Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
PCAPanel | 66 | 187 | 67 | ||
PCAPanel.PCAPrinter | 386 | 18 | 7 |
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.Dimension; | |
26 | import java.awt.Graphics; | |
27 | import java.awt.event.ActionEvent; | |
28 | import java.awt.event.ActionListener; | |
29 | import java.awt.print.PageFormat; | |
30 | import java.awt.print.Printable; | |
31 | import java.awt.print.PrinterException; | |
32 | import java.awt.print.PrinterJob; | |
33 | ||
34 | import javax.swing.ButtonGroup; | |
35 | import javax.swing.JLabel; | |
36 | import javax.swing.JMenuItem; | |
37 | import javax.swing.JProgressBar; | |
38 | import javax.swing.JRadioButtonMenuItem; | |
39 | import javax.swing.SwingConstants; | |
40 | import javax.swing.event.InternalFrameAdapter; | |
41 | import javax.swing.event.InternalFrameEvent; | |
42 | ||
43 | import jalview.analysis.scoremodels.ScoreModels; | |
44 | import jalview.api.AlignViewportI; | |
45 | import jalview.api.analysis.ScoreModelI; | |
46 | import jalview.api.analysis.SimilarityParamsI; | |
47 | import jalview.bin.Console; | |
48 | import jalview.datamodel.Alignment; | |
49 | import jalview.datamodel.AlignmentI; | |
50 | import jalview.datamodel.AlignmentView; | |
51 | import jalview.datamodel.HiddenColumns; | |
52 | import jalview.datamodel.SequenceI; | |
53 | import jalview.gui.ImageExporter.ImageWriterI; | |
54 | import jalview.gui.JalviewColourChooser.ColourChooserListener; | |
55 | import jalview.io.exceptions.ImageOutputException; | |
56 | import jalview.jbgui.GPCAPanel; | |
57 | import jalview.math.RotatableMatrix.Axis; | |
58 | import jalview.util.ImageMaker; | |
59 | import jalview.util.MessageManager; | |
60 | import jalview.viewmodel.AlignmentViewport; | |
61 | import jalview.viewmodel.PCAModel; | |
62 | ||
63 | /** | |
64 | * The panel holding the Principal Component Analysis 3-D visualisation | |
65 | */ | |
66 | public class PCAPanel extends GPCAPanel | |
67 | implements Runnable, IProgressIndicator | |
68 | { | |
69 | private static final int MIN_WIDTH = 470; | |
70 | ||
71 | private static final int MIN_HEIGHT = 250; | |
72 | ||
73 | private RotatableCanvas rc; | |
74 | ||
75 | AlignmentPanel ap; | |
76 | ||
77 | AlignmentViewport av; | |
78 | ||
79 | private PCAModel pcaModel; | |
80 | ||
81 | private int top = 0; | |
82 | ||
83 | private IProgressIndicator progressBar; | |
84 | ||
85 | private boolean working; | |
86 | ||
87 | String newPcaTitle = null; | |
88 | /** | |
89 | * Constructor given sequence data, a similarity (or distance) score model | |
90 | * name, and score calculation parameters | |
91 | * | |
92 | * @param alignPanel | |
93 | * @param modelName | |
94 | * @param params | |
95 | */ | |
96 | 2 | public PCAPanel(AlignmentPanel alignPanel, String modelName, |
97 | SimilarityParamsI params) | |
98 | { | |
99 | 2 | super(); |
100 | 2 | this.setFrameIcon(null); |
101 | 2 | this.av = alignPanel.av; |
102 | 2 | this.ap = alignPanel; |
103 | 2 | boolean nucleotide = av.getAlignment().isNucleotide(); |
104 | ||
105 | 2 | progressBar = new ProgressBar(statusPanel, statusBar); |
106 | ||
107 | 2 | addInternalFrameListener(new InternalFrameAdapter() |
108 | { | |
109 | 2 | @Override |
110 | public void internalFrameClosed(InternalFrameEvent e) | |
111 | { | |
112 | 2 | close_actionPerformed(); |
113 | } | |
114 | }); | |
115 | ||
116 | 2 | boolean selected = av.getSelectionGroup() != null |
117 | && av.getSelectionGroup().getSize() > 0; | |
118 | 2 | AlignmentView seqstrings = av.getAlignmentView(selected); |
119 | 2 | SequenceI[] seqs; |
120 | 2 | if (!selected) |
121 | { | |
