jalviewX
File Desktop.java
Coverage histogram
45% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| Desktop | 137 | 958 | 384 | 997 | ||
| Desktop.MyDesktopManager | 221 | 25 | 19 | 36 | ||
| Desktop.MyDesktopPane | 2482 | 26 | 13 | 29 |
Contributing tests
This file is covered by 127 tests.
.
Source view
| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.gui; | |
| 22 | ||
| 23 | import static jalview.util.UrlConstants.SEQUENCE_ID; | |
| 24 | ||
| 25 | import jalview.api.AlignViewportI; | |
| 26 | import jalview.api.AlignmentViewPanel; | |
| 27 | import jalview.bin.Cache; | |
| 28 | import jalview.bin.Jalview; | |
| 29 | import jalview.gui.ImageExporter.ImageWriterI; | |
| 30 | import jalview.io.DataSourceType; | |
| 31 | import jalview.io.FileFormat; | |
| 32 | import jalview.io.FileFormatException; | |
| 33 | import jalview.io.FileFormatI; | |
| 34 | import jalview.io.FileFormats; | |
| 35 | import jalview.io.FileLoader; | |
| 36 | import jalview.io.FormatAdapter; | |
| 37 | import jalview.io.IdentifyFile; | |
| 38 | import jalview.io.JalviewFileChooser; | |
| 39 | import jalview.io.JalviewFileView; | |
| 40 | import jalview.jbgui.GSplitFrame; | |
| 41 | import jalview.jbgui.GStructureViewer; | |
| 42 | import jalview.structure.StructureSelectionManager; | |
| 43 | import jalview.urls.IdOrgSettings; | |
| 44 | import jalview.util.BrowserLauncher; | |
| 45 | import jalview.util.ImageMaker.TYPE; | |
| 46 | import jalview.util.MessageManager; | |
| 47 | import jalview.util.Platform; | |
| 48 | import jalview.util.UrlConstants; | |
| 49 | import jalview.util.dialogrunner.RunResponse; | |
| 50 | import jalview.viewmodel.AlignmentViewport; | |
| 51 | import jalview.ws.params.ParamManager; | |
| 52 | import jalview.ws.utils.UrlDownloadClient; | |
| 53 | ||
| 54 | import java.awt.BorderLayout; | |
| 55 | import java.awt.Color; | |
| 56 | import java.awt.Dimension; | |
| 57 | import java.awt.FontMetrics; | |
| 58 | import java.awt.Graphics; | |
| 59 | import java.awt.GridLayout; | |
| 60 | import java.awt.Point; | |
| 61 | import java.awt.Rectangle; | |
| 62 | import java.awt.Toolkit; | |
| 63 | import java.awt.Window; | |
| 64 | import java.awt.datatransfer.Clipboard; | |
| 65 | import java.awt.datatransfer.ClipboardOwner; | |
| 66 | import java.awt.datatransfer.DataFlavor; | |
| 67 | import java.awt.datatransfer.Transferable; | |
| 68 | import java.awt.dnd.DnDConstants; | |
| 69 | import java.awt.dnd.DropTargetDragEvent; | |
| 70 | import java.awt.dnd.DropTargetDropEvent; | |
| 71 | import java.awt.dnd.DropTargetEvent; | |
| 72 | import java.awt.dnd.DropTargetListener; | |
| 73 | import java.awt.event.ActionEvent; | |
| 74 | import java.awt.event.ActionListener; | |
| 75 | import java.awt.event.InputEvent; | |
| 76 | import java.awt.event.KeyEvent; | |
| 77 | import java.awt.event.MouseAdapter; | |
| 78 | import java.awt.event.MouseEvent; | |
| 79 | import java.awt.event.WindowAdapter; | |
| 80 | import java.awt.event.WindowEvent; | |
| 81 | import java.beans.PropertyChangeEvent; | |
| 82 | import java.beans.PropertyChangeListener; | |
| 83 | import java.io.BufferedInputStream; | |
| 84 | import java.io.File; | |
| 85 | import java.io.FileOutputStream; | |
| 86 | import java.io.IOException; | |
| 87 | import java.net.URL; | |
| 88 | import java.util.ArrayList; | |
| 89 | import java.util.Hashtable; | |
| 90 | import java.util.List; | |
| 91 | import java.util.ListIterator; | |
| 92 | import java.util.StringTokenizer; | |
| 93 | import java.util.Vector; | |
| 94 | import java.util.concurrent.ExecutorService; | |
