |
1746 | { | |
1747 | 0 | ex.printStackTrace(); |
1748 | } | |
1749 | } | |
1750 | ||
1751 | /** | |
1752 | * Close the specified panel and close up tabs appropriately. | |
1753 | * | |
1754 | * @param panelToClose | |
1755 | */ | |
1756 | 1 | public void closeView(AlignmentPanel panelToClose) |
1757 | { | |
1758 | 1 | int index = tabbedPane.getSelectedIndex(); |
1759 | 1 | int closedindex = tabbedPane.indexOfComponent(panelToClose); |
1760 | 1 | alignPanels.remove(panelToClose); |
1761 | 1 | panelToClose.closePanel(); |
1762 | 1 | panelToClose = null; |
1763 | ||
1764 | 1 | tabbedPane.removeTabAt(closedindex); |
1765 | 1 | tabbedPane.validate(); |
1766 | ||
1767 | 1 | if (index > closedindex || index == tabbedPane.getTabCount()) |
1768 | { | |
1769 | // modify currently selected tab index if necessary. | |
1770 | 1 | index--; |
1771 | } | |
1772 | ||
1773 | 1 | this.tabSelectionChanged(index); |
1774 | } | |
1775 | ||
1776 | /** | |
1777 | * DOCUMENT ME! | |
1778 | */ | |
1779 | 1222 | void updateEditMenuBar() |
1780 | { | |
1781 | ||
1782 | 1222 | if (viewport.getHistoryList().size() > 0) |
1783 | { | |
1784 | 1 | undoMenuItem.setEnabled(true); |
1785 | 1 | CommandI command = viewport.getHistoryList().peek(); |
1786 | 1 | undoMenuItem.setText(MessageManager |
1787 | .formatMessage("label.undo_command", new Object[] | |
1788 | { command.getDescription() })); | |
1789 | } | |
1790 | else | |
1791 | { | |
1792 | 1221 | undoMenuItem.setEnabled(false); |
1793 | 1221 | undoMenuItem.setText(MessageManager.getString("action.undo")); |
1794 | } | |
1795 | ||
1796 | 1222 | if (viewport.getRedoList().size() > 0) |
1797 | { | |
1798 | 0 | redoMenuItem.setEnabled(true); |
1799 | ||
1800 | 0 | CommandI command = viewport.getRedoList().peek(); |
1801 | 0 | redoMenuItem.setText(MessageManager |
1802 | .formatMessage("label.redo_command", new Object[] | |
1803 | { command.getDescription() })); | |
1804 | } | |
1805 | else | |
1806 | { | |
1807 | 1222 | redoMenuItem.setEnabled(false); |
1808 | 1222 | redoMenuItem.setText(MessageManager.getString("action.redo")); |
1809 | } | |
1810 | } | |
1811 | ||
1812 | 1 | @Override |
1813 | public void addHistoryItem(CommandI command) | |
1814 | { | |
1815 | 1 | if (command.getSize() > 0) |
1816 | { | |
1817 | 1 | viewport.addToHistoryList(command); |
1818 | 1 | viewport.clearRedoList(); |
1819 | 1 | updateEditMenuBar(); |
1820 | 1 | viewport.updateHiddenColumns(); |
1821 | // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null | |
1822 | // && viewport.getColumnSelection().getHiddenColumns() != null && | |
1823 | // viewport.getColumnSelection() | |
1824 | // .getHiddenColumns().size() > 0); | |
1825 | } | |
1826 | } | |
1827 | ||
1828 | /** | |
1829 | * | |
1830 | * @return alignment objects for all views | |
1831 | */ | |
1832 | 0 | public AlignmentI[] getViewAlignments() |
1833 | { | |
1834 | 0 | if (alignPanels != null) |
1835 | { | |
1836 | 0 | AlignmentI[] als = new AlignmentI[alignPanels.size()]; |
1837 | 0 | int i = 0; |
1838 | 0 | for (AlignmentPanel ap : alignPanels) |
1839 | { | |
1840 | 0 | als[i++] = ap.av.getAlignment(); |
1841 | } | |
1842 | 0 | return als; |
1843 | } | |
1844 | 0 | if (viewport != null) |
1845 | { | |
1846 | 0 | return new AlignmentI[] { viewport.getAlignment() }; |
1847 | } | |
1848 | 0 | return null; |
1849 | } | |
1850 | ||
1851 | /** | |
1852 | * DOCUMENT ME! | |
1853 | * | |
1854 | * @param e | |
1855 | * DOCUMENT ME! | |
1856 | */ | |
1857 | 0 | @Override |
1858 | protected void undoMenuItem_actionPerformed(ActionEvent e) | |
1859 | { | |
1860 | 0 | if (viewport.getHistoryList().isEmpty()) |
1861 | { | |
1862 | 0 | return; |
1863 | } | |
1864 | 0 | CommandI command = viewport.getHistoryList().pop(); |
1865 | 0 | viewport.addToRedoList(command); |
1866 | 0 | command.undoCommand(getViewAlignments()); |
1867 | ||
1868 | 0 | AlignmentViewport originalSource = getOriginatingSource(command); |
1869 | 0 | updateEditMenuBar(); |
1870 | ||
1871 | 0 | if (originalSource != null) |
1872 | { | |
1873 | 0 | if (originalSource != viewport) |
1874 | { | |
1875 | 0 | Console.warn( |
1876 | "Implementation worry: mismatch of viewport origin for undo"); | |
1877 | } | |
1878 | 0 | originalSource.updateHiddenColumns(); |
1879 | // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != | |
1880 | // null | |
1881 | // && viewport.getColumnSelection().getHiddenColumns() != null && | |
1882 | // viewport.getColumnSelection() | |
1883 | // .getHiddenColumns().size() > 0); | |
1884 | 0 | originalSource.firePropertyChange("alignment", null, |
1885 | originalSource.getAlignment().getSequences()); | |
1886 | } | |
1887 | } | |
1888 | ||
1889 | /** | |
1890 | * DOCUMENT ME! | |
1891 | * | |
1892 | * @param e | |
1893 | * DOCUMENT ME! | |
1894 | */ | |
1895 | 0 | @Override |
1896 | protected void redoMenuItem_actionPerformed(ActionEvent e) | |
1897 | { | |
1898 | 0 | if (viewport.getRedoList().size() < 1) |
1899 | { | |
1900 | 0 | return; |
1901 | } | |
1902 | ||
1903 | 0 | CommandI command = viewport.getRedoList().pop(); |
1904 | 0 | viewport.addToHistoryList(command); |
1905 | 0 | command.doCommand(getViewAlignments()); |
1906 | ||
1907 | 0 | AlignmentViewport originalSource = getOriginatingSource(command); |
1908 | 0 | updateEditMenuBar(); |
1909 | ||
1910 | 0 | if (originalSource != null) |
1911 | { | |
1912 | ||
1913 | 0 | if (originalSource != viewport) |
1914 | { | |
1915 | 0 | Console.warn( |
1916 | "Implementation worry: mismatch of viewport origin for redo"); | |
1917 | } | |
1918 | 0 | originalSource.updateHiddenColumns(); |
1919 | // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != | |
1920 | // null | |
1921 | // && viewport.getColumnSelection().getHiddenColumns() != null && | |
1922 | // viewport.getColumnSelection() | |
1923 | // .getHiddenColumns().size() > 0); | |
1924 | 0 | originalSource.firePropertyChange("alignment", null, |
1925 | originalSource.getAlignment().getSequences()); | |
1926 | } | |
1927 | } | |
1928 | ||
1929 | 0 | AlignmentViewport getOriginatingSource(CommandI command) |
1930 | { | |
1931 | 0 | AlignmentViewport originalSource = null; |
1932 | // For sequence removal and addition, we need to fire | |
1933 | // the property change event FROM the viewport where the | |
1934 | // original alignment was altered | |
1935 | 0 | AlignmentI al = null; |
1936 | 0 | if (command instanceof EditCommand) |
1937 | { | |
1938 | 0 | EditCommand editCommand = (EditCommand) command; |
1939 | 0 | al = editCommand.getAlignment(); |
1940 | 0 | List<Component> comps = PaintRefresher.components |
1941 | .get(viewport.getSequenceSetId()); | |
1942 | ||
1943 | 0 | for (Component comp : comps) |
1944 | { | |
1945 | 0 | if (comp instanceof AlignmentPanel) |
1946 | { | |
1947 | 0 | if (al == ((AlignmentPanel) comp).av.getAlignment()) |
1948 | { | |
1949 | 0 | originalSource = ((AlignmentPanel) comp).av; |
1950 | 0 | break; |
1951 | } | |
1952 | } | |
1953 | } | |
1954 | } | |
1955 | ||
1956 | 0 | if (originalSource == null) |
1957 | { | |
1958 | // The original view is closed, we must validate | |
1959 | // the current view against the closed view first | |
1960 | 0 | if (al != null) |
1961 | { | |
1962 | 0 | PaintRefresher.validateSequences(al, viewport.getAlignment()); |
1963 | } | |
1964 | ||
1965 | 0 | originalSource = viewport; |
1966 | } | |
1967 | ||
1968 | 0 | return originalSource; |
1969 | } | |
1970 | ||
1971 | /** | |
1972 | * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection | |
1973 | * or the sequence under cursor in keyboard mode | |
1974 | * | |
1975 | * @param up | |
1976 | * or down (if !up) | |
1977 | */ | |
1978 | 0 | public void moveSelectedSequences(boolean up) |
1979 | { | |
1980 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
1981 | ||
1982 | 0 | if (sg == null) |
1983 | { | |
1984 | 0 | if (viewport.cursorMode) |
1985 | { | |
1986 | 0 | sg = new SequenceGroup(); |
1987 | 0 | sg.addSequence(viewport.getAlignment().getSequenceAt( |
1988 | alignPanel.getSeqPanel().seqCanvas.cursorY), false); | |
1989 | } | |
1990 | else | |
1991 | { | |
1992 | 0 | return; |
1993 | } | |
1994 | } | |
1995 | ||
1996 | 0 | if (sg.getSize() < 1) |
1997 | { | |
1998 | 0 | return; |
1999 | } | |
2000 | ||
2001 | // TODO: JAL-3733 - add an event to the undo buffer for this ! | |
2002 | ||
2003 | 0 | viewport.getAlignment().moveSelectedSequencesByOne(sg, |
2004 | viewport.getHiddenRepSequences(), up); | |
2005 | 0 | alignPanel.paintAlignment(true, false); |
2006 | } | |
2007 | ||
2008 | 0 | synchronized void slideSequences(boolean right, int size) |
2009 | { | |
2010 | 0 | List<SequenceI> sg = new ArrayList<>(); |
2011 | 0 | if (viewport.cursorMode) |
2012 | { | |
2013 | 0 | sg.add(viewport.getAlignment() |
2014 | .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); | |
2015 | } | |
2016 | 0 | else if (viewport.getSelectionGroup() != null |
2017 | && viewport.getSelectionGroup().getSize() != viewport | |
2018 | .getAlignment().getHeight()) | |
2019 | { | |
2020 | 0 | sg = viewport.getSelectionGroup() |
2021 | .getSequences(viewport.getHiddenRepSequences()); | |
2022 | } | |
2023 | ||
2024 | 0 | if (sg.size() < 1) |
2025 | { | |
2026 | 0 | return; |
2027 | } | |
2028 | ||
2029 | 0 | List<SequenceI> invertGroup = new ArrayList<>(); |
2030 | ||
2031 | 0 | for (SequenceI seq : viewport.getAlignment().getSequences()) |
2032 | { | |
2033 | 0 | if (!sg.contains(seq)) |
2034 | { | |
2035 | 0 | invertGroup.add(seq); |
2036 | } | |
2037 | } | |
2038 | ||
2039 | 0 | SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); |
2040 | ||
2041 | 0 | SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; |
2042 | 0 | for (int i = 0; i < invertGroup.size(); i++) |
2043 | { | |
2044 | 0 | seqs2[i] = invertGroup.get(i); |
2045 | } | |
2046 | ||
2047 | 0 | SlideSequencesCommand ssc; |
2048 | 0 | if (right) |
2049 | { | |
2050 | 0 | ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, |
2051 | viewport.getGapCharacter()); | |
2052 | } | |
2053 | else | |
2054 | { | |
2055 | 0 | ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, |
2056 | viewport.getGapCharacter()); | |
2057 | } | |
2058 | ||
2059 | 0 | int groupAdjustment = 0; |
2060 | 0 | if (ssc.getGapsInsertedBegin() && right) |
2061 | { | |
2062 | 0 | if (viewport.cursorMode) |
2063 | { | |
2064 | 0 | alignPanel.getSeqPanel().moveCursor(size, 0); |
2065 | } | |
2066 | else | |
2067 | { | |
2068 | 0 | groupAdjustment = size; |
2069 | } | |
2070 | } | |
2071 | 0 | else if (!ssc.getGapsInsertedBegin() && !right) |
2072 | { | |
2073 | 0 | if (viewport.cursorMode) |
2074 | { | |
2075 | 0 | alignPanel.getSeqPanel().moveCursor(-size, 0); |
2076 | } | |
2077 | else | |
2078 | { | |
2079 | 0 | groupAdjustment = -size; |
2080 | } | |
2081 | } | |
2082 | ||
2083 | 0 | if (groupAdjustment != 0) |
2084 | { | |
2085 | 0 | viewport.getSelectionGroup().setStartRes( |
2086 | viewport.getSelectionGroup().getStartRes() + groupAdjustment); | |
2087 | 0 | viewport.getSelectionGroup().setEndRes( |
2088 | viewport.getSelectionGroup().getEndRes() + groupAdjustment); | |
2089 | } | |
2090 | ||
2091 | /* | |
2092 | * just extend the last slide command if compatible; but not if in | |
2093 | * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) | |
2094 | */ | |
2095 | 0 | boolean appendHistoryItem = false; |
2096 | 0 | Deque<CommandI> historyList = viewport.getHistoryList(); |
2097 | 0 | boolean inSplitFrame = getSplitViewContainer() != null; |
2098 | 0 | if (!inSplitFrame && historyList != null && historyList.size() > 0 |
2099 | && historyList.peek() instanceof SlideSequencesCommand) | |
2100 | { | |
2101 | 0 | appendHistoryItem = ssc.appendSlideCommand( |
2102 | (SlideSequencesCommand) historyList.peek()); | |
2103 | } | |
2104 | ||
2105 | 0 | if (!appendHistoryItem) |
2106 | { | |
2107 | 0 | addHistoryItem(ssc); |
2108 | } | |
2109 | ||
2110 | 0 | repaint(); |
2111 | } | |
2112 | ||
2113 | /** | |
2114 | * DOCUMENT ME! | |
2115 | * | |
2116 | * @param e | |
2117 | * DOCUMENT ME! | |
2118 | */ | |
2119 | 1 | @Override |
2120 | protected void copy_actionPerformed() | |
2121 | { | |
2122 | 1 | if (viewport.getSelectionGroup() == null) |
2123 | { | |
2124 | 0 | return; |
2125 | } | |
2126 | // TODO: preserve the ordering of displayed alignment annotation in any | |
2127 | // internal paste (particularly sequence associated annotation) | |
2128 | 1 | SequenceI[] seqs = viewport.getSelectionAsNewSequence(); |
2129 | 1 | String[] omitHidden = null; |
2130 | ||
2131 | 1 | if (viewport.hasHiddenColumns()) |
2132 | { | |
2133 | 0 | omitHidden = viewport.getViewAsString(true); |
2134 | } | |
2135 | ||
2136 | 1 | String output = new FormatAdapter().formatSequences(FileFormat.Fasta, |
2137 | seqs, omitHidden, null); | |
2138 | ||
2139 | 1 | StringSelection ss = new StringSelection(output); |
2140 | ||
2141 | 1 | try |
2142 | { | |
2143 | 1 | jalview.gui.Desktop.internalCopy = true; |
2144 | // Its really worth setting the clipboard contents | |
2145 | // to empty before setting the large StringSelection!! | |
2146 | 1 | Toolkit.getDefaultToolkit().getSystemClipboard() |
2147 | .setContents(new StringSelection(""), null); | |
2148 | ||
2149 | 1 | Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, |
2150 | Desktop.instance); | |
2151 | } catch (OutOfMemoryError er) | |
2152 | { | |
2153 | 0 | new OOMWarning("copying region", er); |
2154 | 0 | return; |
2155 | } | |
2156 | ||
2157 | 1 | HiddenColumns hiddenColumns = null; |
2158 | 1 | if (viewport.hasHiddenColumns()) |
2159 | { | |
2160 | 0 | int hiddenOffset = viewport.getSelectionGroup().getStartRes(); |
2161 | 0 | int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); |
2162 | ||
2163 | // create new HiddenColumns object with copy of hidden regions | |
2164 | // between startRes and endRes, offset by startRes | |
2165 | 0 | hiddenColumns = new HiddenColumns( |
2166 | viewport.getAlignment().getHiddenColumns(), hiddenOffset, | |
2167 | hiddenCutoff, hiddenOffset); | |
2168 | } | |
2169 | ||
2170 | 1 | Desktop.jalviewClipboard = new Object[] { seqs, |
2171 | viewport.getAlignment().getDataset(), hiddenColumns }; | |
2172 | 1 | setStatus(MessageManager.formatMessage( |
2173 | "label.copied_sequences_to_clipboard", new Object[] | |
2174 | { Integer.valueOf(seqs.length).toString() })); | |
2175 | } | |
2176 | ||
2177 | /** | |
2178 | * DOCUMENT ME! | |
2179 | * | |
2180 | * @param e | |
2181 | * DOCUMENT ME! | |
2182 | */ | |
2183 | 0 | @Override |
2184 | protected void pasteNew_actionPerformed(ActionEvent e) | |
2185 | { | |
2186 | 0 | paste(true); |
2187 | } | |
2188 | ||
2189 | /** | |
2190 | * DOCUMENT ME! | |
2191 | * | |
2192 | * @param e | |
2193 | * DOCUMENT ME! | |
2194 | */ | |
2195 | 0 | @Override |
2196 | protected void pasteThis_actionPerformed(ActionEvent e) | |
2197 | { | |
2198 | 0 | paste(false); |
2199 | } | |
2200 | ||
2201 | /** | |
2202 | * Paste contents of Jalview clipboard | |
2203 | * | |
2204 | * @param newAlignment | |
2205 | * true to paste to a new alignment, otherwise add to this. | |
2206 | */ | |
2207 | 0 | void paste(boolean newAlignment) |
2208 | { | |
2209 | 0 | boolean externalPaste = true; |
2210 | 0 | try |
2211 | { | |
2212 | 0 | Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); |
2213 | 0 | Transferable contents = c.getContents(this); |
2214 | ||
2215 | 0 | if (contents == null) |
2216 | { | |
2217 | 0 | return; |
2218 | } | |
2219 | ||
2220 | 0 | String str; |
2221 | 0 | FileFormatI format; |
2222 | 0 | try |
2223 | { | |
2224 | 0 | str = (String) contents.getTransferData(DataFlavor.stringFlavor); |
2225 | 0 | if (str.length() < 1) |
2226 | { | |
2227 | 0 | return; |
2228 | } | |
2229 | ||
2230 | 0 | format = new IdentifyFile().identify(str, DataSourceType.PASTE); |
2231 | ||
2232 | } catch (OutOfMemoryError er) | |
2233 | { | |
2234 | 0 | new OOMWarning("Out of memory pasting sequences!!", er); |
2235 | 0 | return; |
2236 | } | |
2237 | ||
2238 | 0 | SequenceI[] sequences; |
2239 | 0 | boolean annotationAdded = false; |
2240 | 0 | AlignmentI alignment = null; |
2241 | ||
2242 | 0 | if (Desktop.jalviewClipboard != null) |
2243 | { | |
2244 | // The clipboard was filled from within Jalview, we must use the | |
2245 | // sequences | |
2246 | // And dataset from the copied alignment | |
2247 | 0 | SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; |
2248 | // be doubly sure that we create *new* sequence objects. | |
2249 | 0 | sequences = new SequenceI[newseq.length]; |
2250 | 0 | for (int i = 0; i < newseq.length; i++) |
2251 | { | |
2252 | 0 | sequences[i] = new Sequence(newseq[i]); |
2253 | } | |
2254 | 0 | alignment = new Alignment(sequences); |
2255 | 0 | externalPaste = false; |
2256 | } | |
2257 | else | |
2258 | { | |
2259 | // parse the clipboard as an alignment. | |
2260 | 0 | alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE, |
2261 | format); | |
2262 | 0 | sequences = alignment.getSequencesArray(); |
2263 | } | |
2264 | ||
2265 | 0 | int alwidth = 0; |
2266 | 0 | ArrayList<Integer> newGraphGroups = new ArrayList<>(); |
2267 | 0 | int fgroup = -1; |
2268 | ||
2269 | 0 | if (newAlignment) |
2270 | { | |
2271 | ||
2272 | 0 | if (Desktop.jalviewClipboard != null) |
2273 | { | |
2274 | // dataset is inherited | |
2275 | 0 | alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); |
2276 | } | |
2277 | else | |
2278 | { | |
2279 | // new dataset is constructed | |
2280 | 0 | alignment.setDataset(null); |
2281 | } | |
2282 | 0 | alwidth = alignment.getWidth() + 1; |
2283 | } | |
2284 | else | |
2285 | { | |
2286 | 0 | AlignmentI pastedal = alignment; // preserve pasted alignment object |
2287 | // Add pasted sequences and dataset into existing alignment. | |
2288 | 0 | alignment = viewport.getAlignment(); |
2289 | 0 | alwidth = alignment.getWidth() + 1; |
2290 | // decide if we need to import sequences from an existing dataset | |
2291 | 0 | boolean importDs = Desktop.jalviewClipboard != null |
2292 | && Desktop.jalviewClipboard[1] != alignment.getDataset(); | |
2293 | // importDs==true instructs us to copy over new dataset sequences from | |
2294 | // an existing alignment | |
2295 | 0 | Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to |
2296 | // create | |
2297 | // minimum dataset set | |
2298 | ||
2299 | 0 | for (int i = 0; i < sequences.length; i++) |
2300 | { | |
2301 | 0 | if (importDs) |
2302 | { | |
2303 | 0 | newDs.addElement(null); |
2304 | } | |
2305 | 0 | SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple |
2306 | // paste | |
2307 | 0 | if (importDs && ds != null) |
2308 | { | |
2309 | 0 | if (!newDs.contains(ds)) |
2310 | { | |
2311 | 0 | newDs.setElementAt(ds, i); |
2312 | 0 | ds = new Sequence(ds); |
2313 | // update with new dataset sequence | |
2314 | 0 | sequences[i].setDatasetSequence(ds); |
2315 | } | |
2316 | else | |
2317 | { | |
2318 | 0 | ds = sequences[newDs.indexOf(ds)].getDatasetSequence(); |
2319 | } | |
2320 | } | |
2321 | else | |
2322 | { | |
2323 | // copy and derive new dataset sequence | |
2324 | 0 | sequences[i] = sequences[i].deriveSequence(); |
2325 | 0 | alignment.getDataset() |
2326 | .addSequence(sequences[i].getDatasetSequence()); | |
2327 | // TODO: avoid creation of duplicate dataset sequences with a | |
2328 | // 'contains' method using SequenceI.equals()/SequenceI.contains() | |
2329 | } | |
2330 | 0 | alignment.addSequence(sequences[i]); // merges dataset |
2331 | } | |
2332 | 0 | if (newDs != null) |
2333 | { | |
2334 | 0 | newDs.clear(); // tidy up |
2335 | } | |
2336 | 0 | if (alignment.getAlignmentAnnotation() != null) |
2337 | { | |
2338 | 0 | for (AlignmentAnnotation alan : alignment |
2339 | .getAlignmentAnnotation()) | |
2340 | { | |
2341 | 0 | if (alan.graphGroup > fgroup) |
2342 | { | |
2343 | 0 | fgroup = alan.graphGroup; |
2344 | } | |