122 | 2 | seqs = av.getAlignment().getSequencesArray(); |
123 | } | |
124 | else | |
125 | { | |
126 | 0 | seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); |
127 | } | |
128 | ||
129 | 2 | ScoreModelI scoreModel = ScoreModels.getInstance() |
130 | .getScoreModel(modelName, ap); | |
131 | 2 | setPcaModel( |
132 | new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params)); | |
133 | ||
134 | 2 | newPcaTitle = alignPanel.alignFrame.formCalculationTitle( |
135 | MessageManager.formatMessage("label.calc_title", "PCA", | |
136 | getPcaModel().getScoreModelName()), | |
137 | selected, ap.alignFrame.getTitle()); | |
138 | ||
139 | 2 | PaintRefresher.Register(this, av.getSequenceSetId()); |
140 | ||
141 | 2 | setRotatableCanvas(new RotatableCanvas(alignPanel)); |
142 | ||
143 | 2 | if (params.getSecondaryStructureSource() != null) |
144 | { | |
145 | // Initialize and set subtitle text | |
146 | 0 | JLabel subtitleLabel = new JLabel( |
147 | " Secondary Structure Provider : " | |
148 | + params.getSecondaryStructureSource(), | |
149 | SwingConstants.LEFT); | |
150 | 0 | this.getContentPane().add(subtitleLabel, BorderLayout.NORTH); |
151 | ||
152 | } | |
153 | 2 | this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER); |
154 | ||
155 | 2 | addKeyListener(getRotatableCanvas()); |
156 | 2 | validate(); |
157 | } | |
158 | ||
159 | /** | |
160 | * Ensure references to potentially very large objects (the PCA matrices) are | |
161 | * nulled when the frame is closed | |
162 | */ | |
163 | 2 | protected void close_actionPerformed() |
164 | { | |
165 | 2 | setPcaModel(null); |
166 | 2 | if (this.rc != null) |
167 | { | |
168 | 2 | this.rc.sequencePoints = null; |
169 | 2 | this.rc.setAxisEndPoints(null); |
170 | 2 | this.rc = null; |
171 | } | |
172 | } | |
173 | ||
174 | 0 | @Override |
175 | protected void bgcolour_actionPerformed() | |
176 | { | |
177 | 0 | String ttl = MessageManager.getString("label.select_background_colour"); |
178 | 0 | ColourChooserListener listener = new ColourChooserListener() |
179 | { | |
180 | 0 | @Override |
181 | public void colourSelected(Color c) | |
182 | { | |
183 | 0 | rc.setBgColour(c); |
184 | 0 | rc.repaint(); |
185 | } | |
186 | }; | |
187 | 0 | JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(), |
188 | listener); | |
189 | } | |
190 | ||
191 | /** | |
192 | * Calculates the PCA and displays the results | |
193 | */ | |
194 | 1 | @Override |
195 | public void run() | |
196 | { | |
197 | 1 | working = true; |
198 | 1 | long progId = System.currentTimeMillis(); |
199 | 1 | IProgressIndicator progress = this; |
200 | 1 | String message = MessageManager.getString("label.pca_recalculating"); |
201 | 1 | if (getParent() == null) |
202 | { | |
203 | 1 | progress = ap.alignFrame; |
204 | 1 | message = MessageManager.getString("label.pca_calculating"); |
205 | } | |
206 | 1 | progress.setProgressBar(message, progId); |
207 | 1 | try |
208 | { | |
209 | 1 | getPcaModel().calculate(); |
210 | ||
211 | 1 | xCombobox.setSelectedIndex(0); |
212 | 1 | yCombobox.setSelectedIndex(1); |
213 | 1 | zCombobox.setSelectedIndex(2); |
214 | ||
215 | 1 | getPcaModel().updateRc(getRotatableCanvas()); |
216 | // rc.invalidate(); | |
217 | 1 | setTop(getPcaModel().getTop()); |
218 | ||
219 | } catch (OutOfMemoryError er) | |
220 | { | |
221 | 0 | new OOMWarning("calculating PCA", er); |
222 | 0 | working = false; |
223 | 0 | return; |
224 | } finally | |
225 | { | |
226 | 1 | progress.setProgressBar("", progId); |
227 | } | |
228 | ||
229 | 1 | repaint(); |
230 | 1 | if (getParent() == null) |
231 | { | |
232 | 1 | Desktop.addInternalFrame(this, newPcaTitle, |
233 | 475, 450); | |