| 95 | import java.util.concurrent.Executors; | |
| 96 | import java.util.concurrent.Semaphore; | |
| 97 | ||
| 98 | import javax.swing.AbstractAction; | |
| 99 | import javax.swing.Action; | |
| 100 | import javax.swing.ActionMap; | |
| 101 | import javax.swing.Box; | |
| 102 | import javax.swing.BoxLayout; | |
| 103 | import javax.swing.DefaultDesktopManager; | |
| 104 | import javax.swing.DesktopManager; | |
| 105 | import javax.swing.InputMap; | |
| 106 | import javax.swing.JButton; | |
| 107 | import javax.swing.JCheckBox; | |
| 108 | import javax.swing.JComboBox; | |
| 109 | import javax.swing.JComponent; | |
| 110 | import javax.swing.JDesktopPane; | |
| 111 | import javax.swing.JFrame; | |
| 112 | import javax.swing.JInternalFrame; | |
| 113 | import javax.swing.JLabel; | |
| 114 | import javax.swing.JMenuItem; | |
| 115 | import javax.swing.JPanel; | |
| 116 | import javax.swing.JPopupMenu; | |
| 117 | import javax.swing.JProgressBar; | |
| 118 | import javax.swing.JTextField; | |
| 119 | import javax.swing.KeyStroke; | |
| 120 | import javax.swing.SwingUtilities; | |
| 121 | import javax.swing.event.HyperlinkEvent; | |
| 122 | import javax.swing.event.HyperlinkEvent.EventType; | |
| 123 | import javax.swing.event.InternalFrameAdapter; | |
| 124 | import javax.swing.event.InternalFrameEvent; | |
| 125 | import javax.swing.event.MenuEvent; | |
| 126 | import javax.swing.event.MenuListener; | |
| 127 | ||
| 128 | import org.stackoverflowusers.file.WindowsShortcut; | |
| 129 | ||
| 130 | /** | |
| 131 | * Jalview Desktop | |
| 132 | * | |
| 133 | * | |
| 134 | * @author $author$ | |
| 135 | * @version $Revision: 1.155 $ | |
| 136 | */ | |
| 137 | public class Desktop extends jalview.jbgui.GDesktop | |
| 138 | implements DropTargetListener, ClipboardOwner, IProgressIndicator, | |
| 139 | jalview.api.StructureSelectionManagerProvider | |
| 140 | { | |
| 141 | private static int DEFAULT_MIN_WIDTH = 300; | |
| 142 | ||
| 143 | private static int DEFAULT_MIN_HEIGHT = 250; | |
| 144 | ||
| 145 | private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; | |
| 146 | ||
| 147 | private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; | |
| 148 | ||
| 149 | private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; | |
| 150 | ||
| 151 | private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); | |
| 152 | ||
| 153 | /** | |
| 154 | * news reader - null if it was never started. | |
| 155 | */ | |
| 156 | private BlogReader jvnews = null; | |
| 157 | ||
| 158 | private File projectFile; | |
| 159 | ||
| 160 | /** | |
| 161 | * @param listener | |
| 162 | * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) | |
| 163 | */ | |
| 164 | 0 |  public void addJalviewPropertyChangeListener( |
| 165 | PropertyChangeListener listener) | |
| 166 | { | |
| 167 | 0 | changeSupport.addJalviewPropertyChangeListener(listener); |
| 168 | } | |
| 169 | ||
| 170 | /** | |
| 171 | * @param propertyName | |
| 172 | * @param listener | |
| 173 | * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, | |
| 174 | * java.beans.PropertyChangeListener) | |
| 175 | */ | |
| 176 | 190 | public void addJalviewPropertyChangeListener(String propertyName, |
| 177 | PropertyChangeListener listener) | |
| 178 | { | |
| 179 | 190 | changeSupport.addJalviewPropertyChangeListener(propertyName, listener); |
| 180 | } | |
| 181 | ||
| 182 | /** | |
| 183 | * @param propertyName | |
| 184 | * @param listener | |
| 185 | * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, | |
| 186 | * java.beans.PropertyChangeListener) | |