2345 | } | |
2346 | } | |
2347 | 0 | if (pastedal.getAlignmentAnnotation() != null) |
2348 | { | |
2349 | // Add any annotation attached to alignment. | |
2350 | 0 | AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation(); |
2351 | 0 | for (int i = 0; i < alann.length; i++) |
2352 | { | |
2353 | 0 | annotationAdded = true; |
2354 | 0 | if (alann[i].sequenceRef == null && !alann[i].autoCalculated) |
2355 | { | |
2356 | 0 | AlignmentAnnotation newann = new AlignmentAnnotation( |
2357 | alann[i]); | |
2358 | 0 | if (newann.graphGroup > -1) |
2359 | { | |
2360 | 0 | if (newGraphGroups.size() <= newann.graphGroup |
2361 | || newGraphGroups.get(newann.graphGroup) == null) | |
2362 | { | |
2363 | 0 | for (int q = newGraphGroups |
2364 | 0 | .size(); q <= newann.graphGroup; q++) |
2365 | { | |
2366 | 0 | newGraphGroups.add(q, null); |
2367 | } | |
2368 | 0 | newGraphGroups.set(newann.graphGroup, |
2369 | Integer.valueOf(++fgroup)); | |
2370 | } | |
2371 | 0 | newann.graphGroup = newGraphGroups.get(newann.graphGroup) |
2372 | .intValue(); | |
2373 | } | |
2374 | ||
2375 | 0 | newann.padAnnotation(alwidth); |
2376 | 0 | alignment.addAnnotation(newann); |
2377 | } | |
2378 | } | |
2379 | } | |
2380 | } | |
2381 | 0 | if (!newAlignment) |
2382 | { | |
2383 | // ///// | |
2384 | // ADD HISTORY ITEM | |
2385 | // | |
2386 | 0 | addHistoryItem(new EditCommand( |
2387 | MessageManager.getString("label.add_sequences"), | |
2388 | Action.PASTE, sequences, 0, alignment.getWidth(), | |
2389 | alignment)); | |
2390 | } | |
2391 | // Add any annotations attached to sequences | |
2392 | 0 | for (int i = 0; i < sequences.length; i++) |
2393 | { | |
2394 | 0 | if (sequences[i].getAnnotation() != null) |
2395 | { | |
2396 | 0 | AlignmentAnnotation newann; |
2397 | 0 | for (int a = 0; a < sequences[i].getAnnotation().length; a++) |
2398 | { | |
2399 | 0 | annotationAdded = true; |
2400 | 0 | newann = sequences[i].getAnnotation()[a]; |
2401 | 0 | newann.adjustForAlignment(); |
2402 | 0 | newann.padAnnotation(alwidth); |
2403 | 0 | if (newann.graphGroup > -1) |
2404 | { | |
2405 | 0 | if (newann.graphGroup > -1) |
2406 | { | |
2407 | 0 | if (newGraphGroups.size() <= newann.graphGroup |
2408 | || newGraphGroups.get(newann.graphGroup) == null) | |
2409 | { | |
2410 | 0 | for (int q = newGraphGroups |
2411 | 0 | .size(); q <= newann.graphGroup; q++) |
2412 | { | |
2413 | 0 | newGraphGroups.add(q, null); |
2414 | } | |
2415 | 0 | newGraphGroups.set(newann.graphGroup, |
2416 | Integer.valueOf(++fgroup)); | |
2417 | } | |
2418 | 0 | newann.graphGroup = newGraphGroups.get(newann.graphGroup) |
2419 | .intValue(); | |
2420 | } | |
2421 | } | |
2422 | // annotation was duplicated earlier | |
2423 | 0 | alignment.addAnnotation(sequences[i].getAnnotation()[a]); |
2424 | // take care of contact matrix too | |
2425 | 0 | ContactMatrixI cm = sequences[i] |
2426 | .getContactMatrixFor(sequences[i].getAnnotation()[a]); | |
2427 | 0 | if (cm != null) |
2428 | { | |
2429 | 0 | alignment.addContactListFor(sequences[i].getAnnotation()[a], |
2430 | cm); | |
2431 | } | |
2432 | ||
2433 | 0 | alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], |
2434 | a); | |
2435 | } | |
2436 | } | |
2437 | } | |
2438 | 0 | if (!newAlignment) |
2439 | { | |
2440 | ||
2441 | // propagate alignment changed. | |
2442 | 0 | viewport.getRanges().setEndSeq(alignment.getHeight() - 1); |
2443 | 0 | if (annotationAdded) |
2444 | { | |
2445 | // Duplicate sequence annotation in all views. | |
2446 | 0 | AlignmentI[] alview = this.getViewAlignments(); |
2447 | 0 | for (int i = 0; i < sequences.length; i++) |
2448 | { | |
2449 | 0 | AlignmentAnnotation sann[] = sequences[i].getAnnotation(); |
2450 | 0 | if (sann == null) |
2451 | { | |
2452 | 0 | continue; |
2453 | } | |
2454 | 0 | for (int avnum = 0; avnum < alview.length; avnum++) |
2455 | { | |
2456 | 0 | if (alview[avnum] != alignment) |
2457 | { | |
2458 | // duplicate in a view other than the one with input focus | |
2459 | 0 | int avwidth = alview[avnum].getWidth() + 1; |
2460 | // this relies on sann being preserved after we | |
2461 | // modify the sequence's annotation array for each duplication | |
2462 | 0 | for (int a = 0; a < sann.length; a++) |
2463 | { | |
2464 | 0 | AlignmentAnnotation newann = new AlignmentAnnotation( |
2465 | sann[a]); | |
2466 | 0 | sequences[i].addAlignmentAnnotation(newann); |
2467 | 0 | newann.padAnnotation(avwidth); |
2468 | 0 | alview[avnum].addAnnotation(newann); // annotation was |
2469 | // duplicated earlier | |
2470 | // TODO JAL-1145 graphGroups are not updated for sequence | |
2471 | // annotation added to several views. This may cause | |
2472 | // strangeness | |
2473 | 0 | alview[avnum].setAnnotationIndex(newann, a); |
2474 | } | |
2475 | } | |
2476 | } | |
2477 | } | |
2478 | 0 | buildSortByAnnotationScoresMenu(); |
2479 | } | |
2480 | 0 | viewport.firePropertyChange("alignment", null, |
2481 | alignment.getSequences()); | |
2482 | 0 | if (alignPanels != null) |
2483 | { | |
2484 | 0 | for (AlignmentPanel ap : alignPanels) |
2485 | { | |
2486 | 0 | ap.validateAnnotationDimensions(false); |
2487 | } | |
2488 | } | |
2489 | else | |
2490 | { | |
2491 | 0 | alignPanel.validateAnnotationDimensions(false); |
2492 | } | |
2493 | ||
2494 | } | |
2495 | else | |
2496 | { | |
2497 | 0 | AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, |
2498 | DEFAULT_HEIGHT); | |
2499 | 0 | String newtitle = new String("Copied sequences"); |
2500 | ||
2501 | 0 | if (Desktop.jalviewClipboard != null |
2502 | && Desktop.jalviewClipboard[2] != null) | |
2503 | { | |
2504 | 0 | HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; |
2505 | 0 | af.viewport.setHiddenColumns(hc); |
2506 | } | |
2507 | ||
2508 | // >>>This is a fix for the moment, until a better solution is | |
2509 | // found!!<<< | |
2510 | 0 | af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() |
2511 | .transferSettings(alignPanel.getSeqPanel().seqCanvas | |
2512 | .getFeatureRenderer()); | |
2513 | ||
2514 | // TODO: maintain provenance of an alignment, rather than just make the | |
2515 | // title a concatenation of operations. | |
2516 | 0 | if (!externalPaste) |
2517 | { | |
2518 | 0 | if (title.startsWith("Copied sequences")) |
2519 | { | |
2520 | 0 | newtitle = title; |
2521 | } | |
2522 | else | |
2523 | { | |
2524 | 0 | newtitle = newtitle.concat("- from " + title); |
2525 | } | |
2526 | } | |
2527 | else | |
2528 | { | |
2529 | 0 | newtitle = new String("Pasted sequences"); |
2530 | } | |
2531 | ||
2532 | 0 | Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, |
2533 | DEFAULT_HEIGHT); | |
2534 | ||
2535 | } | |
2536 | ||
2537 | } catch (Exception ex) | |
2538 | { | |
2539 | 0 | ex.printStackTrace(); |
2540 | 0 | jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); |
2541 | // could be anything being pasted in here | |
2542 | } | |
2543 | ||
2544 | } | |
2545 | ||
2546 | 0 | @Override |
2547 | protected void expand_newalign(ActionEvent e) | |
2548 | { | |
2549 | 0 | try |
2550 | { | |
2551 | 0 | AlignmentI alignment = AlignmentUtils |
2552 | .expandContext(getViewport().getAlignment(), -1); | |
2553 | 0 | AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, |
2554 | DEFAULT_HEIGHT); | |
2555 | 0 | String newtitle = new String("Flanking alignment"); |
2556 | ||
2557 | 0 | if (Desktop.jalviewClipboard != null |
2558 | && Desktop.jalviewClipboard[2] != null) | |
2559 | { | |
2560 | 0 | HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; |
2561 | 0 | af.viewport.setHiddenColumns(hc); |
2562 | } | |
2563 | ||
2564 | // >>>This is a fix for the moment, until a better solution is | |
2565 | // found!!<<< | |
2566 | 0 | af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() |
2567 | .transferSettings(alignPanel.getSeqPanel().seqCanvas | |
2568 | .getFeatureRenderer()); | |
2569 | ||
2570 | // TODO: maintain provenance of an alignment, rather than just make the | |
2571 | // title a concatenation of operations. | |
2572 | { | |
2573 | 0 | if (title.startsWith("Copied sequences")) |
2574 | { | |
2575 | 0 | newtitle = title; |
2576 | } | |
2577 | else | |
2578 | { | |
2579 | 0 | newtitle = newtitle.concat("- from " + title); |
2580 | } | |
2581 | } | |
2582 | ||
2583 | 0 | Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); |
2584 | ||
2585 | } catch (Exception ex) | |
2586 | { | |
2587 | 0 | ex.printStackTrace(); |
2588 | 0 | jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); |
2589 | // could be anything being pasted in here | |
2590 | } catch (OutOfMemoryError oom) | |
2591 | { | |
2592 | 0 | new OOMWarning("Viewing flanking region of alignment", oom); |
2593 | } | |
2594 | } | |
2595 | ||
2596 | /** | |
2597 | * Action Cut (delete and copy) the selected region | |
2598 | */ | |
2599 | 0 | @Override |
2600 | protected void cut_actionPerformed() | |
2601 | { | |
2602 | 0 | copy_actionPerformed(); |
2603 | 0 | delete_actionPerformed(); |
2604 | } | |
2605 | ||
2606 | /** | |
2607 | * Performs menu option to Delete the currently selected region | |
2608 | */ | |
2609 | 0 | @Override |
2610 | protected void delete_actionPerformed() | |
2611 | { | |
2612 | ||
2613 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
2614 | 0 | if (sg == null) |
2615 | { | |
2616 | 0 | return; |
2617 | } | |
2618 | ||
2619 | 0 | Runnable okAction = () -> { |
2620 | 0 | SequenceI[] cut = sg.getSequences() |
2621 | .toArray(new SequenceI[sg.getSize()]); | |
2622 | ||
2623 | 0 | addHistoryItem(new EditCommand( |
2624 | MessageManager.getString("label.cut_sequences"), Action.CUT, | |
2625 | cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, | |
2626 | viewport.getAlignment())); | |
2627 | ||
2628 | 0 | viewport.setSelectionGroup(null); |
2629 | 0 | viewport.sendSelection(); |
2630 | 0 | viewport.getAlignment().deleteGroup(sg); |
2631 | ||
2632 | 0 | viewport.firePropertyChange("alignment", null, |
2633 | viewport.getAlignment().getSequences()); | |
2634 | 0 | if (viewport.getAlignment().getHeight() < 1) |
2635 | { | |
2636 | 0 | try |
2637 | { | |
2638 | 0 | AlignFrame.this.setClosed(true); |
2639 | } catch (Exception ex) | |
2640 | { | |
2641 | } | |
2642 | } | |
2643 | }; | |
2644 | ||
2645 | /* | |
2646 | * If the cut affects all sequences, prompt for confirmation | |
2647 | */ | |
2648 | 0 | boolean wholeHeight = sg.getSize() == viewport.getAlignment() |
2649 | .getHeight(); | |
2650 | 0 | boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes()) |
2651 | + 1) == viewport.getAlignment().getWidth()) ? true : false; | |
2652 | 0 | if (wholeHeight && wholeWidth) |
2653 | { | |
2654 | 0 | JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); |
2655 | 0 | dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION |
2656 | 0 | Object[] options = new Object[] { |
2657 | MessageManager.getString("action.ok"), | |
2658 | MessageManager.getString("action.cancel") }; | |
2659 | 0 | dialog.showDialog(MessageManager.getString("warn.delete_all"), |
2660 | MessageManager.getString("label.delete_all"), | |
2661 | JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, | |
2662 | options, options[0]); | |
2663 | } | |
2664 | else | |
2665 | { | |
2666 | 0 | try |
2667 | { | |
2668 | 0 | okAction.run(); |
2669 | } catch (Exception e) | |
2670 | { | |
2671 | 0 | e.printStackTrace(); |
2672 | } | |
2673 | } | |
2674 | } | |
2675 | ||
2676 | /** | |
2677 | * DOCUMENT ME! | |
2678 | * | |
2679 | * @param e | |
2680 | * DOCUMENT ME! | |
2681 | */ | |
2682 | 0 | @Override |
2683 | protected void deleteGroups_actionPerformed(ActionEvent e) | |
2684 | { | |
2685 | 0 | if (avc.deleteGroups()) |
2686 | { | |
2687 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
2688 | 0 | alignPanel.updateAnnotation(); |
2689 | 0 | alignPanel.paintAlignment(true, true); |
2690 | } | |
2691 | } | |
2692 | ||
2693 | /** | |
2694 | * DOCUMENT ME! | |
2695 | * | |
2696 | * @param e | |
2697 | * DOCUMENT ME! | |
2698 | */ | |
2699 | 6 | @Override |
2700 | public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) | |
2701 | { | |
2702 | 6 | SequenceGroup sg = new SequenceGroup( |
2703 | viewport.getAlignment().getSequences()); | |
2704 | ||
2705 | 6 | sg.setEndRes(viewport.getAlignment().getWidth() - 1); |
2706 | 6 | viewport.setSelectionGroup(sg); |
2707 | 6 | viewport.isSelectionGroupChanged(true); |
2708 | 6 | viewport.sendSelection(); |
2709 | // JAL-2034 - should delegate to | |
2710 | // alignPanel to decide if overview needs | |
2711 | // updating. | |
2712 | 6 | alignPanel.paintAlignment(false, false); |
2713 | 6 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2714 | } | |
2715 | ||
2716 | /** | |
2717 | * DOCUMENT ME! | |
2718 | * | |
2719 | * @param e | |
2720 | * DOCUMENT ME! | |
2721 | */ | |
2722 | 2 | @Override |
2723 | public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) | |
2724 | { | |
2725 | 2 | if (viewport.cursorMode) |
2726 | { | |
2727 | 0 | alignPanel.getSeqPanel().keyboardNo1 = null; |
2728 | 0 | alignPanel.getSeqPanel().keyboardNo2 = null; |
2729 | } | |
2730 | 2 | viewport.setSelectionGroup(null); |
2731 | 2 | viewport.getColumnSelection().clear(); |
2732 | 2 | viewport.setSearchResults(null); |
2733 | 2 | alignPanel.getIdPanel().getIdCanvas().searchResults = null; |
2734 | // JAL-2034 - should delegate to | |
2735 | // alignPanel to decide if overview needs | |
2736 | // updating. | |
2737 | 2 | alignPanel.paintAlignment(false, false); |
2738 | 2 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2739 | 2 | viewport.sendSelection(); |
2740 | } | |
2741 | ||
2742 | /** | |
2743 | * DOCUMENT ME! | |
2744 | * | |
2745 | * @param e | |
2746 | * DOCUMENT ME! | |
2747 | */ | |
2748 | 0 | @Override |
2749 | public void invertSequenceMenuItem_actionPerformed(ActionEvent e) | |
2750 | { | |
2751 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
2752 | ||
2753 | 0 | if (sg == null) |
2754 | { | |
2755 | 0 | selectAllSequenceMenuItem_actionPerformed(null); |
2756 | ||
2757 | 0 | return; |
2758 | } | |
2759 | ||
2760 | 0 | for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) |
2761 | { | |
2762 | 0 | sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); |
2763 | } | |
2764 | // JAL-2034 - should delegate to | |
2765 | // alignPanel to decide if overview needs | |
2766 | // updating. | |
2767 | ||
2768 | 0 | alignPanel.paintAlignment(true, false); |
2769 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2770 | 0 | viewport.sendSelection(); |
2771 | } | |
2772 | ||
2773 | 0 | @Override |
2774 | public void invertColSel_actionPerformed(ActionEvent e) | |
2775 | { | |
2776 | 0 | viewport.invertColumnSelection(); |
2777 | 0 | alignPanel.paintAlignment(true, false); |
2778 | 0 | PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2779 | 0 | viewport.sendSelection(); |
2780 | } | |
2781 | ||
2782 | /** | |
2783 | * DOCUMENT ME! | |
2784 | * | |
2785 | * @param e | |
2786 | * DOCUMENT ME! | |
2787 | */ | |
2788 | 0 | @Override |
2789 | public void remove2LeftMenuItem_actionPerformed(ActionEvent e) | |
2790 | { | |
2791 | 0 | trimAlignment(true); |
2792 | } | |
2793 | ||
2794 | /** | |
2795 | * DOCUMENT ME! | |
2796 | * | |
2797 | * @param e | |
2798 | * DOCUMENT ME! | |
2799 | */ | |
2800 | 0 | @Override |
2801 | public void remove2RightMenuItem_actionPerformed(ActionEvent e) | |
2802 | { | |
2803 | 0 | trimAlignment(false); |
2804 | } | |
2805 | ||
2806 | 0 | void trimAlignment(boolean trimLeft) |
2807 | { | |
2808 | 0 | ColumnSelection colSel = viewport.getColumnSelection(); |
2809 | 0 | int column; |
2810 | ||
2811 | 0 | if (!colSel.isEmpty()) |
2812 | { | |
2813 | 0 | if (trimLeft) |
2814 | { | |
2815 | 0 | column = colSel.getMin(); |
2816 | } | |
2817 | else | |
2818 | { | |
2819 | 0 | column = colSel.getMax(); |
2820 | } | |
2821 | ||
2822 | 0 | SequenceI[] seqs; |
2823 | 0 | if (viewport.getSelectionGroup() != null) |
2824 | { | |
2825 | 0 | seqs = viewport.getSelectionGroup() |
2826 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2827 | } | |
2828 | else | |
2829 | { | |
2830 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2831 | } | |
2832 | ||
2833 | 0 | TrimRegionCommand trimRegion; |
2834 | 0 | if (trimLeft) |
2835 | { | |
2836 | 0 | trimRegion = new TrimRegionCommand("Remove Left", true, seqs, |
2837 | column, viewport.getAlignment()); | |
2838 | 0 | viewport.getRanges().setStartRes(0); |
2839 | } | |
2840 | else | |
2841 | { | |
2842 | 0 | trimRegion = new TrimRegionCommand("Remove Right", false, seqs, |
2843 | column, viewport.getAlignment()); | |
2844 | } | |
2845 | ||
2846 | 0 | setStatus(MessageManager.formatMessage("label.removed_columns", |
2847 | new String[] | |
2848 | { Integer.valueOf(trimRegion.getSize()).toString() })); | |
2849 | ||
2850 | 0 | addHistoryItem(trimRegion); |
2851 | ||
2852 | 0 | for (SequenceGroup sg : viewport.getAlignment().getGroups()) |
2853 | { | |
2854 | 0 | if ((trimLeft && !sg.adjustForRemoveLeft(column)) |
2855 | || (!trimLeft && !sg.adjustForRemoveRight(column))) | |
2856 | { | |
2857 | 0 | viewport.getAlignment().deleteGroup(sg); |
2858 | } | |
2859 | } | |
2860 | ||
2861 | 0 | viewport.firePropertyChange("alignment", null, |
2862 | viewport.getAlignment().getSequences()); | |
2863 | } | |
2864 | } | |
2865 | ||
2866 | /** | |
2867 | * DOCUMENT ME! | |
2868 | * | |
2869 | * @param e | |
2870 | * DOCUMENT ME! | |
2871 | */ | |
2872 | 0 | @Override |
2873 | public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) | |
2874 | { | |
2875 | 0 | int start = 0, end = viewport.getAlignment().getWidth() - 1; |
2876 | ||
2877 | 0 | SequenceI[] seqs; |
2878 | 0 | if (viewport.getSelectionGroup() != null) |
2879 | { | |
2880 | 0 | seqs = viewport.getSelectionGroup() |
2881 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2882 | 0 | start = viewport.getSelectionGroup().getStartRes(); |
2883 | 0 | end = viewport.getSelectionGroup().getEndRes(); |
2884 | } | |
2885 | else | |
2886 | { | |
2887 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2888 | } | |
2889 | ||
2890 | 0 | RemoveGapColCommand removeGapCols = new RemoveGapColCommand( |
2891 | "Remove Gapped Columns", seqs, start, end, | |
2892 | viewport.getAlignment()); | |
2893 | ||
2894 | 0 | addHistoryItem(removeGapCols); |
2895 | ||
2896 | 0 | setStatus(MessageManager.formatMessage("label.removed_empty_columns", |
2897 | new Object[] | |
2898 | { Integer.valueOf(removeGapCols.getSize()).toString() })); | |
2899 | ||
2900 | // This is to maintain viewport position on first residue | |
2901 | // of first sequence | |
2902 | 0 | SequenceI seq = viewport.getAlignment().getSequenceAt(0); |
2903 | 0 | ViewportRanges ranges = viewport.getRanges(); |
2904 | 0 | int startRes = seq.findPosition(ranges.getStartRes()); |
2905 | // ShiftList shifts; | |
2906 | // viewport.getAlignment().removeGaps(shifts=new ShiftList()); | |
2907 | // edit.alColumnChanges=shifts.getInverse(); | |
2908 | // if (viewport.hasHiddenColumns) | |
2909 | // viewport.getColumnSelection().compensateForEdits(shifts); | |
2910 | 0 | ranges.setStartRes(seq.findIndex(startRes) - 1); |
2911 | 0 | viewport.firePropertyChange("alignment", null, |
2912 | viewport.getAlignment().getSequences()); | |
2913 | ||
2914 | } | |
2915 | ||
2916 | /** | |
2917 | * DOCUMENT ME! | |
2918 | * | |
2919 | * @param e | |
2920 | * DOCUMENT ME! | |
2921 | */ | |
2922 | 0 | @Override |
2923 | public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) | |
2924 | { | |
2925 | 0 | int start = 0, end = viewport.getAlignment().getWidth() - 1; |
2926 | ||
2927 | 0 | SequenceI[] seqs; |
2928 | 0 | if (viewport.getSelectionGroup() != null) |
2929 | { | |
2930 | 0 | seqs = viewport.getSelectionGroup() |
2931 | .getSequencesAsArray(viewport.getHiddenRepSequences()); | |
2932 | 0 | start = viewport.getSelectionGroup().getStartRes(); |
