Coverage Report
File AlignFrame.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignFrame | 178 | 1,901 | 743 | ||
| PrintThread | 6451 | 9 | 5 |
Contributing tests
This file is covered by 292 tests.
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| 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 | } |