| 187 | */ | |
| 188 | 96 | public void removeJalviewPropertyChangeListener(String propertyName, |
| 189 | PropertyChangeListener listener) | |
| 190 | { | |
| 191 | 96 | changeSupport.removeJalviewPropertyChangeListener(propertyName, |
| 192 | listener); | |
| 193 | } | |
| 194 | ||
| 195 | /** Singleton Desktop instance */ | |
| 196 | public static Desktop instance; | |
| 197 | ||
| 198 | public static MyDesktopPane desktop; | |
| 199 | ||
| 200 | 0 | public static MyDesktopPane getDesktop() |
| 201 | { | |
| 202 | // BH 2018 could use currentThread() here as a reference to a | |
| 203 | // Hashtable<Thread, MyDesktopPane> in JavaScript | |
| 204 | 0 | return desktop; |
| 205 | } | |
| 206 | ||
| 207 | static int openFrameCount = 0; | |
| 208 | ||
| 209 | static final int xOffset = 30; | |
| 210 | ||
| 211 | static final int yOffset = 30; | |
| 212 | ||
| 213 | public static jalview.ws.jws1.Discoverer discoverer; | |
| 214 | ||
| 215 | public static Object[] jalviewClipboard; | |
| 216 | ||
| 217 | public static boolean internalCopy = false; | |
| 218 | ||
| 219 | static int fileLoadingCount = 0; | |
| 220 | ||
| 221 | class MyDesktopManager implements DesktopManager | |
| 222 | { | |
| 223 | ||
| 224 | private DesktopManager delegate; | |
| 225 | ||
| 226 | 11 | public MyDesktopManager(DesktopManager delegate) |
| 227 | { | |
| 228 | 11 | this.delegate = delegate; |
| 229 | } | |
| 230 | ||
| 231 | 290 | @Override |
| 232 | public void activateFrame(JInternalFrame f) | |
| 233 | { | |
| 234 | 290 | try |
| 235 | { | |
| 236 | 290 | delegate.activateFrame(f); |
| 237 | } catch (NullPointerException npe) | |
| 238 | { | |
| 239 | 0 | Point p = getMousePosition(); |
| 240 | 0 | instance.showPasteMenu(p.x, p.y); |
| 241 | } | |
| 242 | } | |
| 243 | ||
| 244 | 0 | @Override |
| 245 | public void beginDraggingFrame(JComponent f) | |
| 246 | { | |
| 247 | 0 | delegate.beginDraggingFrame(f); |
| 248 | } | |
| 249 | ||
| 250 | 0 | @Override |
| 251 | public void beginResizingFrame(JComponent f, int direction) | |
| 252 | { | |
| 253 | 0 | delegate.beginResizingFrame(f, direction); |
| 254 | } | |
| 255 | ||
| 256 | 145 | @Override |
| 257 | public void closeFrame(JInternalFrame f) | |
| 258 | { | |
| 259 | 145 | delegate.closeFrame(f); |
| 260 | } | |
| 261 | ||
| 262 | 281 | @Override |
| 263 | public void deactivateFrame(JInternalFrame f) | |
| 264 | { | |
| 265 | 281 | delegate.deactivateFrame(f); |
| 266 | } | |
| 267 | ||
| 268 | 0 | @Override |
| 269 | public void deiconifyFrame(JInternalFrame f) | |
| 270 | { | |
| 271 | 0 | delegate.deiconifyFrame(f); |
| 272 | } | |
| 273 | ||
| 274 | 0 | @Override |
| 275 | public void dragFrame(JComponent f, int newX, int newY) | |
| 276 | { | |
| 277 | 0 | if (newY < 0) |
| 278 | { | |
| 279 | 0 | newY = 0; |
| 280 | } | |
| 281 | 0 | delegate.dragFrame(f, newX, newY); |
| 282 | } | |
| 283 | ||
| 284 | 0 | @Override |
| 285 | public void endDraggingFrame(JComponent f) | |
| 286 | { | |
| 287 | 0 | delegate.endDraggingFrame(f); |
| 288 | 0 | desktop.repaint(); |
| 289 | } | |
| 290 | ||
| 291 | 0 | @Override |
| 292 | public void endResizingFrame(JComponent f) | |
| 293 | { | |
| 294 | 0 | delegate.endResizingFrame(f); |
| 295 | 0 | desktop.repaint(); |
| 296 | } | |
| 297 | ||
| 298 | 0 | @Override |
| 299 | public void iconifyFrame(JInternalFrame f) | |
| 300 | { | |
| 301 | 0 | delegate.iconifyFrame(f); |
| 302 | } | |
| 303 | ||
| 304 | 0 | @Override |
| 305 | public void maximizeFrame(JInternalFrame f) | |
| 306 | { | |
| 307 | 0 | delegate.maximizeFrame(f); |