2933 | 0 | end = viewport.getSelectionGroup().getEndRes(); |
2934 | } | |
2935 | else | |
2936 | { | |
2937 | 0 | seqs = viewport.getAlignment().getSequencesArray(); |
2938 | } | |
2939 | ||
2940 | // This is to maintain viewport position on first residue | |
2941 | // of first sequence | |
2942 | 0 | SequenceI seq = viewport.getAlignment().getSequenceAt(0); |
2943 | 0 | int startRes = seq.findPosition(viewport.getRanges().getStartRes()); |
2944 | ||
2945 | 0 | addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, |
2946 | viewport.getAlignment())); | |
2947 | ||
2948 | 0 | viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); |
2949 | ||
2950 | 0 | viewport.firePropertyChange("alignment", null, |
2951 | viewport.getAlignment().getSequences()); | |
2952 | ||
2953 | } | |
2954 | ||
2955 | /** | |
2956 | * DOCUMENT ME! | |
2957 | * | |
2958 | * @param e | |
2959 | * DOCUMENT ME! | |
2960 | */ | |
2961 | 0 | @Override |
2962 | public void padGapsMenuitem_actionPerformed(ActionEvent e) | |
2963 | { | |
2964 | 0 | viewport.setPadGaps(padGapsMenuitem.isSelected()); |
2965 | 0 | viewport.firePropertyChange("alignment", null, |
2966 | viewport.getAlignment().getSequences()); | |
2967 | } | |
2968 | ||
2969 | /** | |
2970 | * Opens a Finder dialog | |
2971 | * | |
2972 | * @param e | |
2973 | */ | |
2974 | 0 | @Override |
2975 | public void findMenuItem_actionPerformed(ActionEvent e) | |
2976 | { | |
2977 | 0 | new Finder(alignPanel, false, null); |
2978 | } | |
2979 | ||
2980 | /** | |
2981 | * Create a new view of the current alignment. | |
2982 | */ | |
2983 | 7 | @Override |
2984 | public void newView_actionPerformed(ActionEvent e) | |
2985 | { | |
2986 | 7 | newView(null, true); |
2987 | } | |
2988 | ||
2989 | /** | |
2990 | * Creates and shows a new view of the current alignment. | |
2991 | * | |
2992 | * @param viewTitle | |
2993 | * title of newly created view; if null, one will be generated | |
2994 | * @param copyAnnotation | |
2995 | * if true then duplicate all annnotation, groups and settings | |
2996 | * @return new alignment panel, already displayed. | |
2997 | */ | |
2998 | 10 | public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) |
2999 | { | |
3000 | /* | |
3001 | * Create a new AlignmentPanel (with its own, new Viewport) | |
3002 | */ | |
3003 | 10 | AlignmentPanel newap = new jalview.project.Jalview2XML() |
3004 | .copyAlignPanel(alignPanel); | |
3005 | 10 | if (!copyAnnotation) |
3006 | { | |
3007 | /* | |
3008 | * remove all groups and annotation except for the automatic stuff | |
3009 | */ | |
3010 | 0 | newap.av.getAlignment().deleteAllGroups(); |
3011 | 0 | newap.av.getAlignment().deleteAllAnnotations(false); |
3012 | } | |
3013 | ||
3014 | 10 | newap.av.setGatherViewsHere(false); |
3015 | ||
3016 | 10 | if (viewport.getViewName() == null) |
3017 | { | |
3018 | 9 | viewport.setViewName( |
3019 | MessageManager.getString("label.view_name_original")); | |
3020 | } | |
3021 | ||
3022 | /* | |
3023 | * Views share the same edits undo and redo stacks | |
3024 | */ | |
3025 | 10 | newap.av.setHistoryList(viewport.getHistoryList()); |
3026 | 10 | newap.av.setRedoList(viewport.getRedoList()); |
3027 | ||
3028 | /* | |
3029 | * copy any visualisation settings that are not saved in the project | |
3030 | */ | |
3031 | 10 | newap.av.setColourAppliesToAllGroups( |
3032 | viewport.getColourAppliesToAllGroups()); | |
3033 | ||
3034 | /* | |
3035 | * Views share the same mappings; need to deregister any new mappings | |
3036 | * created by copyAlignPanel, and register the new reference to the shared | |
3037 | * mappings | |
3038 | */ | |
3039 | 10 | newap.av.replaceMappings(viewport.getAlignment()); |
3040 | ||
3041 | /* | |
3042 | * start up cDNA consensus (if applicable) now mappings are in place | |
3043 | */ | |
3044 | 10 | if (newap.av.initComplementConsensus()) |
3045 | { | |
3046 | 0 | newap.refresh(true); // adjust layout of annotations |
3047 | } | |
3048 | ||
3049 | 10 | newap.av.setViewName(getNewViewName(viewTitle)); |
3050 | ||
3051 | 10 | addAlignmentPanel(newap, true); |
3052 | 10 | newap.alignmentChanged(); |
3053 | ||
3054 | 10 | if (alignPanels.size() == 2) |
3055 | { | |
3056 | 9 | viewport.setGatherViewsHere(true); |
3057 | } | |
3058 | 10 | tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); |
3059 | ||
3060 | 10 | return newap; |
3061 | } | |
3062 | ||
3063 | /** | |
3064 | * Make a new name for the view, ensuring it is unique within the current | |
3065 | * sequenceSetId. (This used to be essential for Jalview Project archives, but | |
3066 | * these now use viewId. Unique view names are still desirable for usability.) | |
3067 | * | |
3068 | * @param viewTitle | |
3069 | * @return | |
3070 | */ | |
3071 | 10 | protected String getNewViewName(String viewTitle) |
3072 | { | |
3073 | 10 | int index = Desktop.getViewCount(viewport.getSequenceSetId()); |
3074 | 10 | boolean addFirstIndex = false; |
3075 | 10 | if (viewTitle == null || viewTitle.trim().length() == 0) |
3076 | { | |
3077 | 7 | viewTitle = MessageManager.getString("action.view"); |
3078 | 7 | addFirstIndex = true; |
3079 | } | |
3080 | else | |
3081 | { | |
3082 | 3 | index = 1;// we count from 1 if given a specific name |
3083 | } | |
3084 | 10 | String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); |
3085 | ||
3086 | 10 | List<Component> comps = PaintRefresher.components |
3087 | .get(viewport.getSequenceSetId()); | |
3088 | ||
3089 | 10 | List<String> existingNames = getExistingViewNames(comps); |
3090 | ||
3091 | 10 | while (existingNames.contains(newViewName)) |
3092 | { | |
3093 | 0 | newViewName = viewTitle + " " + (++index); |
3094 | } | |
3095 | 10 | return newViewName; |
3096 | } | |
3097 | ||
3098 | /** | |
3099 | * Returns a list of distinct view names found in the given list of | |
3100 | * components. View names are held on the viewport of an AlignmentPanel. | |
3101 | * | |
3102 | * @param comps | |
3103 | * @return | |
3104 | */ | |
3105 | 10 | protected List<String> getExistingViewNames(List<Component> comps) |
3106 | { | |
3107 | 10 | List<String> existingNames = new ArrayList<>(); |
3108 | 10 | for (Component comp : comps) |
3109 | { | |
3110 | 63 | if (comp instanceof AlignmentPanel) |
3111 | { | |
3112 | 21 | AlignmentPanel ap = (AlignmentPanel) comp; |
3113 | 21 | if (!existingNames.contains(ap.av.getViewName())) |
3114 | { | |
3115 | 20 | existingNames.add(ap.av.getViewName()); |
3116 | } | |
3117 | } | |
3118 | } | |
3119 | 10 | return existingNames; |
3120 | } | |
3121 | ||
3122 | /** | |
3123 | * Explode tabbed views into separate windows. | |
3124 | */ | |
3125 | 0 | @Override |
3126 | public void expandViews_actionPerformed(ActionEvent e) | |
3127 | { | |
3128 | 0 | Desktop.explodeViews(this); |
3129 | } | |
3130 | ||
3131 | /** | |
3132 | * Gather views in separate windows back into a tabbed presentation. | |
3133 | */ | |
3134 | 0 | @Override |
3135 | public void gatherViews_actionPerformed(ActionEvent e) | |
3136 | { | |
3137 | 0 | Desktop.instance.gatherViews(this); |
3138 | } | |
3139 | ||
3140 | /** | |
3141 | * DOCUMENT ME! | |
3142 | * | |
3143 | * @param e | |
3144 | * DOCUMENT ME! | |
3145 | */ | |
3146 | 0 | @Override |
3147 | public void font_actionPerformed(ActionEvent e) | |
3148 | { | |
3149 | 0 | new FontChooser(alignPanel); |
3150 | } | |
3151 | ||
3152 | /** | |
3153 | * DOCUMENT ME! | |
3154 | * | |
3155 | * @param e | |
3156 | * DOCUMENT ME! | |
3157 | */ | |
3158 | 0 | @Override |
3159 | protected void seqLimit_actionPerformed(ActionEvent e) | |
3160 | { | |
3161 | 0 | viewport.setShowJVSuffix(seqLimits.isSelected()); |
3162 | ||
3163 | 0 | alignPanel.getIdPanel().getIdCanvas() |
3164 | .setPreferredSize(alignPanel.calculateIdWidth()); | |
3165 | 0 | alignPanel.paintAlignment(true, false); |
3166 | } | |
3167 | ||
3168 | 0 | @Override |
3169 | public void idRightAlign_actionPerformed(ActionEvent e) | |
3170 | { | |
3171 | 0 | viewport.setRightAlignIds(idRightAlign.isSelected()); |
3172 | 0 | alignPanel.paintAlignment(false, false); |
3173 | } | |
3174 | ||
3175 | 0 | @Override |
3176 | public void centreColumnLabels_actionPerformed(ActionEvent e) | |
3177 | { | |
3178 | 0 | viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); |
3179 | 0 | alignPanel.paintAlignment(false, false); |
3180 | } | |
3181 | ||
3182 | /* | |
3183 | * (non-Javadoc) | |
3184 | * | |
3185 | * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() | |
3186 | */ | |
3187 | 0 | @Override |
3188 | protected void followHighlight_actionPerformed() | |
3189 | { | |
3190 | /* | |
3191 | * Set the 'follow' flag on the Viewport (and scroll to position if now | |
3192 | * true). | |
3193 | */ | |
3194 | 0 | final boolean state = this.followHighlightMenuItem.getState(); |
3195 | 0 | viewport.setFollowHighlight(state); |
3196 | 0 | if (state) |
3197 | { | |
3198 | 0 | alignPanel.scrollToPosition(viewport.getSearchResults()); |
3199 | } | |
3200 | } | |
3201 | ||
3202 | /** | |
3203 | * DOCUMENT ME! | |
3204 | * | |
3205 | * @param e | |
3206 | * DOCUMENT ME! | |
3207 | */ | |
3208 | 0 | @Override |
3209 | protected void colourTextMenuItem_actionPerformed(ActionEvent e) | |
3210 | { | |
3211 | 0 | viewport.setColourText(colourTextMenuItem.isSelected()); |
3212 | 0 | alignPanel.paintAlignment(false, false); |
3213 | } | |
3214 | ||
3215 | /** | |
3216 | * DOCUMENT ME! | |
3217 | * | |
3218 | * @param e | |
3219 | * DOCUMENT ME! | |
3220 | */ | |
3221 | 7 | @Override |
3222 | public void wrapMenuItem_actionPerformed(ActionEvent e) | |
3223 | { | |
3224 | 7 | setWrapFormat(wrapMenuItem.isSelected(), false); |
3225 | } | |
3226 | ||
3227 | 8 | public void setWrapFormat(boolean b, boolean setMenuItem) |
3228 | { | |
3229 | 8 | scaleAbove.setVisible(b); |
3230 | 8 | scaleLeft.setVisible(b); |
3231 | 8 | scaleRight.setVisible(b); |
3232 | 8 | viewport.setWrapAlignment(b); |
3233 | 8 | alignPanel.updateLayout(); |
3234 | 8 | if (setMenuItem) |
3235 | { | |
3236 | 0 | wrapMenuItem.setSelected(b); |
3237 | } | |
3238 | } | |
3239 | ||
3240 | 0 | @Override |
3241 | public void showAllSeqs_actionPerformed(ActionEvent e) | |
3242 | { | |
3243 | 0 | viewport.showAllHiddenSeqs(); |
3244 | } | |
3245 | ||
3246 | 0 | @Override |
3247 | public void showAllColumns_actionPerformed(ActionEvent e) | |
3248 | { | |
3249 | 0 | viewport.showAllHiddenColumns(); |
3250 | 0 | alignPanel.paintAlignment(true, true); |
3251 | 0 | viewport.sendSelection(); |
3252 | } | |
3253 | ||
3254 | 0 | @Override |
3255 | public void hideSelSequences_actionPerformed(ActionEvent e) | |
3256 | { | |
3257 | 0 | viewport.hideAllSelectedSeqs(); |
3258 | } | |
3259 | ||
3260 | /** | |
3261 | * called by key handler and the hide all/show all menu items | |
3262 | * | |
3263 | * @param toggleSeqs | |
3264 | * @param toggleCols | |
3265 | */ | |
3266 | 0 | protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) |
3267 | { | |
3268 | ||
3269 | 0 | boolean hide = false; |
3270 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
3271 | 0 | if (!toggleSeqs && !toggleCols) |
3272 | { | |
3273 | // Hide everything by the current selection - this is a hack - we do the | |
3274 | // invert and then hide | |
3275 | // first check that there will be visible columns after the invert. | |
3276 | 0 | if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 |
3277 | && sg.getStartRes() <= sg.getEndRes())) | |
3278 | { | |
3279 | // now invert the sequence set, if required - empty selection implies | |
3280 | // that no hiding is required. | |
3281 | 0 | if (sg != null) |
3282 | { | |
3283 | 0 | invertSequenceMenuItem_actionPerformed(null); |
3284 | 0 | sg = viewport.getSelectionGroup(); |
3285 | 0 | toggleSeqs = true; |
3286 | ||
3287 | } | |
3288 | 0 | viewport.expandColSelection(sg, true); |
3289 | // finally invert the column selection and get the new sequence | |
3290 | // selection. | |
3291 | 0 | invertColSel_actionPerformed(null); |
3292 | 0 | toggleCols = true; |
3293 | } | |
3294 | } | |
3295 | ||
3296 | 0 | if (toggleSeqs) |
3297 | { | |
3298 | 0 | if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) |
3299 | { | |
3300 | 0 | hideSelSequences_actionPerformed(null); |
3301 | 0 | hide = true; |
3302 | } | |
3303 | 0 | else if (!(toggleCols && viewport.hasSelectedColumns())) |
3304 | { | |
3305 | 0 | showAllSeqs_actionPerformed(null); |
3306 | } | |
3307 | } | |
3308 | ||
3309 | 0 | if (toggleCols) |
3310 | { | |
3311 | 0 | if (viewport.hasSelectedColumns()) |
3312 | { | |
3313 | 0 | hideSelColumns_actionPerformed(null); |
3314 | 0 | if (!toggleSeqs) |
3315 | { | |
3316 | 0 | viewport.setSelectionGroup(sg); |
3317 | } | |
3318 | } | |
3319 | 0 | else if (!hide) |
3320 | { | |
3321 | 0 | showAllColumns_actionPerformed(null); |
3322 | } | |
3323 | } | |
3324 | } | |
3325 | ||
3326 | /* | |
3327 | * (non-Javadoc) | |
3328 | * | |
3329 | * @see | |
3330 | * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. | |
3331 | * event.ActionEvent) | |
3332 | */ | |
3333 | 0 | @Override |
3334 | public void hideAllButSelection_actionPerformed(ActionEvent e) | |
3335 | { | |
3336 | 0 | toggleHiddenRegions(false, false); |
3337 | 0 | viewport.sendSelection(); |
3338 | } | |
3339 | ||
3340 | /* | |
3341 | * (non-Javadoc) | |
3342 | * | |
3343 | * @see | |
3344 | * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event | |
3345 | * .ActionEvent) | |
3346 | */ | |
3347 | 0 | @Override |
3348 | public void hideAllSelection_actionPerformed(ActionEvent e) | |
3349 | { | |
3350 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
3351 | 0 | viewport.expandColSelection(sg, false); |
3352 | 0 | viewport.hideAllSelectedSeqs(); |
3353 | 0 | viewport.hideSelectedColumns(); |
3354 | 0 | alignPanel.updateLayout(); |
3355 | 0 | alignPanel.paintAlignment(true, true); |
3356 | 0 | viewport.sendSelection(); |
3357 | } | |
3358 | ||
3359 | /* | |
3360 | * (non-Javadoc) | |
3361 | * | |
3362 | * @see | |
3363 | * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. | |
3364 | * ActionEvent) | |
3365 | */ | |
3366 | 0 | @Override |
3367 | public void showAllhidden_actionPerformed(ActionEvent e) | |
3368 | { | |
3369 | 0 | viewport.showAllHiddenColumns(); |
3370 | 0 | viewport.showAllHiddenSeqs(); |
3371 | 0 | alignPanel.paintAlignment(true, true); |
3372 | 0 | viewport.sendSelection(); |
3373 | } | |
3374 | ||
3375 | 2 | @Override |
3376 | public void hideSelColumns_actionPerformed(ActionEvent e) | |
3377 | { | |
3378 | 2 | viewport.hideSelectedColumns(); |
3379 | 2 | alignPanel.updateLayout(); |
3380 | 2 | alignPanel.paintAlignment(true, true); |
3381 | 2 | viewport.sendSelection(); |
3382 | } | |
3383 | ||
3384 | 0 | @Override |
3385 | public void hiddenMarkers_actionPerformed(ActionEvent e) | |
3386 | { | |
3387 | 0 | viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); |
3388 | 0 | repaint(); |
3389 | } | |
3390 | ||
3391 | /** | |
3392 | * DOCUMENT ME! | |
3393 | * | |
3394 | * @param e | |
3395 | * DOCUMENT ME! | |
3396 | */ | |
3397 | 0 | @Override |
3398 | protected void scaleAbove_actionPerformed(ActionEvent e) | |
3399 | { | |
3400 | 0 | viewport.setScaleAboveWrapped(scaleAbove.isSelected()); |
3401 | 0 | alignPanel.updateLayout(); |
3402 | 0 | alignPanel.paintAlignment(true, false); |
3403 | } | |
3404 | ||
3405 | /** | |
3406 | * DOCUMENT ME! | |
3407 | * | |
3408 | * @param e | |
3409 | * DOCUMENT ME! | |
3410 | */ | |
3411 | 0 | @Override |
3412 | protected void scaleLeft_actionPerformed(ActionEvent e) | |
3413 | { | |
3414 | 0 | viewport.setScaleLeftWrapped(scaleLeft.isSelected()); |
3415 | 0 | alignPanel.updateLayout(); |
3416 | 0 | alignPanel.paintAlignment(true, false); |
3417 | } | |
3418 | ||
3419 | /** | |
3420 | * DOCUMENT ME! | |
3421 | * | |
3422 | * @param e | |
3423 | * DOCUMENT ME! | |
3424 | */ | |
3425 | 0 | @Override |
3426 | protected void scaleRight_actionPerformed(ActionEvent e) | |
3427 | { | |
3428 | 0 | viewport.setScaleRightWrapped(scaleRight.isSelected()); |
3429 | 0 | alignPanel.updateLayout(); |
3430 | 0 | alignPanel.paintAlignment(true, false); |
3431 | } | |
3432 | ||
3433 | /** | |
3434 | * DOCUMENT ME! | |
3435 | * | |
3436 | * @param e | |
3437 | * DOCUMENT ME! | |
3438 | */ | |
3439 | 0 | @Override |
3440 | public void viewBoxesMenuItem_actionPerformed(ActionEvent e) | |
3441 | { | |
3442 | 0 | viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); |
3443 | 0 | alignPanel.paintAlignment(false, false); |
3444 | } | |
3445 | ||
3446 | /** | |
3447 | * DOCUMENT ME! | |
3448 | * | |
3449 | * @param e | |
3450 | * DOCUMENT ME! | |
3451 | */ | |
3452 | 0 | @Override |
3453 | public void viewTextMenuItem_actionPerformed(ActionEvent e) | |
3454 | { | |
3455 | 0 | viewport.setShowText(viewTextMenuItem.isSelected()); |
3456 | 0 | alignPanel.paintAlignment(false, false); |
3457 | } | |
3458 | ||
3459 | /** | |
3460 | * DOCUMENT ME! | |
3461 | * | |
3462 | * @param e | |
3463 | * DOCUMENT ME! | |
3464 | */ | |
3465 | 0 | @Override |
3466 | protected void renderGapsMenuItem_actionPerformed(ActionEvent e) | |
3467 | { | |
3468 | 0 | viewport.setRenderGaps(renderGapsMenuItem.isSelected()); |
3469 | 0 | alignPanel.paintAlignment(false, false); |
3470 | } | |
3471 | ||
3472 | public FeatureSettings featureSettings; | |
3473 | ||
3474 | 4 | @Override |
3475 | public FeatureSettingsControllerI getFeatureSettingsUI() | |
3476 | { | |
3477 | 4 | return featureSettings; |
3478 | } | |
3479 | ||
3480 | 0 | @Override |
3481 | public void featureSettings_actionPerformed(ActionEvent e) | |
3482 | { | |
3483 | 0 | showFeatureSettingsUI(); |
3484 | } | |
3485 | ||
3486 | 0 | @Override |
3487 | public FeatureSettingsControllerI showFeatureSettingsUI() | |
3488 | { | |
3489 | 0 | if (featureSettings != null) |
3490 | { | |
3491 | 0 | featureSettings.closeOldSettings(); |
3492 | 0 | featureSettings = null; |
3493 | } | |
3494 | 0 | if (!showSeqFeatures.isSelected()) |
3495 | { | |
3496 | // make sure features are actually displayed | |
3497 | 0 | showSeqFeatures.setSelected(true); |
3498 | 0 | showSeqFeatures_actionPerformed(null); |
3499 | } | |
3500 | 0 | featureSettings = new FeatureSettings(this); |
3501 | 0 | return featureSettings; |
3502 | } | |
3503 | ||
3504 | /** | |
3505 | * Set or clear 'Show Sequence Features' | |
3506 | * | |
3507 | * @param evt | |
3508 | * DOCUMENT ME! | |
3509 | */ | |
3510 | 0 | @Override |
3511 | public void showSeqFeatures_actionPerformed(ActionEvent evt) | |
3512 | { | |
3513 | 0 | viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); |
3514 | 0 | alignPanel.paintAlignment(true, true); |
3515 | } | |
3516 | ||
3517 | /** | |
3518 | * Action on toggle of the 'Show annotations' menu item. This shows or hides | |
3519 | * the annotations panel as a whole. | |
3520 | * | |
3521 | * The options to show/hide all annotations should be enabled when the panel | |
3522 | * is shown, and disabled when the panel is hidden. | |
3523 | * | |
3524 | * @param e | |
3525 | */ | |
3526 | 0 | @Override |
3527 | public void annotationPanelMenuItem_actionPerformed(ActionEvent e) | |
3528 | { | |
3529 | 0 | final boolean setVisible = annotationPanelMenuItem.isSelected(); |
3530 | 0 | viewport.setShowAnnotation(setVisible); |
3531 | 0 | this.showAllSeqAnnotations.setEnabled(setVisible); |
3532 | 0 | this.hideAllSeqAnnotations.setEnabled(setVisible); |
3533 | 0 | this.showAllAlAnnotations.setEnabled(setVisible); |
3534 | 0 | this.hideAllAlAnnotations.setEnabled(setVisible); |
3535 | 0 | alignPanel.updateLayout(); |
3536 | } | |
3537 | ||
3538 | 0 | @Override |
3539 | public void alignmentProperties() | |
3540 | { | |
3541 | 0 | JComponent pane; |
3542 | 0 | StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) |
3543 | ||
3544 | .formatAsHtml(); | |
3545 | 0 | String content = MessageManager.formatMessage("label.html_content", |
