Coverage Report
File PCAPanel.java
Coverage histogram
49% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| PCAPanel | 66 | 187 | 67 | ||
| PCAPanel.PCAPrinter | 386 | 18 | 7 |
Contributing tests
This file is covered by 4 tests.
.
Source view
| 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 | } |