| 308 | } | |
| 309 | ||
| 310 | 0 | @Override |
| 311 | public void minimizeFrame(JInternalFrame f) | |
| 312 | { | |
| 313 | 0 | delegate.minimizeFrame(f); |
| 314 | } | |
| 315 | ||
| 316 | 0 | @Override |
| 317 | public void openFrame(JInternalFrame f) | |
| 318 | { | |
| 319 | 0 | delegate.openFrame(f); |
| 320 | } | |
| 321 | ||
| 322 | 0 | @Override |
| 323 | public void resizeFrame(JComponent f, int newX, int newY, int newWidth, | |
| 324 | int newHeight) | |
| 325 | { | |
| 326 | 0 | if (newY < 0) |
| 327 | { | |
| 328 | 0 | newY = 0; |
| 329 | } | |
| 330 | 0 | delegate.resizeFrame(f, newX, newY, newWidth, newHeight); |
| 331 | } | |
| 332 | ||
| 333 | 0 | @Override |
| 334 | public void setBoundsForFrame(JComponent f, int newX, int newY, | |
| 335 | int newWidth, int newHeight) | |
| 336 | { | |
| 337 | 0 | delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight); |
| 338 | } | |
| 339 | ||
| 340 | // All other methods, simply delegate | |
| 341 | ||
| 342 | } | |
| 343 | ||
| 344 | /** | |
| 345 | * Creates a new Desktop object. | |
| 346 | */ | |
| 347 | 11 | public Desktop() |
| 348 | { | |
| 349 | /** | |
| 350 | * A note to implementors. It is ESSENTIAL that any activities that might block | |
| 351 | * are spawned off as threads rather than waited for during this constructor. | |
| 352 | */ | |
| 353 | 11 | instance = this; |
| 354 | 11 | if (!Jalview.isJS()) |
| 355 | { | |
| 356 | 11 | doVamsasClientCheck(); |
| 357 | } | |
| 358 | ||
| 359 | 11 | doConfigureStructurePrefs(); |
| 360 | 11 | setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); |
| 361 | 11 | setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); |
| 362 | 11 | boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", |
| 363 | false); | |
| 364 | 11 | boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", |
| 365 | false); | |
| 366 | 11 | desktop = new MyDesktopPane(selmemusage); |
| 367 | 11 | showMemusage.setSelected(selmemusage); |
| 368 | 11 | desktop.setBackground(Color.white); |
| 369 | 11 | getContentPane().setLayout(new BorderLayout()); |
| 370 | // alternate config - have scrollbars - see notes in JAL-153 | |
| 371 | // JScrollPane sp = new JScrollPane(); | |
| 372 | // sp.getViewport().setView(desktop); | |
| 373 | // getContentPane().add(sp, BorderLayout.CENTER); | |
| 374 | 11 | getContentPane().add(desktop, BorderLayout.CENTER); |
| 375 | 11 | desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); |
| 376 | ||
| 377 | // This line prevents Windows Look&Feel resizing all new windows to maximum | |
| 378 | // if previous window was maximised | |
| 379 | 11 | desktop.setDesktopManager(new MyDesktopManager( |
| 380 | 11 | (Platform.isWindows() ? new DefaultDesktopManager() |
| 381 | 11 | : Platform.isAMac() |
| 382 | ? new AquaInternalFrameManager( | |
| 383 | desktop.getDesktopManager()) | |
| 384 | : desktop.getDesktopManager()))); | |
| 385 | ||
| 386 | 11 | Rectangle dims = getLastKnownDimensions(""); |
| 387 | 11 | if (dims != null) |
| 388 | { | |
| 389 | 7 | setBounds(dims); |
| 390 | } | |
| 391 | else | |
| 392 | { | |
| 393 | 4 | Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); |
| 394 | 4 | int xPos = Math.max(5, (screenSize.width - 900) / 2); |
| 395 | 4 | int yPos = Math.max(5, (screenSize.height - 650) / 2); |
| 396 | 4 | setBounds(xPos, yPos, 900, 650); |
| 397 | } | |
| 398 | ||
| 399 | 11 | boolean doFullLoad = /** @j2sNative ! */true; |
| 400 | ||
| 401 | 11 | if (doFullLoad) { |
| 402 | ||
| 403 | 11 | jconsole = new Console(this, showjconsole); |