3546 | new Object[] | |
3547 | { contents.toString() }); | |
3548 | 0 | contents = null; |
3549 | ||
3550 | 0 | if (Platform.isJS()) |
3551 | { | |
3552 | 0 | JLabel textLabel = new JLabel(); |
3553 | 0 | textLabel.setText(content); |
3554 | 0 | textLabel.setBackground(Color.WHITE); |
3555 | ||
3556 | 0 | pane = new JPanel(new BorderLayout()); |
3557 | 0 | ((JPanel) pane).setOpaque(true); |
3558 | 0 | pane.setBackground(Color.WHITE); |
3559 | 0 | ((JPanel) pane).add(textLabel, BorderLayout.NORTH); |
3560 | } | |
3561 | else | |
3562 | /** | |
3563 | * Java only | |
3564 | * | |
3565 | * @j2sIgnore | |
3566 | */ | |
3567 | { | |
3568 | 0 | JEditorPane editPane = new JEditorPane("text/html", ""); |
3569 | 0 | editPane.setEditable(false); |
3570 | 0 | editPane.setText(content); |
3571 | 0 | pane = editPane; |
3572 | } | |
3573 | ||
3574 | 0 | JInternalFrame frame = new JInternalFrame(); |
3575 | 0 | frame.setFrameIcon(null); |
3576 | 0 | frame.getContentPane().add(new JScrollPane(pane)); |
3577 | ||
3578 | 0 | Desktop.addInternalFrame(frame, MessageManager |
3579 | .formatMessage("label.alignment_properties", new Object[] | |
3580 | { getTitle() }), 500, 400); | |
3581 | } | |
3582 | ||
3583 | /** | |
3584 | * Opens an Overview panel for the alignment, unless one is open already | |
3585 | * | |
3586 | * @param e | |
3587 | */ | |
3588 | 30 | @Override |
3589 | public void overviewMenuItem_actionPerformed(ActionEvent e) | |
3590 | { | |
3591 | 30 | boolean showHiddenRegions = Cache |
3592 | .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false); | |
3593 | 30 | openOverviewPanel(showHiddenRegions); |
3594 | } | |
3595 | ||
3596 | 43 | public OverviewPanel openOverviewPanel(boolean showHidden) |
3597 | { | |
3598 | 43 | if (alignPanel.overviewPanel != null) |
3599 | { | |
3600 | 0 | return alignPanel.overviewPanel; |
3601 | } | |
3602 | 43 | JInternalFrame frame = new JInternalFrame(); |
3603 | 43 | frame.setFrameIcon(null); |
3604 | 43 | final OverviewPanel overview = new OverviewPanel(alignPanel, frame, |
3605 | showHidden); | |
3606 | 43 | frame.setContentPane(overview); |
3607 | ||
3608 | 43 | alignPanel.setOverviewPanel(overview); |
3609 | 43 | alignPanel.setOverviewTitle(this); |
3610 | ||
3611 | 43 | Desktop.addInternalFrame(frame, overview.getTitle(), true, |
3612 | frame.getWidth(), frame.getHeight(), true, true); | |
3613 | 43 | frame.pack(); |
3614 | 43 | frame.setLayer(JLayeredPane.PALETTE_LAYER); |
3615 | 43 | final AlignmentPanel thePanel = this.alignPanel; |
3616 | 43 | frame.addInternalFrameListener( |
3617 | new javax.swing.event.InternalFrameAdapter() | |
3618 | { | |
3619 | 39 | @Override |
3620 | public void internalFrameClosed( | |
3621 | javax.swing.event.InternalFrameEvent evt) | |
3622 | { | |
3623 | 39 | overview.dispose(); |
3624 | 39 | thePanel.setOverviewPanel(null); |
3625 | } | |
3626 | }); | |
3627 | 43 | if (getKeyListeners().length > 0) |
3628 | { | |
3629 | 15 | frame.addKeyListener(getKeyListeners()[0]); |
3630 | } | |
3631 | ||
3632 | 43 | return overview; |
3633 | } | |
3634 | ||
3635 | 0 | @Override |
3636 | public void textColour_actionPerformed() | |
3637 | { | |
3638 | 0 | new TextColourChooser().chooseColour(alignPanel, null); |
3639 | } | |
3640 | ||
3641 | /* | |
3642 | * public void covariationColour_actionPerformed() { | |
3643 | * changeColour(new | |
3644 | * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation | |
3645 | * ()[0])); } | |
3646 | */ | |
3647 | 0 | @Override |
3648 | public void annotationColour_actionPerformed() | |
3649 | { | |
3650 | 0 | new AnnotationColourChooser(viewport, alignPanel); |
3651 | } | |
3652 | ||
3653 | 0 | @Override |
3654 | public void annotationColumn_actionPerformed(ActionEvent e) | |
3655 | { | |
3656 | 0 | new AnnotationColumnChooser(viewport, alignPanel); |
3657 | } | |
3658 | ||
3659 | /** | |
3660 | * Action on the user checking or unchecking the option to apply the selected | |
3661 | * colour scheme to all groups. If unchecked, groups may have their own | |
3662 | * independent colour schemes. | |
3663 | * | |
3664 | * @param selected | |
3665 | */ | |
3666 | 3 | @Override |
3667 | public void applyToAllGroups_actionPerformed(boolean selected) | |
3668 | { | |
3669 | 3 | viewport.setColourAppliesToAllGroups(selected); |
3670 | } | |
3671 | ||
3672 | /** | |
3673 | * Action on user selecting a colour from the colour menu | |
3674 | * | |
3675 | * @param name | |
3676 | * the name (not the menu item label!) of the colour scheme | |
3677 | */ | |
3678 | 15 | @Override |
3679 | public void changeColour_actionPerformed(String name) | |
3680 | { | |
3681 | /* | |
3682 | * 'User Defined' opens a panel to configure or load a | |
3683 | * user-defined colour scheme | |
3684 | */ | |
3685 | 15 | if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) |
3686 | { | |
3687 | 0 | new UserDefinedColours(alignPanel); |
3688 | 0 | return; |
3689 | } | |
3690 | ||
3691 | /* | |
3692 | * otherwise set the chosen colour scheme (or null for 'None') | |
3693 | */ | |
3694 | 15 | ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, |
3695 | viewport, viewport.getAlignment(), | |
3696 | viewport.getHiddenRepSequences()); | |
3697 | 15 | changeColour(cs); |
3698 | } | |
3699 | ||
3700 | /** | |
3701 | * Actions on setting or changing the alignment colour scheme | |
3702 | * | |
3703 | * @param cs | |
3704 | */ | |
3705 | 179 | @Override |
3706 | public void changeColour(ColourSchemeI cs) | |
3707 | { | |
3708 | // TODO: pull up to controller method | |
3709 | 179 | ColourMenuHelper.setColourSelected(colourMenu, cs); |
3710 | ||
3711 | 179 | viewport.setGlobalColourScheme(cs); |
3712 | ||
3713 | 179 | alignPanel.paintAlignment(true, true); |
3714 | } | |
3715 | ||
3716 | /** | |
3717 | * Show the PID threshold slider panel | |
3718 | */ | |
3719 | 6 | @Override |
3720 | protected void modifyPID_actionPerformed() | |
3721 | { | |
3722 | 6 | SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), |
3723 | alignPanel.getViewName()); | |
3724 | 6 | SliderPanel.showPIDSlider(); |
3725 | } | |
3726 | ||
3727 | /** | |
3728 | * Show the Conservation slider panel | |
3729 | */ | |
3730 | 6 | @Override |
3731 | protected void modifyConservation_actionPerformed() | |
3732 | { | |
3733 | 6 | SliderPanel.setConservationSlider(alignPanel, |
3734 | viewport.getResidueShading(), alignPanel.getViewName()); | |
3735 | 6 | SliderPanel.showConservationSlider(); |
3736 | } | |
3737 | ||
3738 | 0 | @Override |
3739 | protected void modifyConsensusSecondaryStructureThreshold_actionPerformed() | |
3740 | { | |
3741 | 0 | SliderPanel.setConsensusSecondaryStructureSlider(alignPanel, |
3742 | viewport.getResidueShading(), alignPanel.getViewName()); | |
3743 | 0 | SliderPanel.showConsensusSecondaryStructureSlider(); |
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 | 0 | @Override |
3768 | public void colourByConsensusSecondaryStructureMenuItem_actionPerformed( | |
3769 | boolean selected) | |
3770 | { | |
3771 | 0 | modifyConsensusSecondaryStructureThreshold.setEnabled(selected); |
3772 | 0 | viewport.setByConsensusSecondaryStructureSelected(selected); |
3773 | 0 | viewport.getResidueShading() |
3774 | .setConsensusSecondaryStructureColouring(selected); | |
3775 | ||
3776 | 0 | changeColour(viewport.getGlobalColourScheme()); |
3777 | 0 | if (selected) |
3778 | { | |
3779 | 0 | modifyConsensusSecondaryStructureThreshold_actionPerformed(); |
3780 | } | |
3781 | else | |
3782 | { | |
3783 | 0 | SliderPanel.hideConsensusSecondaryStructureSlider(); |
3784 | } | |
3785 | } | |
3786 | ||
3787 | /** | |
3788 | * Action on selecting or deselecting (Colour) Above PID Threshold | |
3789 | */ | |
3790 | 9 | @Override |
3791 | public void abovePIDThreshold_actionPerformed(boolean selected) | |
3792 | { | |
3793 | 9 | modifyPID.setEnabled(selected); |
3794 | 9 | viewport.setAbovePIDThreshold(selected); |
3795 | 9 | if (!selected) |
3796 | { | |
3797 | 3 | viewport.getResidueShading().setThreshold(0, |
3798 | viewport.isIgnoreGapsConsensus()); | |
3799 | } | |
3800 | ||
3801 | 9 | changeColour(viewport.getGlobalColourScheme()); |
3802 | 9 | if (selected) |
3803 | { | |
3804 | 6 | modifyPID_actionPerformed(); |
3805 | } | |
3806 | else | |
3807 | { | |
3808 | 3 | SliderPanel.hidePIDSlider(); |
3809 | } | |
3810 | } | |
3811 | ||
3812 | /** | |
3813 | * DOCUMENT ME! | |
3814 | * | |
3815 | * @param e | |
3816 | * DOCUMENT ME! | |
3817 | */ | |
3818 | 0 | @Override |
3819 | public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) | |
3820 | { | |
3821 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3822 | 0 | AlignmentSorter.sortByPID(viewport.getAlignment(), |
3823 | viewport.getAlignment().getSequenceAt(0)); | |
3824 | 0 | addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, |
3825 | viewport.getAlignment())); | |
3826 | 0 | alignPanel.paintAlignment(true, false); |
3827 | } | |
3828 | ||
3829 | /** | |
3830 | * DOCUMENT ME! | |
3831 | * | |
3832 | * @param e | |
3833 | * DOCUMENT ME! | |
3834 | */ | |
3835 | 0 | @Override |
3836 | public void sortIDMenuItem_actionPerformed(ActionEvent e) | |
3837 | { | |
3838 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3839 | 0 | AlignmentSorter.sortByID(viewport.getAlignment()); |
3840 | 0 | addHistoryItem( |
3841 | new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); | |
3842 | 0 | alignPanel.paintAlignment(true, false); |
3843 | } | |
3844 | ||
3845 | /** | |
3846 | * DOCUMENT ME! | |
3847 | * | |
3848 | * @param e | |
3849 | * DOCUMENT ME! | |
3850 | */ | |
3851 | 0 | @Override |
3852 | public void sortLengthMenuItem_actionPerformed(ActionEvent e) | |
3853 | { | |
3854 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3855 | 0 | AlignmentSorter.sortByLength(viewport.getAlignment()); |
3856 | 0 | addHistoryItem(new OrderCommand("Length Sort", oldOrder, |
3857 | viewport.getAlignment())); | |
3858 | 0 | alignPanel.paintAlignment(true, false); |
3859 | } | |
3860 | ||
3861 | /** | |
3862 | * DOCUMENT ME! | |
3863 | * | |
3864 | * @param e | |
3865 | * DOCUMENT ME! | |
3866 | */ | |
3867 | 0 | @Override |
3868 | public void sortGroupMenuItem_actionPerformed(ActionEvent e) | |
3869 | { | |
3870 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
3871 | 0 | AlignmentSorter.sortByGroup(viewport.getAlignment()); |
3872 | 0 | addHistoryItem(new OrderCommand("Group Sort", oldOrder, |
3873 | viewport.getAlignment())); | |
3874 | ||
3875 | 0 | alignPanel.paintAlignment(true, false); |
3876 | } | |
3877 | ||
3878 | /** | |
3879 | * DOCUMENT ME! | |
3880 | * | |
3881 | * @param e | |
3882 | * DOCUMENT ME! | |
3883 | */ | |
3884 | 0 | @Override |
3885 | public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) | |
3886 | { | |
3887 | 0 | new RedundancyPanel(alignPanel, this); |
3888 | } | |
3889 | ||
3890 | /** | |
3891 | * DOCUMENT ME! | |
3892 | * | |
3893 | * @param e | |
3894 | * DOCUMENT ME! | |
3895 | */ | |
3896 | 0 | @Override |
3897 | public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) | |
3898 | { | |
3899 | 0 | if ((viewport.getSelectionGroup() == null) |
3900 | || (viewport.getSelectionGroup().getSize() < 2)) | |
3901 | { | |
3902 | 0 | JvOptionPane.showInternalMessageDialog(this, |
3903 | MessageManager.getString( | |
3904 | "label.you_must_select_least_two_sequences"), | |
3905 | MessageManager.getString("label.invalid_selection"), | |
3906 | JvOptionPane.WARNING_MESSAGE); | |
3907 | } | |
3908 | else | |
3909 | { | |
3910 | 0 | new Thread(new Runnable() |
3911 | { | |
3912 | 0 | @Override |
3913 | public void run() | |
3914 | { | |
3915 | 0 | JInternalFrame frame = new JInternalFrame(); |
3916 | 0 | frame.setFrameIcon(null); |
3917 | 0 | frame.setContentPane(new PairwiseAlignPanel(viewport)); |
3918 | 0 | Desktop.addInternalFrame(frame, |
3919 | MessageManager.getString("action.pairwise_alignment"), | |
3920 | 600, 500); | |
3921 | } | |
3922 | }).start(); | |
3923 | ||
3924 | } | |
3925 | } | |
3926 | ||
3927 | 0 | @Override |
3928 | public void autoCalculate_actionPerformed(ActionEvent e) | |
3929 | { | |
3930 | 0 | viewport.autoCalculateConsensus = autoCalculate.isSelected(); |
3931 | 0 | if (viewport.autoCalculateConsensus) |
3932 | { | |
3933 | 0 | viewport.firePropertyChange("alignment", null, |
3934 | viewport.getAlignment().getSequences()); | |
3935 | } | |
3936 | } | |
3937 | ||
3938 | 0 | @Override |
3939 | public void sortByTreeOption_actionPerformed(ActionEvent e) | |
3940 | { | |
3941 | 0 | viewport.sortByTree = sortByTree.isSelected(); |
3942 | } | |
3943 | ||
3944 | 0 | @Override |
3945 | protected void listenToViewSelections_actionPerformed(ActionEvent e) | |
3946 | { | |
3947 | 0 | viewport.followSelection = listenToViewSelections.isSelected(); |
3948 | } | |
3949 | ||
3950 | /** | |
3951 | * Constructs a tree panel and adds it to the desktop | |
3952 | * | |
3953 | * @param type | |
3954 | * tree type (NJ or AV) | |
3955 | * @param modelName | |
3956 | * name of score model used to compute the tree | |
3957 | * @param options | |
3958 | * parameters for the distance or similarity calculation | |
3959 | */ | |
3960 | 0 | void newTreePanel(String type, String modelName, |
3961 | SimilarityParamsI options) | |
3962 | { | |
3963 | 0 | String frameTitle = ""; |
3964 | 0 | TreePanel tp; |
3965 | ||
3966 | 0 | boolean onSelection = false; |
3967 | 0 | if (viewport.getSelectionGroup() != null |
3968 | && viewport.getSelectionGroup().getSize() > 0) | |
3969 | { | |
3970 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
3971 | ||
3972 | /* Decide if the selection is a column region */ | |
3973 | 0 | for (SequenceI _s : sg.getSequences()) |
3974 | { | |
3975 | 0 | if (_s.getLength() < sg.getEndRes()) |
3976 | { | |
3977 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
3978 | MessageManager.getString( | |
3979 | "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), | |
3980 | MessageManager.getString( | |
3981 | "label.sequences_selection_not_aligned"), | |
3982 | JvOptionPane.WARNING_MESSAGE); | |
3983 | ||
3984 | 0 | return; |
3985 | } | |
3986 | } | |
3987 | 0 | onSelection = true; |
3988 | } | |
3989 | else | |
3990 | { | |
3991 | 0 | if (viewport.getAlignment().getHeight() < 2) |
3992 | { | |
3993 | 0 | return; |
3994 | } | |
3995 | } | |
3996 | ||
3997 | 0 | tp = new TreePanel(alignPanel, type, modelName, options); |
3998 | ||
3999 | 0 | frameTitle = formCalculationTitle(tp.getPanelTitle(), onSelection, |
4000 | this.title); | |
4001 | ||
4002 | 0 | Desktop.addInternalFrame(tp, frameTitle, 600, 500); |
4003 | } | |
4004 | ||
4005 | /** | |
4006 | * | |
4007 | * @param panelTitle | |
4008 | * - calculation name | |
4009 | * @param onSelection | |
4010 | * - true if a selection was analysed | |
4011 | * @param viewName | |
4012 | * - null or current view name | |
4013 | * @param title | |
4014 | * - alignment frame title | |
4015 | * @return <calculation Name> (?on region) from (?viewName of) alignment name | |
4016 | */ | |
4017 | 2 | public String formCalculationTitle(String panelTitle, boolean onSelection, |
4018 | String title) | |
4019 | { | |
4020 | 2 | String frameTitle = panelTitle; |
4021 | ||
4022 | 2 | frameTitle += (onSelection ? " on region" : ""); |
4023 | ||
4024 | 2 | frameTitle += " from "; |
4025 | ||
4026 | 2 | if (viewport.getViewName() != null) |
4027 | { | |
4028 | 2 | frameTitle += viewport.getViewName() + " of "; |
4029 | } | |
4030 | ||
4031 | 2 | frameTitle += title; |
4032 | 2 | return frameTitle; |
4033 | } | |
4034 | ||
4035 | /** | |
4036 | * DOCUMENT ME! | |
4037 | * | |
4038 | * @param title | |
4039 | * DOCUMENT ME! | |
4040 | * @param order | |
4041 | * DOCUMENT ME! | |
4042 | */ | |
4043 | 0 | public void addSortByOrderMenuItem(String title, |
4044 | final AlignmentOrder order) | |
4045 | { | |
4046 | 0 | final JMenuItem item = new JMenuItem(MessageManager |
4047 | .formatMessage("action.by_title_param", new Object[] | |
4048 | { title })); | |
4049 | 0 | sort.add(item); |
4050 | 0 | item.addActionListener(new java.awt.event.ActionListener() |
4051 | { | |
4052 | 0 | @Override |
4053 | public void actionPerformed(ActionEvent e) | |
4054 | { | |
4055 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
4056 | ||
4057 | // TODO: JBPNote - have to map order entries to curent SequenceI | |
4058 | // pointers | |
4059 | 0 | AlignmentSorter.sortBy(viewport.getAlignment(), order); |
4060 | ||
4061 | 0 | addHistoryItem(new OrderCommand(order.getName(), oldOrder, |
4062 | viewport.getAlignment())); | |
4063 | ||
4064 | 0 | alignPanel.paintAlignment(true, false); |
4065 | } | |
4066 | }); | |
4067 | } | |
4068 | ||
4069 | /** | |
4070 | * Add a new sort by annotation score menu item | |
4071 | * | |
4072 | * @param sort | |
4073 | * the menu to add the option to | |
4074 | * @param scoreLabel | |
4075 | * the label used to retrieve scores for each sequence on the | |
4076 | * alignment | |
4077 | */ | |
4078 | 4 | public void addSortByAnnotScoreMenuItem(JMenu sort, |
4079 | final String scoreLabel) | |
4080 | { | |
4081 | 4 | final JMenuItem item = new JMenuItem(scoreLabel); |
4082 | 4 | sort.add(item); |
4083 | 4 | item.addActionListener(new java.awt.event.ActionListener() |
4084 | { | |
4085 | 0 | @Override |
4086 | public void actionPerformed(ActionEvent e) | |
4087 | { | |
4088 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
4089 | 0 | AlignmentSorter.sortByAnnotationScore(scoreLabel, |
4090 | viewport.getAlignment());// ,viewport.getSelectionGroup()); | |
4091 | 0 | addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, |
4092 | viewport.getAlignment())); | |
4093 | 0 | alignPanel.paintAlignment(true, false); |
4094 | } | |
4095 | }); | |
4096 | } | |
4097 | ||
4098 | /** | |
4099 | * last hash for alignment's annotation array - used to minimise cost of | |
4100 | * rebuild. | |
4101 | */ | |
4102 | protected int _annotationScoreVectorHash; | |
4103 | ||
4104 | /** | |
4105 | * search the alignment and rebuild the sort by annotation score submenu the | |
4106 | * last alignment annotation vector hash is stored to minimize cost of | |
4107 | * rebuilding in subsequence calls. | |
4108 | * | |
4109 | */ | |
4110 | 457 | @Override |
4111 | public void buildSortByAnnotationScoresMenu() | |
4112 | { | |
4113 | 457 | if (viewport.getAlignment().getAlignmentAnnotation() == null) |
4114 | { | |
4115 | 0 | return; |
4116 | } | |
4117 | ||
4118 | 457 | if (viewport.getAlignment().getAlignmentAnnotation() |
4119 | .hashCode() != _annotationScoreVectorHash) | |
4120 | { | |
4121 | 456 | sortByAnnotScore.removeAll(); |
4122 | // almost certainly a quicker way to do this - but we keep it simple | |
4123 | 456 | Hashtable<String, String> scoreSorts = new Hashtable<>(); |
4124 | 456 | AlignmentAnnotation aann[]; |
4125 | 456 | for (SequenceI sqa : viewport.getAlignment().getSequences()) |
4126 | { | |
4127 | 4095 | aann = sqa.getAnnotation(); |
4128 | 4399 | for (int i = 0; aann != null && i < aann.length; i++) |
4129 | { | |
4130 | 304 | if (aann[i].hasScore() && aann[i].sequenceRef != null) |
4131 | { | |
4132 | 152 | scoreSorts.put(aann[i].label, aann[i].label); |
4133 | } | |
4134 | } | |
4135 | } | |
4136 | 456 | Enumeration<String> labels = scoreSorts.keys(); |
4137 | 460 | while (labels.hasMoreElements()) |
4138 | { | |
4139 | 4 | addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement()); |
4140 | } | |
4141 | 456 | sortByAnnotScore.setVisible(scoreSorts.size() > 0); |
4142 | 456 | scoreSorts.clear(); |
4143 | ||
4144 | 456 | _annotationScoreVectorHash = viewport.getAlignment() |
4145 | .getAlignmentAnnotation().hashCode(); | |
4146 | } | |
4147 | } | |
4148 | ||
4149 | /** | |
4150 | * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a | |
4151 | * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code> | |