234 | 1 | this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); |
235 | } | |
236 | 1 | working = false; |
237 | } | |
238 | ||
239 | /** | |
240 | * Updates the PCA display after a change of component to use for x, y or z | |
241 | * axis | |
242 | */ | |
243 | 12 | @Override |
244 | protected void doDimensionChange() | |
245 | { | |
246 | 12 | if (getTop() == 0) |
247 | { | |
248 | 12 | return; |
249 | } | |
250 | ||
251 | 0 | int dim1 = getTop() - xCombobox.getSelectedIndex(); |
252 | 0 | int dim2 = getTop() - yCombobox.getSelectedIndex(); |
253 | 0 | int dim3 = getTop() - zCombobox.getSelectedIndex(); |
254 | 0 | getPcaModel().updateRcView(dim1, dim2, dim3); |
255 | 0 | getRotatableCanvas().resetView(); |
256 | } | |
257 | ||
258 | /** | |
259 | * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for | |
260 | * the given axis (X/Y/Z) | |
261 | * | |
262 | * @param index | |
263 | * @param axis | |
264 | */ | |
265 | 3 | public void setSelectedDimensionIndex(int index, Axis axis) |
266 | { | |
267 | 3 | switch (axis) |
268 | { | |
269 | 1 | case X: |
270 | 1 | xCombobox.setSelectedIndex(index); |
271 | 1 | break; |
272 | 1 | case Y: |
273 | 1 | yCombobox.setSelectedIndex(index); |
274 | 1 | break; |
275 | 1 | case Z: |
276 | 1 | zCombobox.setSelectedIndex(index); |
277 | 1 | break; |
278 | 0 | default: |
279 | } | |
280 | } | |
281 | ||
282 | 0 | @Override |
283 | protected void outputValues_actionPerformed() | |
284 | { | |
285 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
286 | 0 | try |
287 | { | |
288 | 0 | cap.setText(getPcaModel().getDetails()); |
289 | 0 | Desktop.addInternalFrame(cap, |
290 | MessageManager.getString("label.pca_details"), 500, 500); | |
291 | } catch (OutOfMemoryError oom) | |
292 | { | |
293 | 0 | new OOMWarning("opening PCA details", oom); |
294 | 0 | cap.dispose(); |
295 | } | |
296 | } | |
297 | ||
298 | 0 | @Override |
299 | protected void showLabels_actionPerformed() | |
300 | { | |
301 | 0 | getRotatableCanvas().showLabels(showLabels.getState()); |
302 | } | |
303 | ||
304 | 0 | @Override |
305 | protected void print_actionPerformed() | |
306 | { | |
307 | 0 | PCAPrinter printer = new PCAPrinter(); |
308 | 0 | printer.start(); |
309 | } | |
310 | ||
311 | /** | |
312 | * If available, shows the data which formed the inputs for the PCA as a new | |
313 | * alignment | |
314 | */ | |
315 | 0 | @Override |
316 | public void originalSeqData_actionPerformed() | |
317 | { | |
318 | // JAL-2647 disabled after load from project (until save to project done) | |
319 | 0 | if (getPcaModel().getInputData() == null) |
320 | { | |
321 | 0 | Console.info( |
322 | "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); | |
323 | 0 | return; |
324 | } | |
325 | // decide if av alignment is sufficiently different to original data to | |
326 | // warrant a new window to be created | |
327 | // create new alignment window with hidden regions (unhiding hidden regions | |
328 | // yields unaligned seqs) | |
329 | // or create a selection box around columns in alignment view | |
330 | // test Alignment(SeqCigar[]) | |
331 | 0 | char gc = '-'; |
332 | 0 | try |
333 | { | |
334 | // we try to get the associated view's gap character | |
335 | // but this may fail if the view was closed... | |
336 | 0 | gc = av.getGapCharacter(); |
337 | } catch (Exception ex) | |
338 | { | |
339 | } | |
340 | ||
341 | 0 | Object[] alAndColsel = getPcaModel().getInputData() |
342 | .getAlignmentAndHiddenColumns(gc); | |
343 | ||
344 | 0 | if (alAndColsel != null && alAndColsel[0] != null) |
345 | { | |
346 | // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); | |
347 | ||