| 404 | // add essential build information | |
| 405 | 11 | jconsole.setHeader("Jalview Version: " |
| 406 | + jalview.bin.Cache.getProperty("VERSION") + "\n" | |
| 407 | + "Jalview Installation: " | |
| 408 | + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") | |
| 409 | + "\n" + "Build Date: " | |
| 410 | + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n" | |
| 411 | + "Java version: " + System.getProperty("java.version") + "\n" | |
| 412 | + System.getProperty("os.arch") + " " | |
| 413 | + System.getProperty("os.name") + " " | |
| 414 | + System.getProperty("os.version")); | |
| 415 | ||
| 416 | 11 | showConsole(showjconsole); |
| 417 | ||
| 418 | 11 | showNews.setVisible(false); |
| 419 | ||
| 420 | 11 | experimentalFeatures.setSelected(showExperimental()); |
| 421 | ||
| 422 | 11 | getIdentifiersOrgData(); |
| 423 | ||
| 424 | 11 | checkURLLinks(); |
| 425 | ||
| 426 | // Spawn a thread that shows the splashscreen | |
| 427 | ||
| 428 | 11 | SwingUtilities.invokeLater(new Runnable() |
| 429 | { | |
| 430 | 11 | @Override |
| 431 | public void run() | |
| 432 | { | |
| 433 | 11 | new SplashScreen(); |
| 434 | } | |
| 435 | }); | |
| 436 | ||
| 437 | // Thread off a new instance of the file chooser - this reduces the time it | |
| 438 | // takes to open it later on. | |
| 439 | 11 | new Thread(new Runnable() |
| 440 | { | |
| 441 | 11 | @Override |
| 442 | public void run() | |
| 443 | { | |
| 444 | 11 | Cache.log.debug("Filechooser init thread started."); |
| 445 | 11 | String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); |
| 446 | 11 | JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), |
| 447 | fileFormat); | |
| 448 | 11 | Cache.log.debug("Filechooser init thread finished."); |
| 449 | } | |
| 450 | }).start(); | |
| 451 | // Add the service change listener | |
| 452 | 11 | changeSupport.addJalviewPropertyChangeListener("services", |
| 453 | new PropertyChangeListener() | |
| 454 | { | |
| 455 | ||
| 456 | 131 | @Override |
| 457 | public void propertyChange(PropertyChangeEvent evt) | |
| 458 | { | |
| 459 | 131 | Cache.log.debug("Firing service changed event for " |
| 460 | + evt.getNewValue()); | |
| 461 | 131 | JalviewServicesChanged(evt); |
| 462 | } | |
| 463 | ||
| 464 | }); | |
| 465 | ||
| 466 | } | |
| 467 | ||
| 468 | 11 | this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); |
| 469 | ||
| 470 | 11 | this.addWindowListener(new WindowAdapter() |
| 471 | { | |
| 472 | 0 | @Override |
| 473 | public void windowClosing(WindowEvent evt) | |
| 474 | { | |
| 475 | 0 | quit(); |
| 476 | } | |
| 477 | }); | |
| 478 | ||
| 479 | 11 | MouseAdapter ma; |
| 480 | 11 | this.addMouseListener(ma = new MouseAdapter() |
| 481 | { | |
| 482 | 0 | @Override |
| 483 | public void mousePressed(MouseEvent evt) | |
| 484 | { | |
| 485 | 0 | if (evt.isPopupTrigger()) // Mac |
| 486 | { | |
| 487 | 0 | showPasteMenu(evt.getX(), evt.getY()); |
| 488 | } | |
| 489 | } | |
| 490 | ||
| 491 | 0 | @Override |
| 492 | public void mouseReleased(MouseEvent evt) | |
| 493 | { | |
| 494 | 0 | if (evt.isPopupTrigger()) // Windows |
| 495 | { | |
| 496 | 0 | showPasteMenu(evt.getX(), evt.getY()); |
| 497 | } | |
| 498 | } | |
| 499 | }); | |
| 500 | 11 | desktop.addMouseListener(ma); |
| 501 | ||
| 502 | } | |
| 503 | ||
| 504 | /** | |
| 505 | * Answers true if user preferences to enable experimental features is True | |
| 506 | * (on), else false | |
| 507 | * | |
| 508 | * @return | |
| 509 | */ | |
| 510 | 11 | public boolean showExperimental() |
| 511 | { | |