4152 | * call. Listeners are added to remove the menu item when the treePanel is | |
4153 | * closed, and adjust the tree leaf to sequence mapping when the alignment is | |
4154 | * modified. | |
4155 | */ | |
4156 | 0 | @Override |
4157 | public void buildTreeSortMenu() | |
4158 | { | |
4159 | 0 | sortByTreeMenu.removeAll(); |
4160 | ||
4161 | 0 | List<Component> comps = PaintRefresher.components |
4162 | .get(viewport.getSequenceSetId()); | |
4163 | 0 | List<TreePanel> treePanels = new ArrayList<>(); |
4164 | 0 | for (Component comp : comps) |
4165 | { | |
4166 | 0 | if (comp instanceof TreePanel) |
4167 | { | |
4168 | 0 | treePanels.add((TreePanel) comp); |
4169 | } | |
4170 | } | |
4171 | ||
4172 | 0 | if (treePanels.size() < 1) |
4173 | { | |
4174 | 0 | sortByTreeMenu.setVisible(false); |
4175 | 0 | return; |
4176 | } | |
4177 | ||
4178 | 0 | sortByTreeMenu.setVisible(true); |
4179 | ||
4180 | 0 | for (final TreePanel tp : treePanels) |
4181 | { | |
4182 | 0 | final JMenuItem item = new JMenuItem(tp.getTitle()); |
4183 | 0 | item.addActionListener(new java.awt.event.ActionListener() |
4184 | { | |
4185 | 0 | @Override |
4186 | public void actionPerformed(ActionEvent e) | |
4187 | { | |
4188 | 0 | tp.sortByTree_actionPerformed(); |
4189 | 0 | addHistoryItem(tp.sortAlignmentIn(alignPanel)); |
4190 | ||
4191 | } | |
4192 | }); | |
4193 | ||
4194 | 0 | sortByTreeMenu.add(item); |
4195 | } | |
4196 | } | |
4197 | ||
4198 | 0 | public boolean sortBy(AlignmentOrder alorder, String undoname) |
4199 | { | |
4200 | 0 | SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
4201 | 0 | AlignmentSorter.sortBy(viewport.getAlignment(), alorder); |
4202 | 0 | if (undoname != null) |
4203 | { | |
4204 | 0 | addHistoryItem(new OrderCommand(undoname, oldOrder, |
4205 | viewport.getAlignment())); | |
4206 | } | |
4207 | 0 | alignPanel.paintAlignment(true, false); |
4208 | 0 | return true; |
4209 | } | |
4210 | ||
4211 | /** | |
4212 | * Work out whether the whole set of sequences or just the selected set will | |
4213 | * be submitted for multiple alignment. | |
4214 | * | |
4215 | */ | |
4216 | 0 | public jalview.datamodel.AlignmentView gatherSequencesForAlignment() |
4217 | { | |
4218 | // Now, check we have enough sequences | |
4219 | 0 | AlignmentView msa = null; |
4220 | ||
4221 | 0 | if ((viewport.getSelectionGroup() != null) |
4222 | && (viewport.getSelectionGroup().getSize() > 1)) | |
4223 | { | |
4224 | // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to | |
4225 | // some common interface! | |
4226 | /* | |
4227 | * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new | |
4228 | * SequenceI[sz = seqs.getSize(false)]; | |
4229 | * | |
4230 | * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) | |
4231 | * seqs.getSequenceAt(i); } | |
4232 | */ | |
4233 | 0 | msa = viewport.getAlignmentView(true); |
4234 | } | |
4235 | 0 | else if (viewport.getSelectionGroup() != null |
4236 | && viewport.getSelectionGroup().getSize() == 1) | |
4237 | { | |
4238 | 0 | int option = JvOptionPane.showConfirmDialog(this, |
4239 | MessageManager.getString("warn.oneseq_msainput_selection"), | |
4240 | MessageManager.getString("label.invalid_selection"), | |
4241 | JvOptionPane.OK_CANCEL_OPTION); | |
4242 | 0 | if (option == JvOptionPane.OK_OPTION) |
4243 | { | |
4244 | 0 | msa = viewport.getAlignmentView(false); |
4245 | } | |
4246 | } | |
4247 | else | |
4248 | { | |
4249 | 0 | msa = viewport.getAlignmentView(false); |
4250 | } | |
4251 | 0 | return msa; |
4252 | } | |
4253 | ||
4254 | /** | |
4255 | * Decides what is submitted to a secondary structure prediction service: the | |
4256 | * first sequence in the alignment, or in the current selection, or, if the | |
4257 | * alignment is 'aligned' (ie padded with gaps), then the currently selected | |
4258 | * region or the whole alignment. (where the first sequence in the set is the | |
4259 | * one that the prediction will be for). | |
4260 | */ | |
4261 | 0 | public AlignmentView gatherSeqOrMsaForSecStrPrediction() |
4262 | { | |
4263 | 0 | AlignmentView seqs = null; |
4264 | ||
4265 | 0 | if ((viewport.getSelectionGroup() != null) |
4266 | && (viewport.getSelectionGroup().getSize() > 0)) | |
4267 | { | |
4268 | 0 | seqs = viewport.getAlignmentView(true); |
4269 | } | |
4270 | else | |
4271 | { | |
4272 | 0 | seqs = viewport.getAlignmentView(false); |
4273 | } | |
4274 | // limit sequences - JBPNote in future - could spawn multiple prediction | |
4275 | // jobs | |
4276 | // TODO: viewport.getAlignment().isAligned is a global state - the local | |
4277 | // selection may well be aligned - we preserve 2.0.8 behaviour for moment. | |
4278 | 0 | if (!viewport.getAlignment().isAligned(false)) |
4279 | { | |
4280 | 0 | seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); |
4281 | // TODO: if seqs.getSequences().length>1 then should really have warned | |
4282 | // user! | |
4283 | ||
4284 | } | |
4285 | 0 | return seqs; |
4286 | } | |
4287 | ||
4288 | //// *************************************************** | |
4289 | //// TODO REFACTOR TREE I/O TO CONTROLLER/SEPARATE CLASS | |
4290 | //// *************************************************** | |
4291 | ||
4292 | /** | |
4293 | * DOCUMENT ME! | |
4294 | * | |
4295 | * @param e | |
4296 | * DOCUMENT ME! | |
4297 | */ | |
4298 | 0 | @Override |
4299 | protected void loadTreeMenuItem_actionPerformed(ActionEvent e) | |
4300 | { | |
4301 | // Pick the tree file | |
4302 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
4303 | Cache.getProperty("LAST_DIRECTORY")); | |
4304 | 0 | chooser.setFileView(new JalviewFileView()); |
4305 | 0 | chooser.setDialogTitle( |
4306 | MessageManager.getString("label.select_newick_like_tree_file")); | |
4307 | 0 | chooser.setToolTipText( |
4308 | MessageManager.getString("label.load_tree_file")); | |
4309 | ||
4310 | 0 | chooser.setResponseHandler(0, () -> { |
4311 | 0 | String filePath = chooser.getSelectedFile().getPath(); |
4312 | 0 | Cache.setProperty("LAST_DIRECTORY", filePath); |
4313 | 0 | NewickFile fin = null; |
4314 | 0 | try |
4315 | { | |
4316 | 0 | fin = new NewickFile(new FileParse(chooser.getSelectedFile(), |
4317 | DataSourceType.FILE)); | |
4318 | 0 | viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); |
4319 | } catch (Exception ex) | |
4320 | { | |
4321 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), |
4322 | MessageManager.getString("label.problem_reading_tree_file"), | |
4323 | JvOptionPane.WARNING_MESSAGE); | |
4324 | 0 | ex.printStackTrace(); |
4325 | } | |
4326 | 0 | if (fin != null && fin.hasWarningMessage()) |
4327 | { | |
4328 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
4329 | fin.getWarningMessage(), | |
4330 | MessageManager | |
4331 | .getString("label.possible_problem_with_tree_file"), | |
4332 | JvOptionPane.WARNING_MESSAGE); | |
4333 | } | |
4334 | }); | |
4335 | 0 | chooser.showOpenDialog(this); |
4336 | } | |
4337 | ||
4338 | 2 | public TreePanel showNewickTree(NewickFile nf, String treeTitle) |
4339 | { | |
4340 | 2 | return showNewickTree(nf, treeTitle, 600, 500, 4, 5); |
4341 | } | |
4342 | ||
4343 | 14 | public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w, |
4344 | int h, int x, int y) | |
4345 | { | |
4346 | 14 | return showNewickTree(nf, treeTitle, null, w, h, x, y); |
4347 | } | |
4348 | ||
4349 | /** | |
4350 | * Add a treeviewer for the tree extracted from a Newick file object to the | |
4351 | * current alignment view | |
4352 | * | |
4353 | * @param nf | |
4354 | * the tree | |
4355 | * @param title | |
4356 | * tree viewer title | |
4357 | * @param input | |
4358 | * Associated alignment input data (or null) | |
4359 | * @param w | |
4360 | * width | |
4361 | * @param h | |
4362 | * height | |
4363 | * @param x | |
4364 | * position | |
4365 | * @param y | |
4366 | * position | |
4367 | * @return TreePanel handle | |
4368 | */ | |
4369 | 14 | public TreePanel showNewickTree(NewickFile nf, String treeTitle, |
4370 | AlignmentView input, int w, int h, int x, int y) | |
4371 | { | |
4372 | 14 | TreePanel tp = null; |
4373 | ||
4374 | 14 | try |
4375 | { | |
4376 | 14 | nf.parse(); |
4377 | ||
4378 | 14 | if (nf.getTree() != null) |
4379 | { | |
4380 | 14 | tp = new TreePanel(alignPanel, nf, treeTitle, input); |
4381 | ||
4382 | 14 | tp.setSize(w, h); |
4383 | ||
4384 | 14 | if (x > 0 && y > 0) |
4385 | { | |
4386 | 14 | tp.setLocation(x, y); |
4387 | } | |
4388 | ||
4389 | 14 | Desktop.addInternalFrame(tp, treeTitle, w, h); |
4390 | } | |
4391 | } catch (Exception ex) | |
4392 | { | |
4393 | 0 | ex.printStackTrace(); |
4394 | } | |
4395 | ||
4396 | 14 | return tp; |
4397 | } | |
4398 | ||
4399 | 0 | public TreePanel showNewickTreeForAnnotation(NewickFile nf, |
4400 | String treeTitle, AlignmentView input, int w, int h, int x, int y) | |
4401 | { | |
4402 | 0 | TreePanel tp = null; |
4403 | ||
4404 | 0 | try |
4405 | { | |
4406 | 0 | nf.parse(); |
4407 | ||
4408 | 0 | if (nf.getTree() != null) |
4409 | { | |
4410 | 0 | tp = TreePanel.newTreeForAnnotations(alignPanel, nf, treeTitle, |
4411 | input); | |
4412 | // TODO - refactor layout code to one place for tree view methods | |
4413 | 0 | tp.setSize(w, h); |
4414 | ||
4415 | 0 | if (x > 0 && y > 0) |
4416 | { | |
4417 | 0 | tp.setLocation(x, y); |
4418 | } | |
4419 | ||
4420 | 0 | Desktop.addInternalFrame(tp, treeTitle, w, h); |
4421 | } | |
4422 | } catch (Exception ex) | |
4423 | { | |
4424 | 0 | ex.printStackTrace(); |
4425 | } | |
4426 | ||
4427 | 0 | return tp; |
4428 | } | |
4429 | ||
4430 | 0 | public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm) |
4431 | { | |
4432 | 0 | int x = 4, y = 5; |
4433 | 0 | int w = 400, h = 500; |
4434 | ||
4435 | 0 | try |
4436 | { | |
4437 | 0 | NewickFile fin = new NewickFile( |
4438 | new FileParse(cm.getNewick(), DataSourceType.PASTE)); | |
4439 | 0 | String title = aa.label + " " + cm.getTreeMethod() + " tree" |
4440 | 0 | + (aa.sequenceRef != null |
4441 | ? (" for " + aa.sequenceRef.getDisplayId(false)) | |
4442 | : ""); | |
4443 | ||
4444 | 0 | showColumnWiseTree(fin, aa, title, w, h, x, y); |
4445 | } catch (Throwable xx) | |
4446 | { | |
4447 | 0 | Console.error("Unexpected exception showing tree for contact matrix", |
4448 | xx); | |
4449 | } | |
4450 | } | |
4451 | ||
4452 | 0 | public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, |
4453 | String treeTitle, int w, int h, int x, int y) | |
4454 | { | |
4455 | 0 | try |
4456 | { | |
4457 | 0 | nf.parse(); |
4458 | 0 | if (nf.getTree() == null) |
4459 | { | |
4460 | 0 | return null; |
4461 | } | |
4462 | 0 | TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle); |
4463 | ||
4464 | 0 | tp.setSize(w, h); |
4465 | ||
4466 | 0 | if (x > 0 && y > 0) |
4467 | { | |
4468 | 0 | tp.setLocation(x, y); |
4469 | } | |
4470 | ||
4471 | 0 | Desktop.addInternalFrame(tp, treeTitle, w, h); |
4472 | 0 | return tp; |
4473 | } catch (Throwable xx) | |
4474 | { | |
4475 | 0 | Console.error("Unexpected exception showing tree for contact matrix", |
4476 | xx); | |
4477 | } | |
4478 | 0 | return null; |
4479 | } | |
4480 | //// *************************************************** | |
4481 | //// TODO REFACTOR TREE I/O TO CONTROLLER/SEPARATE CLASS - END OF METHODS | |
4482 | //// *************************************************** | |
4483 | ||
4484 | private boolean buildingMenu = false; | |
4485 | ||
4486 | /** | |
4487 | * Generates menu items and listener event actions for web service clients | |
4488 | * | |
4489 | */ | |
4490 | 2700 | public void BuildWebServiceMenu() |
4491 | { | |
4492 | 2708 | while (buildingMenu) |
4493 | { | |
4494 | 8 | try |
4495 | { | |
4496 | 8 | jalview.bin.Console |
4497 | .errPrintln("Waiting for building menu to finish."); | |
4498 | 8 | Thread.sleep(10); |
4499 | } catch (Exception e) | |
4500 | { | |
4501 | } | |
4502 | } | |
4503 | 2700 | final AlignFrame me = this; |
4504 | 2700 | buildingMenu = true; |
4505 | 2700 | new Thread(new Runnable() |
4506 | { | |
4507 | 2700 | @Override |
4508 | public void run() | |
4509 | { | |
4510 | 2700 | final List<JMenuItem> legacyItems = new ArrayList<>(); |
4511 | 2700 | try |
4512 | { | |
4513 | // jalview.bin.Console.errPrintln("Building ws menu again " | |
4514 | // + Thread.currentThread()); | |
4515 | // TODO: add support for context dependent disabling of services based | |
4516 | // on | |
4517 | // alignment and current selection | |
4518 | // TODO: add additional serviceHandle parameter to specify abstract | |
4519 | // handler | |
4520 | // class independently of AbstractName | |
4521 | // TODO: add in rediscovery GUI function to restart discoverer | |
4522 | // TODO: group services by location as well as function and/or | |
4523 | // introduce | |
4524 | // object broker mechanism. | |
4525 | 2700 | final Vector<JMenu> wsmenu = new Vector<>(); |
4526 | 2699 | final IProgressIndicator af = me; |
4527 | ||
4528 | /* | |
4529 | * do not i18n these strings - they are hard-coded in class | |
4530 | * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and | |
4531 | * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() | |
4532 | */ | |
4533 | 2699 | final JMenu msawsmenu = new JMenu("Alignment"); |
4534 | 2700 | final JMenu secstrmenu = new JMenu( |
4535 | "Secondary Structure Prediction"); | |
4536 | 2700 | final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); |
4537 | 2700 | final JMenu analymenu = new JMenu("Analysis"); |
4538 | 2700 | final JMenu dismenu = new JMenu("Protein Disorder"); |
4539 | // JAL-940 - only show secondary structure prediction services from | |
4540 | // the legacy server | |
4541 | 2700 | if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) |
4542 | // && | |
4543 | 2700 | Discoverer.services != null && (Discoverer.services.size() > 0)) |
4544 | { | |
4545 | // TODO: refactor to allow list of AbstractName/Handler bindings to | |
4546 | // be | |
4547 | // stored or retrieved from elsewhere | |
4548 | // No MSAWS used any more: | |
4549 | // Vector msaws = null; // (Vector) | |
4550 | // Discoverer.services.get("MsaWS"); | |
4551 | 2700 | Vector<ServiceHandle> secstrpr = Discoverer.services |
4552 | .get("SecStrPred"); | |
4553 | 2700 | if (secstrpr != null) |
4554 | { | |
4555 | // Add any secondary structure prediction services | |
4556 | 5400 | for (int i = 0, j = secstrpr.size(); i < j; i++) |
4557 | { | |
4558 | 2700 | final ext.vamsas.ServiceHandle sh = secstrpr.get(i); |
4559 | 2700 | jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer |
4560 | .getServiceClient(sh); | |
4561 | 2700 | int p = secstrmenu.getItemCount(); |
4562 | 2700 | impl.attachWSMenuEntry(secstrmenu, me); |
4563 | 2700 | int q = secstrmenu.getItemCount(); |
4564 | 5400 | for (int litm = p; litm < q; litm++) |
4565 | { | |
4566 | 2700 | legacyItems.add(secstrmenu.getItem(litm)); |
4567 | } | |
4568 | } | |
4569 | } | |
4570 | } | |
4571 | ||
4572 | // Add all submenus in the order they should appear on the web | |
4573 | // services menu | |
4574 | 2700 | wsmenu.add(msawsmenu); |
4575 | 2700 | wsmenu.add(secstrmenu); |
4576 | 2700 | wsmenu.add(dismenu); |
4577 | 2700 | wsmenu.add(analymenu); |
4578 | // No search services yet | |
4579 | // wsmenu.add(seqsrchmenu); | |
4580 | ||
4581 | 2700 | javax.swing.SwingUtilities.invokeLater(new Runnable() |
4582 | { | |
4583 | 2700 | @Override |
4584 | public void run() | |
4585 | { | |
4586 | 2700 | try |
4587 | { | |
4588 | 2700 | webService.removeAll(); |
4589 | // first, add discovered services onto the webservices menu | |
4590 | 2700 | if (wsmenu.size() > 0) |
4591 | { | |
4592 | 13500 | for (int i = 0, j = wsmenu.size(); i < j; i++) |
4593 | { | |
4594 | 10800 | webService.add(wsmenu.get(i)); |
4595 | } | |
4596 | } | |
4597 | else | |
4598 | { | |
4599 | 0 | webService.add(me.webServiceNoServices); |
4600 | } | |
4601 | // TODO: move into separate menu builder class. | |
4602 | { | |
4603 | // logic for 2.11.1.4 is | |
4604 | // always look to see if there is a discover. if there isn't | |
4605 | // we can't show any Jws2 services | |
4606 | // if there are services available, show them - regardless of | |
4607 | // the 'show JWS2 preference' | |
4608 | // if the discoverer is running then say so | |
4609 | // otherwise offer to trigger discovery if 'show JWS2' is not | |
4610 | // enabled | |
4611 | 2700 | Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); |
4612 | 2700 | if (jws2servs != null) |
4613 | { | |
4614 | 2700 | if (jws2servs.hasServices()) |
4615 | { | |
4616 | 1723 | jws2servs.attachWSMenuEntry(webService, me); |
4617 | 1717 | for (Jws2Instance sv : jws2servs.getServices()) |
4618 | { | |
4619 | 4515 | if (sv.description.toLowerCase(Locale.ROOT) |
4620 | .contains("jpred")) | |
4621 | { | |
4622 | 0 | for (JMenuItem jmi : legacyItems) |
4623 | { | |
4624 | 0 | jmi.setVisible(false); |
4625 | } | |
4626 | } | |
4627 | } | |
4628 | } | |
4629 | ||
4630 | 2694 | if (jws2servs.isRunning()) |
4631 | { | |
4632 | 721 | JMenuItem tm = new JMenuItem( |
4633 | "Still discovering JABA Services"); | |
4634 | 721 | tm.setEnabled(false); |
4635 | 721 | webService.add(tm); |
4636 | } | |
4637 | 1973 | else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true)) |
4638 | { | |
4639 | 0 | JMenuItem enableJws2 = new JMenuItem( |
4640 | "Discover Web Services"); | |
4641 | 0 | enableJws2.setToolTipText( |
4642 | "Select to start JABA Web Service discovery (or enable option in Web Service preferences)"); | |
4643 | 0 | enableJws2.setEnabled(true); |
4644 | 0 | enableJws2.addActionListener(new ActionListener() |
4645 | { | |
4646 | ||
4647 | 0 | @Override |
4648 | public void actionPerformed(ActionEvent e) | |
4649 | { | |
4650 | // start service discoverer, but ignore preference | |
4651 | 0 | Desktop.instance.startServiceDiscovery(false, |
4652 | true); | |
4653 | } | |
4654 | }); | |
4655 | 0 | webService.add(enableJws2); |
4656 | } | |
4657 | } | |
4658 | } | |
4659 | 2694 | build_urlServiceMenu(me.webService); |
4660 | 2694 | build_fetchdbmenu(webService); |
4661 | 2694 | for (JMenu item : wsmenu) |
4662 | { | |
4663 | 10776 | if (item.getItemCount() == 0) |
4664 | { | |
4665 | 3636 | item.setEnabled(false); |
4666 | } | |
4667 | else | |
4668 | { | |
4669 | 7140 | item.setEnabled(true); |
4670 | } | |
4671 | } | |
4672 | } catch (Exception e) | |
4673 | { | |
4674 | 6 | Console.debug( |
4675 | "Exception during web service menu building process.", | |
4676 | e); | |
4677 | } | |
4678 | } | |
4679 | }); | |
4680 | } catch (Exception e) | |
4681 | { | |
4682 | } | |
4683 | 2700 | buildingMenu = false; |
4684 | } | |
4685 | }).start(); | |
4686 | ||
4687 | } | |
4688 | ||
4689 | /** | |
4690 | * construct any groupURL type service menu entries. | |
4691 | * | |
4692 | * @param webService | |
4693 | */ | |
4694 | 2694 | protected void build_urlServiceMenu(JMenu webService) |
4695 | { | |
4696 | // TODO: remove this code when 2.7 is released | |
4697 | // DEBUG - alignmentView | |
4698 | /* | |
4699 | * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final | |
4700 | * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { | |
4701 | * | |
4702 | * @Override public void actionPerformed(ActionEvent e) { | |
4703 | * jalview.datamodel.AlignmentView | |
4704 | * .testSelectionViews(af.viewport.getAlignment(), | |
4705 | * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } | |
4706 | * | |
4707 | * }); webService.add(testAlView); | |
4708 | */ | |
4709 | // TODO: refactor to RestClient discoverer and merge menu entries for | |
4710 | // rest-style services with other types of analysis/calculation service | |
4711 | // SHmmr test client - still being implemented. | |
4712 | // DEBUG - alignmentView | |
4713 | ||
4714 | 2694 | for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient |
4715 | .getRestClients()) | |