348 | 0 | AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); |
349 | 0 | AlignmentI dataset = (av != null && av.getAlignment() != null) |
350 | ? av.getAlignment().getDataset() | |
351 | : null; | |
352 | 0 | if (dataset != null) |
353 | { | |
354 | 0 | al.setDataset(dataset); |
355 | } | |
356 | ||
357 | 0 | if (true) |
358 | { | |
359 | // make a new frame! | |
360 | 0 | AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], |
361 | AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); | |
362 | ||
363 | // >>>This is a fix for the moment, until a better solution is | |
364 | // found!!<<< | |
365 | // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); | |
366 | ||
367 | // af.addSortByOrderMenuItem(ServiceName + " Ordering", | |
368 | // msaorder); | |
369 | ||
370 | 0 | Desktop.addInternalFrame(af, MessageManager.formatMessage( |
371 | "label.original_data_for_params", new String[] | |
372 | { this.title }), AlignFrame.DEFAULT_WIDTH, | |
373 | AlignFrame.DEFAULT_HEIGHT); | |
374 | } | |
375 | } | |
376 | /* | |
377 | * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i < | |
378 | * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 + | |
379 | * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] + | |
380 | * "\n"); } | |
381 | * | |
382 | * Desktop.addInternalFrame(cap, "Original Data", 400, 400); | |
383 | */ | |
384 | } | |
385 | ||
386 | class PCAPrinter extends Thread implements Printable | |
387 | { | |
388 | 0 | @Override |
389 | public void run() | |
390 | { | |
391 | 0 | PrinterJob printJob = PrinterJob.getPrinterJob(); |
392 | 0 | PageFormat defaultPage = printJob.defaultPage(); |
393 | 0 | PageFormat pf = printJob.pageDialog(defaultPage); |
394 | ||
395 | 0 | if (defaultPage == pf) |
396 | { | |
397 | /* | |
398 | * user cancelled | |
399 | */ | |
400 | 0 | return; |
401 | } | |
402 | ||
403 | 0 | printJob.setPrintable(this, pf); |
404 | ||
405 | 0 | if (printJob.printDialog()) |
406 | { | |
407 | 0 | try |
408 | { | |
409 | 0 | printJob.print(); |
410 | } catch (Exception PrintException) | |
411 | { | |
412 | 0 | PrintException.printStackTrace(); |
413 | } | |
414 | } | |
415 | } | |
416 | ||
417 | 0 | @Override |
418 | public int print(Graphics pg, PageFormat pf, int pi) | |
419 | throws PrinterException | |
420 | { | |
421 | 0 | pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); |
422 | ||
423 | 0 | getRotatableCanvas().drawBackground(pg); |
424 | 0 | getRotatableCanvas().drawScene(pg); |
425 | 0 | if (getRotatableCanvas().drawAxes) |
426 | { | |
427 | 0 | getRotatableCanvas().drawAxes(pg); |
428 | } | |
429 | ||
430 | 0 | if (pi == 0) |
431 | { | |
432 | 0 | return Printable.PAGE_EXISTS; |
433 | } | |
434 | else | |
435 | { | |
436 | 0 | return Printable.NO_SUCH_PAGE; |
437 | } | |
438 | } | |
439 | } | |
440 | ||
441 | 0 | public void makePCAImage(ImageMaker.TYPE type) |
442 | { | |
443 | 0 | int width = getRotatableCanvas().getWidth(); |
444 | 0 | int height = getRotatableCanvas().getHeight(); |
445 | 0 | ImageWriterI writer = new ImageWriterI() |
446 | { | |
447 | 0 | @Override |
448 | public void exportImage(Graphics g) throws Exception | |
449 | { | |
450 | 0 | RotatableCanvas canvas = getRotatableCanvas(); |
451 | 0 | canvas.drawBackground(g); |
452 | 0 | canvas.drawScene(g); |
453 | 0 | if (canvas.drawAxes) |
454 | { | |
455 | 0 | canvas.drawAxes(g); |
456 | } | |
457 | } | |
458 | }; | |
459 | 0 | String pca = MessageManager.getString("label.pca"); |
460 | 0 | ImageExporter exporter = new ImageExporter(writer, null, type, pca); |
461 | 0 | try |
462 | { | |
463 | 0 | exporter.doExport(null, this, width, height, pca); |