| 512 | 11 | String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, |
| 513 | Boolean.FALSE.toString()); | |
| 514 | 11 | return Boolean.valueOf(experimental).booleanValue(); |
| 515 | } | |
| 516 | ||
| 517 | 11 | public void doConfigureStructurePrefs() |
| 518 | { | |
| 519 | // configure services | |
| 520 | 11 | StructureSelectionManager ssm = StructureSelectionManager |
| 521 | .getStructureSelectionManager(this); | |
| 522 | 11 | if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true)) |
| 523 | { | |
| 524 | 11 | ssm.setAddTempFacAnnot(jalview.bin.Cache |
| 525 | .getDefault(Preferences.ADD_TEMPFACT_ANN, true)); | |
| 526 | 11 | ssm.setProcessSecondaryStructure(jalview.bin.Cache |
| 527 | .getDefault(Preferences.STRUCT_FROM_PDB, true)); | |
| 528 | 11 | ssm.setSecStructServices( |
| 529 | jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true)); | |
| 530 | } | |
| 531 | else | |
| 532 | { | |
| 533 | 0 | ssm.setAddTempFacAnnot(false); |
| 534 | 0 | ssm.setProcessSecondaryStructure(false); |
| 535 | 0 | ssm.setSecStructServices(false); |
| 536 | } | |
| 537 | } | |
| 538 | ||
| 539 | 4 | public void checkForNews() |
| 540 | { | |
| 541 | 4 | final Desktop me = this; |
| 542 | // Thread off the news reader, in case there are connection problems. | |
| 543 | 4 | addDialogThread(new Runnable() |
| 544 | { | |
| 545 | 3 | @Override |
| 546 | public void run() | |
| 547 | { | |
| 548 | 3 | Cache.log.debug("Starting news thread."); |
| 549 | 3 | jvnews = new BlogReader(me); |
| 550 | 3 | showNews.setVisible(true); |
| 551 | 3 | Cache.log.debug("Completed news thread."); |
| 552 | } | |
| 553 | }); | |
| 554 | } | |
| 555 | ||
| 556 | 11 | public void getIdentifiersOrgData() |
| 557 | { | |
| 558 | // Thread off the identifiers fetcher | |
| 559 | 11 | addDialogThread(new Runnable() |
| 560 | { | |
| 561 | 5 | @Override |
| 562 | public void run() | |
| 563 | { | |
| 564 | 5 | Cache.log.debug("Downloading data from identifiers.org"); |
| 565 | 5 | UrlDownloadClient client = new UrlDownloadClient(); |
| 566 | 5 | try |
| 567 | { | |
| 568 | 5 | client.download(IdOrgSettings.getUrl(), |
| 569 | IdOrgSettings.getDownloadLocation()); | |
| 570 | } catch (IOException e) | |
| 571 | { | |
| 572 | 0 | Cache.log.debug("Exception downloading identifiers.org data" |
| 573 | + e.getMessage()); | |
| 574 | } | |
| 575 | } | |
| 576 | }); | |
| 577 | } | |
| 578 | ||
| 579 | 0 | @Override |
| 580 | protected void showNews_actionPerformed(ActionEvent e) | |
| 581 | { | |
| 582 | 0 | showNews(showNews.isSelected()); |
| 583 | } | |
| 584 | ||
| 585 | 0 | void showNews(boolean visible) |
| 586 | { | |
| 587 | 0 | Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); |
| 588 | 0 | showNews.setSelected(visible); |
| 589 | 0 | if (visible && !jvnews.isVisible()) |
| 590 | { | |
| 591 | 0 | new Thread(new Runnable() |
| 592 | { | |
| 593 | 0 | @Override |
| 594 | public void run() | |
| 595 | { | |
| 596 | 0 | long now = System.currentTimeMillis(); |
| 597 | 0 | Desktop.instance.setProgressBar( |
| 598 | MessageManager.getString("status.refreshing_news"), now); | |
| 599 | 0 | jvnews.refreshNews(); |
| 600 | 0 | Desktop.instance.setProgressBar(null, now); |
| 601 | 0 | jvnews.showNews(); |
| 602 | } | |
| 603 | }).start(); | |
| 604 | } | |
| 605 | } | |
| 606 | ||
| 607 | /** | |
| 608 | * recover the last known dimensions for a jalview window | |
| 609 | * | |
| 610 | * @param windowName | |
| 611 | * - empty string is desktop, all other windows have unique prefix | |
| 612 | * @return null or last known dimensions scaled to current geometry (if last | |