4716 | { | |
4717 | 2694 | client.attachWSMenuEntry( |
4718 | JvSwingUtils.findOrCreateMenu(webService, client.getAction()), | |
4719 | this); | |
4720 | } | |
4721 | } | |
4722 | ||
4723 | /** | |
4724 | * Searches the alignment sequences for xRefs and builds the Show | |
4725 | * Cross-References menu (formerly called Show Products), with database | |
4726 | * sources for which cross-references are found (protein sources for a | |
4727 | * nucleotide alignment and vice versa) | |
4728 | * | |
4729 | * @return true if Show Cross-references menu should be enabled | |
4730 | */ | |
4731 | 672 | public boolean canShowProducts() |
4732 | { | |
4733 | 672 | SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); |
4734 | 672 | AlignmentI dataset = viewport.getAlignment().getDataset(); |
4735 | ||
4736 | 672 | showProducts.removeAll(); |
4737 | 672 | final boolean dna = viewport.getAlignment().isNucleotide(); |
4738 | ||
4739 | 672 | if (seqs == null || seqs.length == 0) |
4740 | { | |
4741 | // nothing to see here. | |
4742 | 0 | return false; |
4743 | } | |
4744 | ||
4745 | 672 | boolean showp = false; |
4746 | 672 | try |
4747 | { | |
4748 | 672 | List<String> ptypes = new CrossRef(seqs, dataset) |
4749 | .findXrefSourcesForSequences(dna); | |
4750 | ||
4751 | 672 | for (final String source : ptypes) |
4752 | { | |
4753 | 6 | showp = true; |
4754 | 6 | final AlignFrame af = this; |
4755 | 6 | JMenuItem xtype = new JMenuItem(source); |
4756 | 6 | xtype.addActionListener(new ActionListener() |
4757 | { | |
4758 | 0 | @Override |
4759 | public void actionPerformed(ActionEvent e) | |
4760 | { | |
4761 | 0 | showProductsFor(af.viewport.getSequenceSelection(), dna, |
4762 | source); | |
4763 | } | |
4764 | }); | |
4765 | 6 | showProducts.add(xtype); |
4766 | } | |
4767 | 672 | showProducts.setVisible(showp); |
4768 | 672 | showProducts.setEnabled(showp); |
4769 | } catch (Exception e) | |
4770 | { | |
4771 | 0 | Console.warn( |
4772 | "canShowProducts threw an exception - please report to help@jalview.org", | |
4773 | e); | |
4774 | 0 | return false; |
4775 | } | |
4776 | 672 | return showp; |
4777 | } | |
4778 | ||
4779 | /** | |
4780 | * Finds and displays cross-references for the selected sequences (protein | |
4781 | * products for nucleotide sequences, dna coding sequences for peptides). | |
4782 | * | |
4783 | * @param sel | |
4784 | * the sequences to show cross-references for | |
4785 | * @param dna | |
4786 | * true if from a nucleotide alignment (so showing proteins) | |
4787 | * @param source | |
4788 | * the database to show cross-references for | |
4789 | */ | |
4790 | 0 | protected void showProductsFor(final SequenceI[] sel, final boolean _odna, |
4791 | final String source) | |
4792 | { | |
4793 | 0 | new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this)) |
4794 | .start(); | |
4795 | } | |
4796 | ||
4797 | /** | |
4798 | * Construct and display a new frame containing the translation of this | |
4799 | * frame's DNA sequences to their aligned protein (amino acid) equivalents. | |
4800 | */ | |
4801 | 1 | @Override |
4802 | public void showTranslation_actionPerformed(GeneticCodeI codeTable) | |
4803 | { | |
4804 | 1 | AlignmentI al = null; |
4805 | 1 | try |
4806 | { | |
4807 | 1 | Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); |
4808 | ||
4809 | 1 | al = dna.translateCdna(codeTable); |
4810 | } catch (Exception ex) | |
4811 | { | |
4812 | 0 | Console.error("Exception during translation. Please report this !", |
4813 | ex); | |
4814 | 0 | final String msg = MessageManager.getString( |
4815 | "label.error_when_translating_sequences_submit_bug_report"); | |
4816 | 0 | final String errorTitle = MessageManager |
4817 | .getString("label.implementation_error") | |
4818 | + MessageManager.getString("label.translation_failed"); | |
4819 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, |
4820 | JvOptionPane.ERROR_MESSAGE); | |
4821 | 0 | return; |
4822 | } | |
4823 | 1 | if (al == null || al.getHeight() == 0) |
4824 | { | |
4825 | 0 | final String msg = MessageManager.getString( |
4826 | "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); | |
4827 | 0 | final String errorTitle = MessageManager |
4828 | .getString("label.translation_failed"); | |
4829 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, |
4830 | JvOptionPane.WARNING_MESSAGE); | |
4831 | } | |
4832 | else | |
4833 | { | |
4834 | 1 | AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); |
4835 | 1 | af.setFileFormat(this.currentFileFormat); |
4836 | 1 | final String newTitle = MessageManager |
4837 | .formatMessage("label.translation_of_params", new Object[] | |
4838 | { this.getTitle(), codeTable.getId() }); | |
4839 | 1 | af.setTitle(newTitle); |
4840 | 1 | if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) |
4841 | { | |
4842 | 1 | final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); |
4843 | 1 | viewport.openSplitFrame(af, new Alignment(seqs)); |
4844 | } | |
4845 | else | |
4846 | { | |
4847 | 0 | Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, |
4848 | DEFAULT_HEIGHT); | |
4849 | } | |
4850 | } | |
4851 | } | |
4852 | ||
4853 | /** | |
4854 | * Set the file format | |
4855 | * | |
4856 | * @param format | |
4857 | */ | |
4858 | 327 | public void setFileFormat(FileFormatI format) |
4859 | { | |
4860 | 327 | this.currentFileFormat = format; |
4861 | } | |
4862 | ||
4863 | /** | |
4864 | * Try to load a features file onto the alignment. | |
4865 | * | |
4866 | * @param file | |
4867 | * contents or path to retrieve file or a File object | |
4868 | * @param sourceType | |
4869 | * access mode of file (see jalview.io.AlignFile) | |
4870 | * @return true if features file was parsed correctly. | |
4871 | */ | |
4872 | 4 | public boolean parseFeaturesFile(Object file, DataSourceType sourceType) |
4873 | { | |
4874 | // BH 2018 | |
4875 | 4 | return avc.parseFeaturesFile(file, sourceType, |
4876 | Cache.getDefault("RELAXEDSEQIDMATCHING", false)); | |
4877 | ||
4878 | } | |
4879 | ||
4880 | 5 | @Override |
4881 | public void refreshFeatureUI(boolean enableIfNecessary) | |
4882 | { | |
4883 | // note - currently this is only still here rather than in the controller | |
4884 | // because of the featureSettings hard reference that is yet to be | |
4885 | // abstracted | |
4886 | 5 | if (enableIfNecessary) |
4887 | { | |
4888 | 5 | viewport.setShowSequenceFeatures(true); |
4889 | 5 | showSeqFeatures.setSelected(true); |
4890 | } | |
4891 | ||
4892 | } | |
4893 | ||
4894 | 0 | @Override |
4895 | public void dragEnter(DropTargetDragEvent evt) | |
4896 | { | |
4897 | } | |
4898 | ||
4899 | 0 | @Override |
4900 | public void dragExit(DropTargetEvent evt) | |
4901 | { | |
4902 | } | |
4903 | ||
4904 | 0 | @Override |
4905 | public void dragOver(DropTargetDragEvent evt) | |
4906 | { | |
4907 | } | |
4908 | ||
4909 | 0 | @Override |
4910 | public void dropActionChanged(DropTargetDragEvent evt) | |
4911 | { | |
4912 | } | |
4913 | ||
4914 | 0 | @Override |
4915 | public void drop(DropTargetDropEvent evt) | |
4916 | { | |
4917 | // JAL-1552 - acceptDrop required before getTransferable call for | |
4918 | // Java's Transferable for native dnd | |
4919 | 0 | evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); |
4920 | 0 | Transferable t = evt.getTransferable(); |
4921 | ||
4922 | 0 | final AlignFrame thisaf = this; |
4923 | 0 | final List<Object> files = new ArrayList<>(); |
4924 | 0 | List<DataSourceType> protocols = new ArrayList<>(); |
4925 | ||
4926 | 0 | try |
4927 | { | |
4928 | 0 | Desktop.transferFromDropTarget(files, protocols, evt, t); |
4929 | } catch (Exception e) | |
4930 | { | |
4931 | 0 | e.printStackTrace(); |
4932 | } | |
4933 | 0 | if (files != null) |
4934 | { | |
4935 | 0 | new Thread(new Runnable() |
4936 | { | |
4937 | 0 | @Override |
4938 | public void run() | |
4939 | { | |
4940 | 0 | try |
4941 | { | |
4942 | // check to see if any of these files have names matching sequences | |
4943 | // in | |
4944 | // the alignment | |
4945 | 0 | SequenceIdMatcher idm = new SequenceIdMatcher( |
4946 | viewport.getAlignment().getSequencesArray()); | |
4947 | /** | |
4948 | * Object[] { String,SequenceI} | |
4949 | */ | |
4950 | 0 | ArrayList<Object[]> filesmatched = new ArrayList<>(); |
4951 | 0 | ArrayList<Object[]> filesnotmatched = new ArrayList<>(); |
4952 | 0 | for (int i = 0; i < files.size(); i++) |
4953 | { | |
4954 | // BH 2018 | |
4955 | 0 | Object file = files.get(i); |
4956 | 0 | String fileName = file.toString(); |
4957 | 0 | String pdbfn = ""; |
4958 | 0 | DataSourceType protocol = (file instanceof File |
4959 | ? DataSourceType.FILE | |
4960 | : FormatAdapter.checkProtocol(fileName)); | |
4961 | 0 | if (protocol == DataSourceType.FILE) |
4962 | { | |
4963 | 0 | File fl; |
4964 | 0 | if (file instanceof File) |
4965 | { | |
4966 | 0 | fl = (File) file; |
4967 | 0 | Platform.cacheFileData(fl); |
4968 | } | |
4969 | else | |
4970 | { | |
4971 | 0 | fl = new File(fileName); |
4972 | } | |
4973 | 0 | pdbfn = fl.getName(); |
4974 | } | |
4975 | 0 | else if (protocol == DataSourceType.URL) |
4976 | { | |
4977 | 0 | URL url = new URL(fileName); |
4978 | 0 | pdbfn = url.getFile(); |
4979 | } | |
4980 | 0 | if (pdbfn.length() > 0) |
4981 | { | |
4982 | // attempt to find a match in the alignment | |
4983 | 0 | SequenceI[] mtch = idm.findAllIdMatches(pdbfn); |
4984 | 0 | int l = 0, c = pdbfn.indexOf("."); |
4985 | 0 | while (mtch == null && c != -1) |
4986 | { | |
4987 | 0 | do |
4988 | { | |
4989 | 0 | l = c; |
4990 | ? | } while ((c = pdbfn.indexOf(".", l)) > l); |
4991 | 0 | if (l > -1) |
4992 | { | |
4993 | 0 | pdbfn = pdbfn.substring(0, l); |
4994 | } | |
4995 | 0 | mtch = idm.findAllIdMatches(pdbfn); |
4996 | } | |
4997 | 0 | FileFormatI type = null; |
4998 | 0 | if (mtch != null) |
4999 | { | |
5000 | 0 | try |
5001 | { | |
5002 | 0 | type = new IdentifyFile().identify(file, protocol); |
5003 | } catch (Exception ex) | |
5004 | { | |
5005 | 0 | type = null; |
5006 | } | |
5007 | 0 | if (type != null && type.isStructureFile()) |
5008 | { | |
5009 | 0 | filesmatched.add(new Object[] { file, protocol, mtch }); |
5010 | 0 | continue; |
5011 | } | |
5012 | } | |
5013 | // File wasn't named like one of the sequences or wasn't a PDB | |
5014 | // file. | |
5015 | 0 | filesnotmatched.add(new Object[] { file, protocol, type }); |
5016 | } | |
5017 | } | |
5018 | 0 | int assocfiles = 0; |
5019 | 0 | if (filesmatched.size() > 0) |
5020 | { | |
5021 | 0 | boolean autoAssociate = Cache |
5022 | .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); | |
5023 | 0 | if (!autoAssociate) |
5024 | { | |
5025 | 0 | String msg = MessageManager.formatMessage( |
5026 | "label.automatically_associate_structure_files_with_sequences_same_name", | |
5027 | new Object[] | |
5028 | { Integer.valueOf(filesmatched.size()) | |
5029 | .toString() }); | |
5030 | 0 | String ttl = MessageManager.getString( |
5031 | "label.automatically_associate_structure_files_by_name"); | |
5032 | 0 | int choice = JvOptionPane.showConfirmDialog(thisaf, msg, |
5033 | ttl, JvOptionPane.YES_NO_OPTION); | |
5034 | 0 | autoAssociate = choice == JvOptionPane.YES_OPTION; |
5035 | } | |
5036 | 0 | if (autoAssociate) |
5037 | { | |
5038 | 0 | for (Object[] fm : filesmatched) |
5039 | { | |
5040 | // try and associate | |
5041 | // TODO: may want to set a standard ID naming formalism for | |
5042 | // associating PDB files which have no IDs. | |
5043 | 0 | for (SequenceI toassoc : (SequenceI[]) fm[2]) |
5044 | { | |
5045 | 0 | PDBEntry pe = new AssociatePdbFileWithSeq() |
5046 | .associatePdbWithSeq(fm[0].toString(), | |
5047 | (DataSourceType) fm[1], toassoc, false, | |
5048 | Desktop.instance); | |
5049 | 0 | if (pe != null) |
5050 | { | |
5051 | 0 | jalview.bin.Console.errPrintln("Associated file : " |
5052 | + (fm[0].toString()) + " with " | |
5053 | + toassoc.getDisplayId(true)); | |
5054 | 0 | assocfiles++; |
5055 | } | |
5056 | } | |
5057 | // TODO: do we need to update overview ? only if features are | |
5058 | // shown I guess | |
5059 | 0 | alignPanel.paintAlignment(true, false); |
5060 | } | |
5061 | } | |
5062 | else | |
5063 | { | |
5064 | /* | |
5065 | * add declined structures as sequences | |
5066 | */ | |
5067 | 0 | for (Object[] o : filesmatched) |
5068 | { | |
5069 | 0 | filesnotmatched.add(new Object[] { o[0], o[1] }); |
5070 | } | |
5071 | } | |
5072 | } | |
5073 | 0 | if (filesnotmatched.size() > 0) |
5074 | { | |
5075 | 0 | if (assocfiles > 0 && (Cache.getDefault( |
5076 | "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) | |
5077 | || JvOptionPane.showConfirmDialog(thisaf, | |
5078 | "<html>" + MessageManager.formatMessage( | |
5079 | "label.ignore_unmatched_dropped_files_info", | |
5080 | new Object[] | |
5081 | { Integer.valueOf( | |
5082 | filesnotmatched.size()) | |
5083 | .toString() }) | |
5084 | + "</html>", | |
5085 | MessageManager.getString( | |
5086 | "label.ignore_unmatched_dropped_files"), | |
5087 | JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) | |
5088 | { | |
5089 | 0 | return; |
5090 | } | |
5091 | 0 | for (Object[] fn : filesnotmatched) |
5092 | { | |
5093 | 0 | loadJalviewDataFile(fn[0], (DataSourceType) fn[1], |
5094 | (FileFormatI) fn[2], null); | |
5095 | } | |
5096 | ||
5097 | } | |
5098 | } catch (Exception ex) | |
5099 | { | |
5100 | 0 | ex.printStackTrace(); |
5101 | } | |
5102 | } | |
5103 | }).start(); | |
5104 | } | |
5105 | } | |
5106 | ||
5107 | /** | |
5108 | * Attempt to load a "dropped" file or URL string, by testing in turn for | |
5109 | * <ul> | |
5110 | * <li>an Annotation file</li> | |
5111 | * <li>a JNet file</li> | |
5112 | * <li>a features file</li> | |
5113 | * <li>else try to interpret as an alignment file</li> | |
5114 | * </ul> | |
5115 | * | |
5116 | * @param file | |
5117 | * either a filename or a URL string. | |
5118 | */ | |
5119 | 7 | public void loadJalviewDataFile(Object file, DataSourceType sourceType, |
5120 | FileFormatI format, SequenceI assocSeq) | |
5121 | { | |
5122 | // BH 2018 was String file | |
5123 | 7 | try |
5124 | { | |
5125 | 7 | if (sourceType == null) |
5126 | { | |
5127 | 2 | sourceType = FormatAdapter.checkProtocol(file); |
5128 | } | |
5129 | // if the file isn't identified, or not positively identified as some | |
5130 | // other filetype (PFAM is default unidentified alignment file type) then | |
5131 | // try to parse as annotation. | |
5132 | 7 | boolean isAnnotation = (format == null |
5133 | || FileFormat.Pfam.equals(format)) | |
5134 | ? new AnnotationFile().annotateAlignmentView(viewport, | |
5135 | file, sourceType) | |
5136 | : false; | |
5137 | ||
5138 | 7 | if (!isAnnotation) |
5139 | { | |
5140 | // first see if its a T-COFFEE score file | |
5141 | 3 | TCoffeeScoreFile tcf = null; |
5142 | 3 | try |
5143 | { | |
5144 | 3 | tcf = new TCoffeeScoreFile(file, sourceType); |
5145 | 3 | if (tcf.isValid()) |
5146 | { | |
5147 | 1 | if (tcf.annotateAlignment(viewport.getAlignment(), true)) |
5148 | { | |
5149 | 1 | buildColourMenu(); |
5150 | 1 | changeColour( |
5151 | new TCoffeeColourScheme(viewport.getAlignment())); | |
5152 | 1 | isAnnotation = true; |
5153 | 1 | setStatus(MessageManager.getString( |
5154 | "label.successfully_pasted_tcoffee_scores_to_alignment")); | |
5155 | } | |
5156 | else | |
5157 | { | |
5158 | // some problem - if no warning its probable that the ID matching | |
5159 | // process didn't work | |
5160 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
5161 | 0 | tcf.getWarningMessage() == null |
5162 | ? MessageManager.getString( | |
5163 | "label.check_file_matches_sequence_ids_alignment") | |
5164 | : tcf.getWarningMessage(), | |
5165 | MessageManager.getString( | |
5166 | "label.problem_reading_tcoffee_score_file"), | |
5167 | JvOptionPane.WARNING_MESSAGE); | |
5168 | } | |
5169 | } | |
5170 | else | |
5171 | { | |
5172 | 2 | tcf = null; |
5173 | } | |
5174 | } catch (Exception x) | |
5175 | { | |
5176 | 0 | Console.debug( |
5177 | "Exception when processing data source as T-COFFEE score file", | |
5178 | x); | |
5179 | 0 | tcf = null; |
5180 | } | |
5181 | 3 | if (tcf == null) |
5182 | { | |
5183 | // try to see if its a JNet 'concise' style annotation file *before* | |
5184 | // we | |
5185 | // try to parse it as a features file | |
5186 | 2 | if (format == null) |
5187 | { | |
5188 | 2 | format = new IdentifyFile().identify(file, sourceType); |
5189 | } | |
5190 | 2 | if (FileFormat.FeatureSettings == format) |
5191 | { | |
5192 | 0 | if (featureSettings != null) |
5193 | { | |
5194 | 0 | featureSettings.load(file, sourceType); |
5195 | } | |
5196 | else | |
5197 | { | |
5198 | 0 | FeatureSettings.loadFeatureSettingsFile(getFeatureRenderer(), |
5199 | fileObject, sourceType); | |
5200 | } | |
5201 | } | |
5202 | 2 | else if (FileFormat.ScoreMatrix == format) |
5203 | { | |
5204 | 0 | ScoreMatrixFile sm = new ScoreMatrixFile( |
5205 | new FileParse(file, sourceType)); | |
5206 | 0 | sm.parse(); |
5207 | // todo: i18n this message | |
5208 | 0 | setStatus(MessageManager.formatMessage( |
5209 | "label.successfully_loaded_matrix", | |
5210 | sm.getMatrixName())); | |
5211 | } | |
5212 | 2 | else if (FileFormat.Jnet.equals(format)) |
5213 | { | |
5214 | 0 | JPredFile predictions = new JPredFile(file, sourceType); |
5215 | 0 | new JnetAnnotationMaker(); |
5216 | 0 | JnetAnnotationMaker.add_annotation(predictions, |
5217 | viewport.getAlignment(), 0, false); | |
5218 | 0 | viewport.getAlignment().setupJPredAlignment(); |
5219 | 0 | isAnnotation = true; |
5220 | } | |
5221 | // else if (IdentifyFile.FeaturesFile.equals(format)) | |
5222 | 2 | else if (FileFormat.Features.equals(format)) |
5223 | { | |
5224 | 2 | if (parseFeaturesFile(file, sourceType)) |
5225 | { | |
5226 | 2 | SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); |
5227 | 2 | if (splitFrame != null) |
5228 | { | |
5229 | 0 | splitFrame.repaint(); |
5230 | } | |
5231 | else | |
5232 | { | |
5233 | 2 | alignPanel.paintAlignment(true, true); |
5234 | } | |
5235 | } | |
5236 | } | |
5237 | else | |
5238 | { | |
5239 | 0 | new FileLoader().LoadFile(viewport, file, sourceType, format); |
5240 | } | |
5241 | } | |
5242 | } | |
5243 | 7 | if (isAnnotation) |
5244 | { | |
5245 | ||
5246 | 5 | alignPanel.adjustAnnotationHeight(); |
5247 | 5 | viewport.updateSequenceIdColours(); |
5248 | 5 | viewport.updateAnnotationColours(); |
5249 | 5 | buildSortByAnnotationScoresMenu(); |
5250 | 5 | alignPanel.paintAlignment(true, true); |
5251 | } | |
5252 | } catch (Exception ex) | |
5253 | { | |
5254 | 0 | ex.printStackTrace(); |
5255 | } catch (OutOfMemoryError oom) | |
5256 | { | |
5257 | 0 | try |
5258 | { | |
5259 | 0 | System.gc(); |
5260 | } catch (Exception x) | |
5261 | { | |
5262 | } | |
5263 | 0 | new OOMWarning( |
5264 | "loading data " | |
5265 | 0 | + (sourceType != null |
5266 | 0 | ? (sourceType == DataSourceType.PASTE |
5267 | ? "from clipboard." | |
5268 | : "using " + sourceType + " from " | |
5269 | + file) | |
5270 | : ".") | |
5271 | 0 | + (format != null |
5272 | ? "(parsing as '" + format + "' file)" | |
5273 | : ""), | |
5274 | oom, Desktop.desktop); | |
5275 | } | |
5276 | } | |
5277 | ||
5278 | /** | |
5279 | * Method invoked by the ChangeListener on the tabbed pane, in other words | |
5280 | * when a different tabbed pane is selected by the user or programmatically. | |
5281 | */ | |
5282 | 160 | @Override |
5283 | public void tabSelectionChanged(int index) | |
5284 | { | |
5285 | 160 | if (index > -1) |
5286 | { | |
5287 | /* | |
5288 | * update current Overview window title (if there is one) | |
5289 | * to add view name "Original" if necessary | |
5290 | */ | |
5291 | 105 | alignPanel.setOverviewTitle(this); |
5292 | ||
5293 | /* | |
5294 | * switch panels and set Overview title (if there is one | |