464 | } catch (ImageOutputException ioex) | |
465 | { | |
466 | 0 | Console.error("Unexpected error whilst writing " + type.toString(), |
467 | ioex); | |
468 | } | |
469 | } | |
470 | ||
471 | 0 | @Override |
472 | protected void viewMenu_menuSelected() | |
473 | { | |
474 | 0 | buildAssociatedViewMenu(); |
475 | } | |
476 | ||
477 | /** | |
478 | * Builds the menu showing the choice of possible views (for the associated | |
479 | * sequence data) to which the PCA may be linked | |
480 | */ | |
481 | 0 | void buildAssociatedViewMenu() |
482 | { | |
483 | 0 | AlignmentPanel[] aps = PaintRefresher |
484 | .getAssociatedPanels(av.getSequenceSetId()); | |
485 | 0 | if (aps.length == 1 && getRotatableCanvas().av == aps[0].av) |
486 | { | |
487 | 0 | associateViewsMenu.setVisible(false); |
488 | 0 | return; |
489 | } | |
490 | ||
491 | 0 | associateViewsMenu.setVisible(true); |
492 | ||
493 | 0 | if ((viewMenu |
494 | .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) | |
495 | { | |
496 | 0 | viewMenu.insertSeparator(viewMenu.getItemCount() - 1); |
497 | } | |
498 | ||
499 | 0 | associateViewsMenu.removeAll(); |
500 | ||
501 | 0 | JRadioButtonMenuItem item; |
502 | 0 | ButtonGroup buttonGroup = new ButtonGroup(); |
503 | 0 | int iSize = aps.length; |
504 | ||
505 | 0 | for (int i = 0; i < iSize; i++) |
506 | { | |
507 | 0 | final AlignmentPanel panel = aps[i]; |
508 | 0 | item = new JRadioButtonMenuItem(panel.av.getViewName(), |
509 | panel.av == getRotatableCanvas().av); | |
510 | 0 | buttonGroup.add(item); |
511 | 0 | item.addActionListener(new ActionListener() |
512 | { | |
513 | 0 | @Override |
514 | public void actionPerformed(ActionEvent evt) | |
515 | { | |
516 | 0 | selectAssociatedView(panel); |
517 | } | |
518 | }); | |
519 | ||
520 | 0 | associateViewsMenu.add(item); |
521 | } | |
522 | ||
523 | 0 | final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( |
524 | "All Views"); | |
525 | ||
526 | 0 | buttonGroup.add(itemf); |
527 | ||
528 | 0 | itemf.setSelected(getRotatableCanvas().isApplyToAllViews()); |
529 | 0 | itemf.addActionListener(new ActionListener() |
530 | { | |
531 | 0 | @Override |
532 | public void actionPerformed(ActionEvent evt) | |
533 | { | |
534 | 0 | getRotatableCanvas().setApplyToAllViews(itemf.isSelected()); |
535 | } | |
536 | }); | |
537 | 0 | associateViewsMenu.add(itemf); |
538 | ||
539 | } | |
540 | ||
541 | /* | |
542 | * (non-Javadoc) | |
543 | * | |
544 | * @see | |
545 | * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent | |
546 | * ) | |
547 | */ | |
548 | 0 | @Override |
549 | protected void outputPoints_actionPerformed() | |
550 | { | |
551 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
552 | 0 | try |
553 | { | |
554 | 0 | cap.setText(getPcaModel().getPointsasCsv(false, |
555 | xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), | |
556 | zCombobox.getSelectedIndex())); | |
557 | 0 | Desktop.addInternalFrame(cap, MessageManager |
558 | .formatMessage("label.points_for_params", new String[] | |
559 | { this.getTitle() }), 500, 500); | |
560 | } catch (OutOfMemoryError oom) | |
561 | { | |
562 | 0 | new OOMWarning("exporting PCA points", oom); |
563 | 0 | cap.dispose(); |
564 | } | |
565 | } | |
566 | ||
567 | /* | |
568 | * (non-Javadoc) | |
569 | * | |
570 | * @see | |
571 | * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event | |
572 | * .ActionEvent) | |
573 | */ | |
574 | 0 | @Override |
575 | protected void outputProjPoints_actionPerformed() | |
576 | { | |
577 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
578 | 0 | try |
579 | { | |
580 | 0 | cap.setText(getPcaModel().getPointsasCsv(true, |