5295 | * because it was opened automatically) | |
5296 | */ | |
5297 | 105 | alignPanel = alignPanels.get(index); |
5298 | 105 | alignPanel.setOverviewTitle(this); |
5299 | ||
5300 | 105 | viewport = alignPanel.av; |
5301 | 105 | avc.setViewportAndAlignmentPanel(viewport, alignPanel); |
5302 | 105 | setMenusFromViewport(viewport); |
5303 | 105 | if (featureSettings != null && featureSettings.isOpen() |
5304 | && featureSettings.fr.getViewport() != viewport) | |
5305 | { | |
5306 | 0 | if (viewport.isShowSequenceFeatures()) |
5307 | { | |
5308 | // refresh the featureSettings to reflect UI change | |
5309 | 0 | showFeatureSettingsUI(); |
5310 | } | |
5311 | else | |
5312 | { | |
5313 | // close feature settings for this view. | |
5314 | 0 | featureSettings.close(); |
5315 | } | |
5316 | } | |
5317 | ||
5318 | } | |
5319 | ||
5320 | /* | |
5321 | * 'focus' any colour slider that is open to the selected viewport | |
5322 | */ | |
5323 | 160 | if (viewport.getConservationSelected()) |
5324 | { | |
5325 | 2 | SliderPanel.setConservationSlider(alignPanel, |
5326 | viewport.getResidueShading(), alignPanel.getViewName()); | |
5327 | } | |
5328 | else | |
5329 | { | |
5330 | 158 | SliderPanel.hideConservationSlider(); |
5331 | } | |
5332 | 160 | if (viewport.getByConsensusSecondaryStructureSelected()) |
5333 | { | |
5334 | 0 | SliderPanel.setConsensusSecondaryStructureSlider(alignPanel, |
5335 | viewport.getResidueShading(), alignPanel.getViewName()); | |
5336 | } | |
5337 | else | |
5338 | { | |
5339 | 160 | SliderPanel.hideConsensusSecondaryStructureSlider(); |
5340 | } | |
5341 | 160 | if (viewport.getAbovePIDThreshold()) |
5342 | { | |
5343 | 2 | SliderPanel.setPIDSliderSource(alignPanel, |
5344 | viewport.getResidueShading(), alignPanel.getViewName()); | |
5345 | } | |
5346 | else | |
5347 | { | |
5348 | 158 | SliderPanel.hidePIDSlider(); |
5349 | } | |
5350 | ||
5351 | /* | |
5352 | * If there is a frame linked to this one in a SplitPane, switch it to the | |
5353 | * same view tab index. No infinite recursion of calls should happen, since | |
5354 | * tabSelectionChanged() should not get invoked on setting the selected | |
5355 | * index to an unchanged value. Guard against setting an invalid index | |
5356 | * before the new view peer tab has been created. | |
5357 | */ | |
5358 | 160 | final AlignViewportI peer = viewport.getCodingComplement(); |
5359 | 160 | if (peer != null) |
5360 | { | |
5361 | 0 | AlignFrame linkedAlignFrame = ((AlignViewport) peer) |
5362 | .getAlignPanel().alignFrame; | |
5363 | 0 | if (linkedAlignFrame.tabbedPane.getTabCount() > index) |
5364 | { | |
5365 | 0 | linkedAlignFrame.tabbedPane.setSelectedIndex(index); |
5366 | } | |
5367 | } | |
5368 | } | |
5369 | ||
5370 | /** | |
5371 | * On right mouse click on view tab, prompt for and set new view name. | |
5372 | */ | |
5373 | 0 | @Override |
5374 | public void tabbedPane_mousePressed(MouseEvent e) | |
5375 | { | |
5376 | 0 | if (e.isPopupTrigger()) |
5377 | { | |
5378 | 0 | String msg = MessageManager.getString("label.enter_view_name"); |
5379 | 0 | String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex()); |
5380 | 0 | String reply = JvOptionPane.showInputDialog(msg, ttl); |
5381 | ||
5382 | 0 | if (reply != null) |
5383 | { | |
5384 | 0 | viewport.setViewName(reply); |
5385 | // TODO warn if reply is in getExistingViewNames()? | |
5386 | 0 | tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); |
5387 | } | |
5388 | } | |
5389 | } | |
5390 | ||
5391 | 185 | public AlignViewport getCurrentView() |
5392 | { | |
5393 | 185 | return viewport; |
5394 | } | |
5395 | ||
5396 | /** | |
5397 | * Open the dialog for regex description parsing. | |
5398 | */ | |
5399 | 0 | @Override |
5400 | protected void extractScores_actionPerformed(ActionEvent e) | |
5401 | { | |
5402 | 0 | ParseProperties pp = new jalview.analysis.ParseProperties( |
5403 | viewport.getAlignment()); | |
5404 | // TODO: verify regex and introduce GUI dialog for version 2.5 | |
5405 | // if (pp.getScoresFromDescription("col", "score column ", | |
5406 | // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", | |
5407 | // true)>0) | |
5408 | 0 | if (pp.getScoresFromDescription("description column", |
5409 | "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0) | |
5410 | { | |
5411 | 0 | buildSortByAnnotationScoresMenu(); |
5412 | } | |
5413 | } | |
5414 | ||
5415 | /* | |
5416 | * (non-Javadoc) | |
5417 | * | |
5418 | * @see | |
5419 | * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent | |
5420 | * ) | |
5421 | */ | |
5422 | 0 | @Override |
5423 | protected void showDbRefs_actionPerformed(ActionEvent e) | |
5424 | { | |
5425 | 0 | viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); |
5426 | } | |
5427 | ||
5428 | /* | |
5429 | * (non-Javadoc) | |
5430 | * | |
5431 | * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. | |
5432 | * ActionEvent) | |
5433 | */ | |
5434 | 0 | @Override |
5435 | protected void showNpFeats_actionPerformed(ActionEvent e) | |
5436 | { | |
5437 | 0 | viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); |
5438 | } | |
5439 | ||
5440 | /** | |
5441 | * find the viewport amongst the tabs in this alignment frame and close that | |
5442 | * tab | |
5443 | * | |
5444 | * @param av | |
5445 | */ | |
5446 | 0 | public boolean closeView(AlignViewportI av) |
5447 | { | |
5448 | 0 | if (viewport == av) |
5449 | { | |
5450 | 0 | this.closeMenuItem_actionPerformed(false); |
5451 | 0 | return true; |
5452 | } | |
5453 | 0 | Component[] comp = tabbedPane.getComponents(); |
5454 | 0 | for (int i = 0; comp != null && i < comp.length; i++) |
5455 | { | |
5456 | 0 | if (comp[i] instanceof AlignmentPanel) |
5457 | { | |
5458 | 0 | if (((AlignmentPanel) comp[i]).av == av) |
5459 | { | |
5460 | // close the view. | |
5461 | 0 | closeView((AlignmentPanel) comp[i]); |
5462 | 0 | return true; |
5463 | } | |
5464 | } | |
5465 | } | |
5466 | 0 | return false; |
5467 | } | |
5468 | ||
5469 | 2694 | protected void build_fetchdbmenu(JMenu webService) |
5470 | { | |
5471 | // Temporary hack - DBRef Fetcher always top level ws entry. | |
5472 | // TODO We probably want to store a sequence database checklist in | |
5473 | // preferences and have checkboxes.. rather than individual sources selected | |
5474 | // here | |
5475 | 2694 | final JMenu rfetch = new JMenu( |
5476 | MessageManager.getString("action.fetch_db_references")); | |
5477 | 2694 | rfetch.setToolTipText(MessageManager.getString( |
5478 | "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); | |
5479 | 2694 | webService.add(rfetch); |
5480 | ||
5481 | 2694 | final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem( |
5482 | MessageManager.getString("option.trim_retrieved_seqs")); | |
5483 | 2694 | trimrs.setToolTipText( |
5484 | MessageManager.getString("label.trim_retrieved_sequences")); | |
5485 | 2694 | trimrs.setSelected( |
5486 | Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); | |
5487 | 2694 | trimrs.addActionListener(new ActionListener() |
5488 | { | |
5489 | 0 | @Override |
5490 | public void actionPerformed(ActionEvent e) | |
5491 | { | |
5492 | 0 | trimrs.setSelected(trimrs.isSelected()); |
5493 | 0 | Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, |
5494 | Boolean.valueOf(trimrs.isSelected()).toString()); | |
5495 | } | |
5496 | }); | |
5497 | 2694 | rfetch.add(trimrs); |
5498 | 2694 | JMenuItem fetchr = new JMenuItem( |
5499 | MessageManager.getString("label.standard_databases")); | |
5500 | 2694 | fetchr.setToolTipText( |
5501 | MessageManager.getString("label.fetch_embl_uniprot")); | |
5502 | 2694 | fetchr.addActionListener(new ActionListener() |
5503 | { | |
5504 | ||
5505 | 0 | @Override |
5506 | public void actionPerformed(ActionEvent e) | |
5507 | { | |
5508 | 0 | new Thread(new Runnable() |
5509 | { | |
5510 | 0 | @Override |
5511 | public void run() | |
5512 | { | |
5513 | 0 | boolean isNucleotide = alignPanel.alignFrame.getViewport() |
5514 | .getAlignment().isNucleotide(); | |
5515 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher( |
5516 | alignPanel.av.getSequenceSelection(), | |
5517 | alignPanel.alignFrame, null, | |
5518 | alignPanel.alignFrame.featureSettings, isNucleotide); | |
5519 | 0 | dbRefFetcher.addListener(new FetchFinishedListenerI() |
5520 | { | |
5521 | 0 | @Override |
5522 | public void finished() | |
5523 | { | |
5524 | ||
5525 | 0 | for (FeatureSettingsModelI srcSettings : dbRefFetcher |
5526 | .getFeatureSettingsModels()) | |
5527 | { | |
5528 | ||
5529 | 0 | alignPanel.av.mergeFeaturesStyle(srcSettings); |
5530 | } | |
5531 | 0 | AlignFrame.this.setMenusForViewport(); |
5532 | } | |
5533 | }); | |
5534 | 0 | dbRefFetcher.fetchDBRefs(false); |
5535 | } | |
5536 | }).start(); | |
5537 | ||
5538 | } | |
5539 | ||
5540 | }); | |
5541 | 2694 | rfetch.add(fetchr); |
5542 | 2694 | new Thread(new Runnable() |
5543 | { | |
5544 | 2694 | @Override |
5545 | public void run() | |
5546 | { | |
5547 | 2694 | final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher |
5548 | .getSequenceFetcherSingleton(); | |
5549 | 2694 | javax.swing.SwingUtilities.invokeLater(new Runnable() |
5550 | { | |
5551 | 2694 | @Override |
5552 | public void run() | |
5553 | { | |
5554 | 2694 | String[] dbclasses = sf.getNonAlignmentSources(); |
5555 | 2694 | List<DbSourceProxy> otherdb; |
5556 | 2694 | JMenu dfetch = new JMenu(); |
5557 | 2694 | JMenu ifetch = new JMenu(); |
5558 | 2694 | JMenuItem fetchr = null; |
5559 | 2694 | int comp = 0, icomp = 0, mcomp = 15; |
5560 | 2694 | String mname = null; |
5561 | 2694 | int dbi = 0; |
5562 | 2694 | for (String dbclass : dbclasses) |
5563 | { | |
5564 | 13470 | otherdb = sf.getSourceProxy(dbclass); |
5565 | // add a single entry for this class, or submenu allowing 'fetch | |
5566 | // all' or pick one | |
5567 | 13470 | if (otherdb == null || otherdb.size() < 1) |
5568 | { | |
5569 | 0 | continue; |
5570 | } | |
5571 | 13470 | if (mname == null) |
5572 | { | |
5573 | 2694 | mname = "From " + dbclass; |
5574 | } | |
5575 | 13470 | if (otherdb.size() == 1) |
5576 | { | |
5577 | 13470 | final DbSourceProxy[] dassource = otherdb |
5578 | .toArray(new DbSourceProxy[0]); | |
5579 | 13470 | DbSourceProxy src = otherdb.get(0); |
5580 | 13470 | fetchr = new JMenuItem(src.getDbSource()); |
5581 | 13470 | fetchr.addActionListener(new ActionListener() |
5582 | { | |
5583 | ||
5584 | 0 | @Override |
5585 | public void actionPerformed(ActionEvent e) | |
5586 | { | |
5587 | 0 | new Thread(new Runnable() |
5588 | { | |
5589 | ||
5590 | 0 | @Override |
5591 | public void run() | |
5592 | { | |
5593 | 0 | boolean isNucleotide = alignPanel.alignFrame |
5594 | .getViewport().getAlignment() | |
5595 | .isNucleotide(); | |
5596 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher( |
5597 | alignPanel.av.getSequenceSelection(), | |
5598 | alignPanel.alignFrame, dassource, | |
5599 | alignPanel.alignFrame.featureSettings, | |
5600 | isNucleotide); | |
5601 | 0 | dbRefFetcher |
5602 | .addListener(new FetchFinishedListenerI() | |
5603 | { | |
5604 | 0 | @Override |
5605 | public void finished() | |
5606 | { | |
5607 | 0 | FeatureSettingsModelI srcSettings = dassource[0] |
5608 | .getFeatureColourScheme(); | |
5609 | 0 | alignPanel.av.mergeFeaturesStyle( |
5610 | srcSettings); | |
5611 | 0 | AlignFrame.this.setMenusForViewport(); |
5612 | } | |
5613 | }); | |
5614 | 0 | dbRefFetcher.fetchDBRefs(false); |
5615 | } | |
5616 | }).start(); | |
5617 | } | |
5618 | ||
5619 | }); | |
5620 | 13470 | fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, |
5621 | MessageManager.formatMessage( | |
5622 | "label.fetch_retrieve_from", new Object[] | |
5623 | { src.getDbName() }))); | |
5624 | 13470 | dfetch.add(fetchr); |
5625 | 13470 | comp++; |
5626 | } | |
5627 | else | |
5628 | { | |
5629 | 0 | final DbSourceProxy[] dassource = otherdb |
5630 | .toArray(new DbSourceProxy[0]); | |
5631 | // fetch all entry | |
5632 | 0 | DbSourceProxy src = otherdb.get(0); |
5633 | 0 | fetchr = new JMenuItem(MessageManager |
5634 | .formatMessage("label.fetch_all_param", new Object[] | |
5635 | { src.getDbSource() })); | |
5636 | 0 | fetchr.addActionListener(new ActionListener() |
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, dassource, | |
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(JvSwingUtils.wrapTooltip(true, |
5671 | MessageManager.formatMessage( | |
5672 | "label.fetch_retrieve_from_all_sources", | |
5673 | new Object[] | |
5674 | { Integer.valueOf(otherdb.size()) | |
5675 | .toString(), | |
5676 | src.getDbSource(), src.getDbName() }))); | |
5677 | 0 | dfetch.add(fetchr); |
5678 | 0 | comp++; |
5679 | // and then build the rest of the individual menus | |
5680 | 0 | ifetch = new JMenu(MessageManager.formatMessage( |
5681 | "label.source_from_db_source", new Object[] | |
5682 | { src.getDbSource() })); | |
5683 | 0 | icomp = 0; |
5684 | 0 | String imname = null; |
5685 | 0 | int i = 0; |
5686 | 0 | for (DbSourceProxy sproxy : otherdb) |
5687 | { | |
5688 | 0 | String dbname = sproxy.getDbName(); |
5689 | 0 | String sname = dbname.length() > 5 |
5690 | ? dbname.substring(0, 5) + "..." | |
5691 | : dbname; | |
5692 | 0 | String msname = dbname.length() > 10 |
5693 | ? dbname.substring(0, 10) + "..." | |
5694 | : dbname; | |
5695 | 0 | if (imname == null) |
5696 | { | |
5697 | 0 | imname = MessageManager |
5698 | .formatMessage("label.from_msname", new Object[] | |
5699 | { sname }); | |
5700 | } | |
5701 | 0 | fetchr = new JMenuItem(msname); |
5702 | 0 | final DbSourceProxy[] dassrc = { sproxy }; |
5703 | 0 | fetchr.addActionListener(new ActionListener() |
5704 | { | |
5705 | ||
5706 | 0 | @Override |
5707 | public void actionPerformed(ActionEvent e) | |
5708 | { | |
5709 | 0 | new Thread(new Runnable() |
5710 | { | |
5711 | ||
5712 | 0 | @Override |
5713 | public void run() | |
5714 | { | |
5715 | 0 | boolean isNucleotide = alignPanel.alignFrame |
5716 | .getViewport().getAlignment() | |
5717 | .isNucleotide(); | |
5718 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher( |
5719 | alignPanel.av.getSequenceSelection(), | |
5720 | alignPanel.alignFrame, dassrc, | |
5721 | alignPanel.alignFrame.featureSettings, | |
5722 | isNucleotide); | |
5723 | 0 | dbRefFetcher |
5724 | .addListener(new FetchFinishedListenerI() | |
5725 | { | |
5726 | 0 | @Override |
5727 | public void finished() | |
5728 | { | |
5729 | 0 | AlignFrame.this.setMenusForViewport(); |
5730 | } | |
5731 | }); | |
5732 | 0 | dbRefFetcher.fetchDBRefs(false); |
5733 | } | |
5734 | }).start(); | |
5735 | } | |
5736 | ||
5737 | }); | |
5738 | 0 | fetchr.setToolTipText( |
5739 | "<html>" + MessageManager.formatMessage( | |
5740 | "label.fetch_retrieve_from", new Object[] | |
5741 | { dbname })); | |
5742 | 0 | ifetch.add(fetchr); |
5743 | 0 | ++i; |
5744 | 0 | if (++icomp >= mcomp || i == (otherdb.size())) |
5745 | { | |
5746 | 0 | ifetch.setText(MessageManager.formatMessage( |
5747 | "label.source_to_target", imname, sname)); | |
5748 | 0 | dfetch.add(ifetch); |
5749 | 0 | ifetch = new JMenu(); |
5750 | 0 | imname = null; |
5751 | 0 | icomp = 0; |
5752 | 0 | comp++; |
5753 | } | |
5754 | } | |
5755 | } | |
5756 | 13470 | ++dbi; |
5757 | 13470 | if (comp >= mcomp || dbi >= (dbclasses.length)) |
5758 | { | |
5759 | 2694 | dfetch.setText(MessageManager.formatMessage( |
5760 | "label.source_to_target", mname, dbclass)); | |
5761 | 2694 | rfetch.add(dfetch); |
5762 | 2694 | dfetch = new JMenu(); |
5763 | 2694 | mname = null; |
5764 | 2694 | comp = 0; |
5765 | } | |
5766 | } | |
5767 | } | |
5768 | }); | |
5769 | } | |
5770 | }).start(); | |
5771 | ||
5772 | } | |
5773 | ||
5774 | /** | |
5775 | * Left justify the whole alignment. | |
5776 | */ | |
5777 | 0 | @Override |
5778 | protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) | |
5779 | { | |
5780 | 0 | avc.justify_Region(true); |
5781 | } | |
5782 | ||
5783 | /** | |
5784 | * Right justify the whole alignment. | |
5785 | */ | |
5786 | 0 | @Override |
5787 | protected void justifyRightMenuItem_actionPerformed(ActionEvent e) | |
5788 | { | |
5789 | 0 | avc.justify_Region(false); |
5790 | } | |
5791 | ||
5792 | 12 | @Override |
5793 | public void setShowSeqFeatures(boolean b) | |
5794 | { | |
5795 | 12 | showSeqFeatures.setSelected(b); |
5796 | 12 | viewport.setShowSequenceFeatures(b); |
5797 | } | |
5798 | ||
5799 | /* | |
5800 | * (non-Javadoc) | |
5801 | * | |
5802 | * @see | |
5803 | * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. | |
5804 | * awt.event.ActionEvent) | |
5805 | */ | |
5806 | 0 | @Override |
5807 | protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) | |
5808 | { | |
5809 | 0 | viewport.setShowUnconserved(showNonconservedMenuItem.getState()); |
5810 | 0 | alignPanel.paintAlignment(false, false); |
5811 | } | |
5812 | ||
5813 | 0 | @Override |
5814 | protected void showStructureProvider_actionPerformed(ActionEvent e) | |
5815 | { | |
5816 | 0 | viewport.setShowStructureProvider(showStrucProvider.getState()); |
5817 | 0 | alignPanel.paintAlignment(false, false); |
5818 | ||
5819 | } | |
5820 | ||
5821 | 0 | @Override |
5822 | protected void updateShowSecondaryStructureMenu(JMenu showSS, | |
5823 | ButtonGroup ssButtonGroup) | |
5824 | { | |
5825 | ||
5826 | 0 | List<String> ssSources = new ArrayList<String>(); |
5827 | 0 | AlignmentAnnotation[] anns = alignPanel.getAlignment() |
5828 | .getAlignmentAnnotation(); | |
5829 | 0 | Map<String, JCheckBoxMenuItem> checkboxMap = getCheckboxesInMenu( |
5830 | showSS); | |
5831 | ||
5832 | 0 | ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(anns); |
5833 | ||
5834 | 0 | if (ssSources == null) |
5835 | { | |
5836 | 0 | showSS.removeAll(); |
5837 | 0 | ssButtonGroup.clearSelection(); |
5838 | 0 | return; |
5839 | } | |
5840 | ||
5841 | 0 | List<String> selectedCheckBoxes = getSelectedOptions(checkboxMap); |
5842 | ||
5843 | // Add checkboxes for categories | |
5844 | 0 | for (String ssSource : ssSources) |
5845 | { | |
5846 | ||
5847 | 0 | if (checkboxMap.get(ssSource) == null) |
5848 | { | |
5849 | 0 | JCheckBoxMenuItem checkBox = new JCheckBoxMenuItem(ssSource); |
5850 | 0 | checkBox.setSelected(false); |
5851 | ||
5852 | 0 | checkBox.addItemListener(e -> { |
5853 | 0 | if (e.getStateChange() == ItemEvent.SELECTED) |
5854 | { | |
5855 | ||
5856 | 0 | showOrHideSecondaryStructureForSource(ssSource, true); |
5857 | ||
5858 | } | |
5859 | else | |
5860 | { | |
5861 | ||
5862 | 0 | showOrHideSecondaryStructureForSource(ssSource, false); |
5863 | ||
5864 | } | |
5865 | }); | |
5866 | 0 | showSS.add(checkBox); |
5867 | } | |
5868 | } | |
5869 | // Iterate over the keys of checkboxMap | |
5870 | 0 | for (String key : checkboxMap.keySet()) |
5871 | { | |
5872 | // Check if the key is not in ssSources | |
5873 | 0 | if (!ssSources.contains(key)) |
5874 | { | |
5875 | 0 | showSS.remove(checkboxMap.get(key)); |
5876 | 0 | checkboxMap.remove(key); |
5877 | 0 | selectedCheckBoxes.remove(key); |
5878 | } | |
5879 | 0 | if (selectedCheckBoxes.contains(key)) |
5880 | { | |
5881 | 0 | checkboxMap.get(key).setSelected(true); |
5882 | } | |
5883 | else | |
5884 | { | |
5885 | 0 | checkboxMap.get(key).setSelected(false); |
5886 | } | |
5887 | ||
5888 | 0 | ssButtonGroup.clearSelection(); |
5889 | } | |
5890 | ||
5891 | } | |
5892 | ||
5893 | 0 | private List<String> getSelectedOptions( |
5894 | Map<String, JCheckBoxMenuItem> checkboxMap) | |
5895 | { | |
5896 | 0 | List<String> selectedOptions = new ArrayList<>(); |
5897 | 0 | for (String key : checkboxMap.keySet()) |
5898 | { | |
5899 | 0 | JCheckBoxMenuItem checkbox = checkboxMap.get(key); |
5900 | 0 | if (checkbox.isSelected()) |
5901 | { | |
5902 | 0 | selectedOptions.add(key); |
5903 | } | |
5904 | } | |
5905 | 0 | return selectedOptions; |
5906 | } | |
5907 | ||