581 | xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), | |
582 | zCombobox.getSelectedIndex())); | |
583 | 0 | Desktop.addInternalFrame(cap, MessageManager.formatMessage( |
584 | "label.transformed_points_for_params", new String[] | |
585 | { this.getTitle() }), 500, 500); | |
586 | } catch (OutOfMemoryError oom) | |
587 | { | |
588 | 0 | new OOMWarning("exporting transformed PCA points", oom); |
589 | 0 | cap.dispose(); |
590 | } | |
591 | } | |
592 | ||
593 | /* | |
594 | * (non-Javadoc) | |
595 | * | |
596 | * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) | |
597 | */ | |
598 | 0 | @Override |
599 | public void setProgressBar(String message, long id) | |
600 | { | |
601 | 0 | progressBar.setProgressBar(message, id); |
602 | // if (progressBars == null) | |
603 | // { | |
604 | // progressBars = new Hashtable(); | |
605 | // progressBarHandlers = new Hashtable(); | |
606 | // } | |
607 | // | |
608 | // JPanel progressPanel; | |
609 | // Long lId = Long.valueOf(id); | |
610 | // GridLayout layout = (GridLayout) statusPanel.getLayout(); | |
611 | // if (progressBars.get(lId) != null) | |
612 | // { | |
613 | // progressPanel = (JPanel) progressBars.get(Long.valueOf(id)); | |
614 | // statusPanel.remove(progressPanel); | |
615 | // progressBars.remove(lId); | |
616 | // progressPanel = null; | |
617 | // if (message != null) | |
618 | // { | |
619 | // statusBar.setText(message); | |
620 | // } | |
621 | // if (progressBarHandlers.contains(lId)) | |
622 | // { | |
623 | // progressBarHandlers.remove(lId); | |
624 | // } | |
625 | // layout.setRows(layout.getRows() - 1); | |
626 | // } | |
627 | // else | |
628 | // { | |
629 | // progressPanel = new JPanel(new BorderLayout(10, 5)); | |
630 | // | |
631 | // JProgressBar progressBar = new JProgressBar(); | |
632 | // progressBar.setIndeterminate(true); | |
633 | // | |
634 | // progressPanel.add(new JLabel(message), BorderLayout.WEST); | |
635 | // progressPanel.add(progressBar, BorderLayout.CENTER); | |
636 | // | |
637 | // layout.setRows(layout.getRows() + 1); | |
638 | // statusPanel.add(progressPanel); | |
639 | // | |
640 | // progressBars.put(lId, progressPanel); | |
641 | // } | |
642 | // // update GUI | |
643 | // // setMenusForViewport(); | |
644 | // validate(); | |
645 | } | |
646 | ||
647 | 0 | @Override |
648 | public void registerHandler(final long id, | |
649 | final IProgressIndicatorHandler handler) | |
650 | { | |
651 | 0 | progressBar.registerHandler(id, handler); |
652 | // if (progressBarHandlers == null || | |
653 | // !progressBars.contains(Long.valueOf(id))) | |
654 | // { | |
655 | // throw new | |
656 | // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); | |
657 | // } | |
658 | // progressBarHandlers.put(Long.valueOf(id), handler); | |
659 | // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id)); | |
660 | // if (handler.canCancel()) | |
661 | // { | |
662 | // JButton cancel = new JButton( | |
663 | // MessageManager.getString("action.cancel")); | |
664 | // final IProgressIndicator us = this; | |
665 | // cancel.addActionListener(new ActionListener() | |
666 | // { | |
667 | // | |
668 | // @Override | |
669 | // public void actionPerformed(ActionEvent e) | |
670 | // { | |
671 | // handler.cancelActivity(id); | |
672 | // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", | |
673 | // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); | |
674 | // } | |
675 | // }); | |
676 | // progressPanel.add(cancel, BorderLayout.EAST); | |
677 | // } | |
678 | } | |
679 | ||
680 | /** | |
681 | * | |
682 | * @return true if any progress bars are still active | |
683 | */ | |
684 | 0 | @Override |
685 | public boolean operationInProgress() | |
686 | { | |
687 | 0 | return progressBar.operationInProgress(); |
688 | } | |
689 | ||
690 | 0 | @Override |
691 | protected void resetButton_actionPerformed() | |
692 | { | |
693 | 0 | int t = getTop(); |
694 | 0 | setTop(0); // ugly - prevents dimensionChanged events from being processed |
695 | 0 | xCombobox.setSelectedIndex(0); |
696 | 0 | yCombobox.setSelectedIndex(1); |
697 | 0 | setTop(t); |
698 | 0 | zCombobox.setSelectedIndex(2); |
699 | } | |
700 | ||
701 | /** | |
702 | * Answers true if PCA calculation is in progress, else false | |
703 | * | |
704 | * @return | |
705 | */ | |
706 | 0 | public boolean isWorking() |
707 | { | |
708 | 0 | return working; |
709 | } | |
710 | ||
711 | /** | |
712 | * Answers the selected checkbox item index for PCA dimension for the X, Y or | |
713 | * Z axis of the display | |
714 | * | |
715 | * @param axis | |
716 | * @return | |
717 | */ | |
718 | 3 | public int getSelectedDimensionIndex(Axis axis) |
719 | { | |
720 | 3 | switch (axis) |
721 | { | |
722 | 1 | case X: |
723 | 1 | return xCombobox.getSelectedIndex(); |
724 | 1 | case Y: |
725 | 1 | return yCombobox.getSelectedIndex(); |
726 | 1 | default: |
727 | 1 | return zCombobox.getSelectedIndex(); |
728 | } | |
729 | } | |
730 | ||
731 | 1 | public void setShowLabels(boolean show) |
732 | { | |
733 | 1 | showLabels.setSelected(show); |
734 | } | |
735 | ||
736 | /** | |
737 | * Sets the input data used to calculate the PCA. This is provided for | |
738 | * 'restore from project', which does not currently support this (AL-2647), so | |
739 | * sets the value to null, and hides the menu option for "Input Data...". J | |
740 | * | |
741 | * @param data | |
742 | */ | |
743 | 1 | public void setInputData(AlignmentView data) |
744 | { | |
745 | 1 | getPcaModel().setInputData(data); |
746 | 1 | originalSeqData.setVisible(data != null); |
747 | } | |
748 | ||
749 | 10 | public AlignViewportI getAlignViewport() |
750 | { | |
751 | 10 | return av; |
752 | } | |
753 | ||
754 | 10 | public PCAModel getPcaModel() |
755 | { | |
756 | 10 | return pcaModel; |
757 | } | |
758 | ||
759 | 4 | public void setPcaModel(PCAModel pcaModel) |
760 | { | |
761 | 4 | this.pcaModel = pcaModel; |
762 | } | |
763 | ||
764 | 24 | public RotatableCanvas getRotatableCanvas() |
765 | { | |
766 | 24 | return rc; |
767 | } | |
768 | ||
769 | 2 | public void setRotatableCanvas(RotatableCanvas rc) |
770 | { | |
771 | 2 | this.rc = rc; |
772 | } | |
773 | ||
774 | 12 | public int getTop() |
775 | { | |
776 | 12 | return top; |
777 | } | |
778 | ||
779 | 2 | public void setTop(int top) |
780 | { | |
781 | 2 | this.top = top; |
782 | } | |
783 | ||
784 | /** | |
785 | * set the associated view for this PCA. | |
786 | * | |
787 | * @param panel | |
788 | */ | |
789 | 1 | public void selectAssociatedView(AlignmentPanel panel) |
790 | { | |
791 | 1 | getRotatableCanvas().setApplyToAllViews(false); |
792 | ||
793 | 1 | ap = panel; |
794 | 1 | av = panel.av; |
795 | ||
796 | 1 | getRotatableCanvas().av = panel.av; |
797 | 1 | getRotatableCanvas().ap = panel; |
798 | 1 | PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId()); |
799 | } | |
800 | ||
801 | 0 | @Override |
802 | public JProgressBar getProgressBar(long id) | |
803 | { | |
804 | 0 | return progressBar.getProgressBar(id); |
805 | } | |
806 | ||
807 | 0 | public String getMessage(long id) |
808 | { | |
809 | 0 | return progressBar.getMessage(id); |
810 | } | |
811 | ||
812 | 0 | public void setProgressBarMessage(long id, String message) |
813 | { | |
814 | 0 | progressBar.setProgressBarMessage(id, message); |
815 | } | |
816 | } |