5908 | 0 | private Map<String, JCheckBoxMenuItem> getCheckboxesInMenu(JMenu menu) |
5909 | { | |
5910 | 0 | Map<String, JCheckBoxMenuItem> checkboxMap = new HashMap<>(); |
5911 | 0 | for (Component component : menu.getMenuComponents()) |
5912 | { | |
5913 | 0 | if (component instanceof JCheckBoxMenuItem) |
5914 | { | |
5915 | 0 | JCheckBoxMenuItem checkbox = (JCheckBoxMenuItem) component; |
5916 | 0 | checkboxMap.put(checkbox.getText(), checkbox); |
5917 | } | |
5918 | } | |
5919 | 0 | return checkboxMap; |
5920 | } | |
5921 | ||
5922 | 0 | @Override |
5923 | protected void showOrHideSecondaryStructureForSource( | |
5924 | String ssSourceSelection, boolean visible) | |
5925 | { | |
5926 | ||
5927 | 0 | String noneOption = MessageManager |
5928 | .getString("option.ss_providers_none"); | |
5929 | 0 | String allOption = MessageManager.getString("option.ss_providers_all"); |
5930 | ||
5931 | 0 | AlignmentAnnotation[] annotations = alignPanel.getAlignment() |
5932 | .getAlignmentAnnotation(); | |
5933 | ||
5934 | 0 | for (AlignmentAnnotation aa : annotations) |
5935 | { | |
5936 | ||
5937 | 0 | if (aa.groupRef != null) |
5938 | { | |
5939 | 0 | continue; |
5940 | } | |
5941 | ||
5942 | 0 | boolean isSSConsensus = aa.label.startsWith( |
5943 | MessageManager.getString("label.ssconsensus_label")); | |
5944 | 0 | boolean matchesSSSourceSelection = aa.description |
5945 | .startsWith(ssSourceSelection); | |
5946 | ||
5947 | 0 | if (isSSConsensus && (matchesSSSourceSelection |
5948 | || ssSourceSelection.equals(noneOption))) | |
5949 | { | |
5950 | ||
5951 | 0 | if (ssSourceSelection.equals(allOption)) |
5952 | { | |
5953 | 0 | aa.visible = true; |
5954 | 0 | break; |
5955 | } | |
5956 | ||
5957 | 0 | if (!aa.description.startsWith(allOption)) |
5958 | 0 | aa.visible = visible; |
5959 | ||
5960 | } | |
5961 | ||
5962 | 0 | for (String label : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) |
5963 | { | |
5964 | ||
5965 | 0 | if (label.equals(aa.label)) |
5966 | { | |
5967 | ||
5968 | 0 | String ssSource = AlignmentUtils |
5969 | .extractSSSourceFromAnnotationDescription(aa); | |
5970 | ||
5971 | 0 | if (ssSource != null && (ssSource.equals(ssSourceSelection) |
5972 | || ssSourceSelection.equals(noneOption))) | |
5973 | { | |
5974 | 0 | aa.visible = visible; |
5975 | } | |
5976 | } | |
5977 | } | |
5978 | ||
5979 | } | |
5980 | ||
5981 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
5982 | 0 | alignPanel.updateAnnotation(); |
5983 | 0 | alignPanel.paintAlignment(true, true); |
5984 | ||
5985 | } | |
5986 | ||
5987 | 0 | protected void showSSConsensus_actionPerformed(ActionEvent e) |
5988 | { | |
5989 | 0 | viewport.setShowSSConsensus(showSSConsensus.getState()); |
5990 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
5991 | } | |
5992 | ||
5993 | /* | |
5994 | * (non-Javadoc) | |
5995 | * | |
5996 | * @see | |
5997 | * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event | |
5998 | * .ActionEvent) | |
5999 | */ | |
6000 | 0 | @Override |
6001 | protected void showGroupConsensus_actionPerformed(ActionEvent e) | |
6002 | { | |
6003 | 0 | viewport.setShowGroupConsensus(showGroupConsensus.getState()); |
6004 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
6005 | ||
6006 | } | |
6007 | ||
6008 | 0 | @Override |
6009 | protected void showGroupSSConsensus_actionPerformed(ActionEvent e) | |
6010 | { | |
6011 | 0 | viewport.setShowGroupSSConsensus(showGroupSSConsensus.getState()); |
6012 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
6013 | ||
6014 | } | |
6015 | ||
6016 | /* | |
6017 | * (non-Javadoc) | |
6018 | * | |
6019 | * @see | |
6020 | * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt | |
6021 | * .event.ActionEvent) | |
6022 | */ | |
6023 | 0 | @Override |
6024 | protected void showGroupConservation_actionPerformed(ActionEvent e) | |
6025 | { | |
6026 | 0 | viewport.setShowGroupConservation(showGroupConservation.getState()); |
6027 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
6028 | } | |
6029 | ||
6030 | /* | |
6031 | * (non-Javadoc) | |
6032 | * | |
6033 | * @see | |
6034 | * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt | |
6035 | * .event.ActionEvent) | |
6036 | */ | |
6037 | 0 | @Override |
6038 | protected void showConsensusHistogram_actionPerformed(ActionEvent e) | |
6039 | { | |
6040 | 0 | viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); |
6041 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
6042 | } | |
6043 | ||
6044 | ||
6045 | /* | |
6046 | * (non-Javadoc) | |
6047 | * | |
6048 | * @see | |
6049 | * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt | |
6050 | * .event.ActionEvent) | |
6051 | */ | |
6052 | 0 | @Override |
6053 | protected void showSequenceLogo_actionPerformed(ActionEvent e) | |
6054 | { | |
6055 | 0 | viewport.setShowSequenceLogo(showSequenceLogo.getState()); |
6056 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
6057 | } | |
6058 | ||
6059 | 0 | @Override |
6060 | protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) | |
6061 | { | |
6062 | 0 | showSequenceLogo.setState(true); |
6063 | 0 | viewport.setShowSequenceLogo(true); |
6064 | 0 | viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); |
6065 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
6066 | } | |
6067 | ||
6068 | 0 | @Override |
6069 | protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) | |
6070 | { | |
6071 | 0 | alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
6072 | } | |
6073 | ||
6074 | /* | |
6075 | * (non-Javadoc) | |
6076 | * | |
6077 | * @see | |
6078 | * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt | |
6079 | * .event.ActionEvent) | |
6080 | */ | |
6081 | 0 | @Override |
6082 | protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) | |
6083 | { | |
6084 | 0 | if (avc.makeGroupsFromSelection()) |
6085 | { | |
6086 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
6087 | 0 | alignPanel.updateAnnotation(); |
6088 | 0 | alignPanel.paintAlignment(true, |
6089 | viewport.needToUpdateStructureViews()); | |
6090 | } | |
6091 | } | |
6092 | ||
6093 | 0 | public void clearAlignmentSeqRep() |
6094 | { | |
6095 | // TODO refactor alignmentseqrep to controller | |
6096 | 0 | if (viewport.getAlignment().hasSeqrep()) |
6097 | { | |
6098 | 0 | viewport.getAlignment().setSeqrep(null); |
6099 | 0 | PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
6100 | 0 | alignPanel.updateAnnotation(); |
6101 | 0 | alignPanel.paintAlignment(true, true); |
6102 | } | |
6103 | } | |
6104 | ||
6105 | 0 | @Override |
6106 | protected void createGroup_actionPerformed(ActionEvent e) | |
6107 | { | |
6108 | 0 | if (avc.createGroup()) |
6109 | { | |
6110 | 0 | if (applyAutoAnnotationSettings.isSelected()) |
6111 | { | |
6112 | 0 | alignPanel.updateAnnotation(true, false); |
6113 | } | |
6114 | 0 | alignPanel.alignmentChanged(); |
6115 | } | |
6116 | } | |
6117 | ||
6118 | 0 | @Override |
6119 | protected void unGroup_actionPerformed(ActionEvent e) | |
6120 | { | |
6121 | 0 | if (avc.unGroup()) |
6122 | { | |
6123 | 0 | alignPanel.alignmentChanged(); |
6124 | } | |
6125 | } | |
6126 | ||
6127 | /** | |
6128 | * make the given alignmentPanel the currently selected tab | |
6129 | * | |
6130 | * @param alignmentPanel | |
6131 | */ | |
6132 | 0 | public void setDisplayedView(AlignmentPanel alignmentPanel) |
6133 | { | |
6134 | 0 | if (!viewport.getSequenceSetId() |
6135 | .equals(alignmentPanel.av.getSequenceSetId())) | |
6136 | { | |
6137 | 0 | throw new Error(MessageManager.getString( |
6138 | "error.implementation_error_cannot_show_view_alignment_frame")); | |
6139 | } | |
6140 | 0 | if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels |
6141 | .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) | |
6142 | { | |
6143 | 0 | tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); |
6144 | } | |
6145 | } | |
6146 | ||
6147 | /** | |
6148 | * Action on selection of menu options to Show or Hide annotations. | |
6149 | * | |
6150 | * @param visible | |
6151 | * @param forSequences | |
6152 | * update sequence-related annotations | |
6153 | * @param forAlignment | |
6154 | * update non-sequence-related annotations | |
6155 | */ | |
6156 | 302 | @Override |
6157 | public void setAnnotationsVisibility(boolean visible, | |
6158 | boolean forSequences, boolean forAlignment) | |
6159 | { | |
6160 | 302 | AlignmentAnnotation[] anns = alignPanel.getAlignment() |
6161 | .getAlignmentAnnotation(); | |
6162 | 302 | if (anns == null) |
6163 | { | |
6164 | 0 | return; |
6165 | } | |
6166 | 302 | for (AlignmentAnnotation aa : anns) |
6167 | { | |
6168 | /* | |
6169 | * don't display non-positional annotations on an alignment | |
6170 | */ | |
6171 | 1138 | if (aa.annotations == null) |
6172 | { | |
6173 | 0 | continue; |
6174 | } | |
6175 | 1138 | boolean apply = (aa.sequenceRef == null && forAlignment) |
6176 | || (aa.sequenceRef != null && forSequences); | |
6177 | 1138 | if (apply) |
6178 | { | |
6179 | 569 | aa.visible = visible; |
6180 | } | |
6181 | } | |
6182 | 302 | alignPanel.validateAnnotationDimensions(true); |
6183 | // TODO this triggers relayout of annotation panel - otherwise annotation | |
6184 | // label height is different to panel height | |
6185 | 302 | alignPanel.fontChanged(); |
6186 | 302 | alignPanel.alignmentChanged(); |
6187 | } | |
6188 | ||
6189 | /** | |
6190 | * Store selected annotation sort order for the view and repaint. | |
6191 | */ | |
6192 | 0 | @Override |
6193 | protected void sortAnnotations_actionPerformed() | |
6194 | { | |
6195 | 0 | this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); |
6196 | 0 | this.alignPanel.av |
6197 | .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); | |
6198 | 0 | alignPanel.paintAlignment(false, false); |
6199 | } | |
6200 | ||
6201 | /** | |
6202 | * | |
6203 | * @return alignment panels in this alignment frame | |
6204 | */ | |
6205 | 235 | public List<? extends AlignmentViewPanel> getAlignPanels() |
6206 | { | |
6207 | // alignPanels is never null | |
6208 | // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; | |
6209 | 235 | return alignPanels; |
6210 | } | |
6211 | ||
6212 | /** | |
6213 | * Open a new alignment window, with the cDNA associated with this (protein) | |
6214 | * alignment, aligned as is the protein. | |
6215 | */ | |
6216 | 0 | protected void viewAsCdna_actionPerformed() |
6217 | { | |
6218 | // TODO no longer a menu action - refactor as required | |
6219 | 0 | final AlignmentI alignment = getViewport().getAlignment(); |
6220 | 0 | List<AlignedCodonFrame> mappings = alignment.getCodonFrames(); |
6221 | 0 | if (mappings == null) |
6222 | { | |
6223 | 0 | return; |
6224 | } | |
6225 | 0 | List<SequenceI> cdnaSeqs = new ArrayList<>(); |
6226 | 0 | for (SequenceI aaSeq : alignment.getSequences()) |
6227 | { | |
6228 | 0 | for (AlignedCodonFrame acf : mappings) |
6229 | { | |
6230 | 0 | SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); |
6231 | 0 | if (dnaSeq != null) |
6232 | { | |
6233 | /* | |
6234 | * There is a cDNA mapping for this protein sequence - add to new | |
6235 | * alignment. It will share the same dataset sequence as other mapped | |
6236 | * cDNA (no new mappings need to be created). | |
6237 | */ | |
6238 | 0 | final Sequence newSeq = new Sequence(dnaSeq); |
6239 | 0 | newSeq.setDatasetSequence(dnaSeq); |
6240 | 0 | cdnaSeqs.add(newSeq); |
6241 | } | |
6242 | } | |
6243 | } | |
6244 | 0 | if (cdnaSeqs.size() == 0) |
6245 | { | |
6246 | // show a warning dialog no mapped cDNA | |
6247 | 0 | return; |
6248 | } | |
6249 | 0 | AlignmentI cdna = new Alignment( |
6250 | cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()])); | |
6251 | 0 | GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, |
6252 | AlignFrame.DEFAULT_HEIGHT); | |
6253 | 0 | cdna.alignAs(alignment); |
6254 | 0 | String newtitle = "cDNA " + MessageManager.getString("label.for") + " " |
6255 | + this.title; | |
6256 | 0 | Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH, |
6257 | AlignFrame.DEFAULT_HEIGHT); | |
6258 | } | |
6259 | ||
6260 | /** | |
6261 | * Set visibility of dna/protein complement view (available when shown in a | |
6262 | * split frame). | |
6263 | * | |
6264 | * @param show | |
6265 | */ | |
6266 | 0 | @Override |
6267 | protected void showComplement_actionPerformed(boolean show) | |
6268 | { | |
6269 | 0 | SplitContainerI sf = getSplitViewContainer(); |
6270 | 0 | if (sf != null) |
6271 | { | |
6272 | 0 | sf.setComplementVisible(this, show); |
6273 | } | |
6274 | } | |
6275 | ||
6276 | /** | |
6277 | * Generate the reverse (optionally complemented) of the selected sequences, | |
6278 | * and add them to the alignment | |
6279 | */ | |
6280 | 0 | @Override |
6281 | protected void showReverse_actionPerformed(boolean complement) | |
6282 | { | |
6283 | 0 | AlignmentI al = null; |
6284 | 0 | try |
6285 | { | |
6286 | 0 | Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); |
6287 | 0 | al = dna.reverseCdna(complement); |
6288 | 0 | viewport.addAlignment(al, ""); |
6289 | 0 | addHistoryItem(new EditCommand( |
6290 | MessageManager.getString("label.add_sequences"), Action.PASTE, | |
6291 | al.getSequencesArray(), 0, al.getWidth(), | |
6292 | viewport.getAlignment())); | |
6293 | } catch (Exception ex) | |
6294 | { | |
6295 | 0 | jalview.bin.Console.errPrintln(ex.getMessage()); |
6296 | 0 | return; |
6297 | } | |
6298 | } | |
6299 | ||
6300 | /** | |
6301 | * Try to run a script in the Groovy console, having first ensured that this | |
6302 | * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to | |
6303 | * be targeted at this alignment. | |
6304 | */ | |
6305 | 0 | @Override |
6306 | protected void runGroovy_actionPerformed() | |
6307 | { | |
6308 | 0 | Jalview.getInstance().setCurrentAlignFrame(this); |
6309 | 0 | groovy.console.ui.Console console = Desktop.getGroovyConsole(); |
6310 | 0 | if (console != null) |
6311 | { | |
6312 | 0 | try |
6313 | { | |
6314 | 0 | console.setVariable(JalviewObjectI.currentAlFrameName, this); |
6315 | 0 | console.runScript(); |
6316 | } catch (Exception ex) | |
6317 | { | |
6318 | 0 | jalview.bin.Console.errPrintln((ex.toString())); |
6319 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
6320 | MessageManager.getString("label.couldnt_run_groovy_script"), | |
6321 | MessageManager.getString("label.groovy_support_failed"), | |
6322 | JvOptionPane.ERROR_MESSAGE); | |
6323 | } | |
6324 | } | |
6325 | else | |
6326 | { | |
6327 | 0 | jalview.bin.Console |
6328 | .errPrintln("Can't run Groovy script as console not found"); | |
6329 | } | |
6330 | } | |
6331 | ||
6332 | /** | |
6333 | * Hides columns containing (or not containing) a specified feature, provided | |
6334 | * that would not leave all columns hidden | |
6335 | * | |
6336 | * @param featureType | |
6337 | * @param columnsContaining | |
6338 | * @return | |
6339 | */ | |
6340 | 7 | public boolean hideFeatureColumns(String featureType, |
6341 | boolean columnsContaining) | |
6342 | { | |
6343 | 7 | boolean notForHiding = avc.markColumnsContainingFeatures( |
6344 | columnsContaining, false, false, featureType); | |
6345 | 7 | if (notForHiding) |
6346 | { | |
6347 | 5 | if (avc.markColumnsContainingFeatures(!columnsContaining, false, |
6348 | false, featureType)) | |
6349 | { | |
6350 | 4 | getViewport().hideSelectedColumns(); |
6351 | 4 | return true; |
6352 | } | |
6353 | } | |
6354 | 3 | return false; |
6355 | } | |
6356 | ||
6357 | 0 | @Override |
6358 | protected void selectHighlightedColumns_actionPerformed( | |
6359 | ActionEvent actionEvent) | |
6360 | { | |
6361 | // include key modifier check in case user selects from menu | |
6362 | 0 | avc.markHighlightedColumns( |
6363 | (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true, | |
6364 | (actionEvent.getModifiers() & (ActionEvent.META_MASK | |
6365 | | ActionEvent.CTRL_MASK)) != 0); | |
6366 | } | |
6367 | ||
6368 | 0 | @Override |
6369 | protected void copyHighlightedColumns_actionPerformed( | |
6370 | ActionEvent actionEvent) | |
6371 | { | |
6372 | 0 | avc.copyHighlightedRegionsToClipboard(); |
6373 | } | |
6374 | ||
6375 | /** | |
6376 | * Rebuilds the Colour menu, including any user-defined colours which have | |
6377 | * been loaded either on startup or during the session | |
6378 | */ | |
6379 | 453 | public void buildColourMenu() |
6380 | { | |
6381 | 453 | colourMenu.removeAll(); |
6382 | ||
6383 | 453 | colourMenu.add(applyToAllGroups); |
6384 | 453 | colourMenu.add(textColour); |
6385 | 453 | colourMenu.addSeparator(); |
6386 | ||
6387 | 453 | ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, |
6388 | viewport.getAlignment(), false); | |
6389 | ||
6390 | 453 | colourMenu.add(annotationColour); |
6391 | 453 | bg.add(annotationColour); |
6392 | 453 | colourMenu.addSeparator(); |
6393 | 453 | colourMenu.add(conservationMenuItem); |
6394 | 453 | colourMenu.add(modifyConservation); |
6395 | 453 | colourMenu.add(byConsensusSecondaryStructureMenuItem); |
6396 | 453 | colourMenu.add(modifyConsensusSecondaryStructureThreshold); |
6397 | 453 | colourMenu.add(abovePIDThreshold); |
6398 | 453 | colourMenu.add(modifyPID); |
6399 | ||
6400 | 453 | ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); |
6401 | 453 | ColourMenuHelper.setColourSelected(colourMenu, colourScheme); |
6402 | } | |
6403 | ||
6404 | /** | |
6405 | * Open a dialog (if not already open) that allows the user to select and | |
6406 | * calculate PCA or Tree analysis | |
6407 | */ | |
6408 | 0 | protected void openTreePcaDialog() |
6409 | { | |
6410 | 0 | if (alignPanel.getCalculationDialog() == null) |
6411 | { | |
6412 | 0 | new CalculationChooser(AlignFrame.this); |
6413 | } | |
6414 | } | |
6415 | ||
6416 | 0 | @Override |
6417 | protected void loadVcf_actionPerformed() | |
6418 | { | |
6419 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
6420 | Cache.getProperty("LAST_DIRECTORY")); | |
6421 | 0 | chooser.setFileView(new JalviewFileView()); |
6422 | 0 | chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); |
6423 | 0 | chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); |
6424 | 0 | final AlignFrame us = this; |
6425 | 0 | chooser.setResponseHandler(0, () -> { |
6426 | 0 | String choice = chooser.getSelectedFile().getPath(); |
6427 | 0 | Cache.setProperty("LAST_DIRECTORY", choice); |
6428 | 0 | SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); |
6429 | 0 | new VCFLoader(choice).loadVCF(seqs, us); |
6430 | }); | |
6431 | 0 | chooser.showOpenDialog(null); |
6432 | ||
6433 | } | |
6434 | ||
6435 | private Rectangle lastFeatureSettingsBounds = null; | |
6436 | ||
6437 | 1 | @Override |
6438 | public void setFeatureSettingsGeometry(Rectangle bounds) | |
6439 | { | |
6440 | 1 | lastFeatureSettingsBounds = bounds; |
6441 | } | |
6442 | ||
6443 | 2 | @Override |
6444 | public Rectangle getFeatureSettingsGeometry() | |
6445 | { | |
6446 | 2 | return lastFeatureSettingsBounds; |
6447 | } | |
6448 | ||
6449 | } | |
6450 | ||
6451 | class PrintThread extends Thread | |
6452 | { | |
6453 | AlignmentPanel ap; | |
6454 | ||
6455 | 0 | public PrintThread(AlignmentPanel ap) |
6456 | { | |
6457 | 0 | this.ap = ap; |
6458 | } | |
6459 | ||
6460 | static PageFormat pf; | |
6461 | ||
6462 | 0 | @Override |
6463 | public void run() | |
6464 | { | |
6465 | 0 | PrinterJob printJob = PrinterJob.getPrinterJob(); |
6466 | ||
6467 | 0 | if (pf != null) |
6468 | { | |
6469 | 0 | printJob.setPrintable(ap, pf); |
6470 | } | |
6471 | else | |
6472 | { | |
6473 | 0 | printJob.setPrintable(ap); |
6474 | } | |
6475 | ||
6476 | 0 | if (printJob.printDialog()) |
6477 | { | |
6478 | 0 | try |
6479 | { | |
6480 | 0 | printJob.print(); |
6481 | } catch (Exception PrintException) | |
6482 | { | |
6483 | 0 | PrintException.printStackTrace(); |
6484 | } | |
6485 | } | |
6486 | } | |
6487 | } |