| 613 | * window geom was known) | |
| 614 | */ | |
| 615 | 22 | Rectangle getLastKnownDimensions(String windowName) |
| 616 | { | |
| 617 | // TODO: lock aspect ratio for scaling desktop Bug #0058199 | |
| 618 | 22 | Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); |
| 619 | 22 | String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X"); |
| 620 | 22 | String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y"); |
| 621 | 22 | String width = jalview.bin.Cache |
| 622 | .getProperty(windowName + "SCREEN_WIDTH"); | |
| 623 | 22 | String height = jalview.bin.Cache |
| 624 | .getProperty(windowName + "SCREEN_HEIGHT"); | |
| 625 | 22 | if ((x != null) && (y != null) && (width != null) && (height != null)) |
| 626 | { | |
| 627 | 14 | int ix = Integer.parseInt(x), iy = Integer.parseInt(y), |
| 628 | iw = Integer.parseInt(width), ih = Integer.parseInt(height); | |
| 629 | 14 | if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null) |
| 630 | { | |
| 631 | // attempt #1 - try to cope with change in screen geometry - this | |
| 632 | // version doesn't preserve original jv aspect ratio. | |
| 633 | // take ratio of current screen size vs original screen size. | |
| 634 | 14 | double sw = ((1f * screenSize.width) / (1f * Integer.parseInt( |
| 635 | jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH")))); | |
| 636 | 14 | double sh = ((1f * screenSize.height) / (1f * Integer.parseInt( |
| 637 | jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT")))); | |
| 638 | // rescale the bounds depending upon the current screen geometry. | |
| 639 | 14 | ix = (int) (ix * sw); |
| 640 | 14 | iw = (int) (iw * sw); |
| 641 | 14 | iy = (int) (iy * sh); |
| 642 | 14 | ih = (int) (ih * sh); |
| 643 | 14 | while (ix >= screenSize.width) |
| 644 | { | |
| 645 | 0 | jalview.bin.Cache.log.debug( |
| 646 | "Window geometry location recall error: shifting horizontal to within screenbounds."); | |
| 647 | 0 | ix -= screenSize.width; |
| 648 | } | |
| 649 | 14 | while (iy >= screenSize.height) |
| 650 | { | |
| 651 | 0 | jalview.bin.Cache.log.debug( |
| 652 | "Window geometry location recall error: shifting vertical to within screenbounds."); | |
| 653 | 0 | iy -= screenSize.height; |
| 654 | } | |
| 655 | 14 | jalview.bin.Cache.log.debug( |
| 656 | "Got last known dimensions for " + windowName + ": x:" + ix | |
| 657 | + " y:" + iy + " width:" + iw + " height:" + ih); | |
| 658 | } | |
| 659 | // return dimensions for new instance | |
| 660 | 14 | return new Rectangle(ix, iy, iw, ih); |
| 661 | } | |
| 662 | 8 | return null; |
| 663 | } | |
| 664 | ||
| 665 | 11 | private void doVamsasClientCheck() |
| 666 | { | |
| 667 | 11 | if (Cache.vamsasJarsPresent()) |
| 668 | { | |
| 669 | 11 | setupVamsasDisconnectedGui(); |
| 670 | 11 | VamsasMenu.setVisible(true); |
| 671 | 11 | final Desktop us = this; |
| 672 | 11 | VamsasMenu.addMenuListener(new MenuListener() |
| 673 | { | |
| 674 | // this listener remembers when the menu was first selected, and | |
| 675 | // doesn't rebuild the session list until it has been cleared and | |
| 676 | // reselected again. | |
| 677 | boolean refresh = true; | |
| 678 | ||
| 679 | 0 | @Override |
| 680 | public void menuCanceled(MenuEvent e) | |
| 681 | { | |
| 682 | 0 | refresh = true; |
| 683 | } | |
| 684 | ||
| 685 | 0 | @Override |
| 686 | public void menuDeselected(MenuEvent e) | |
| 687 | { | |
| 688 | 0 | refresh = true; |
| 689 | } | |
| 690 | ||
| 691 | 0 | @Override |
| 692 | public void menuSelected(MenuEvent e) | |
| 693 | { | |
| 694 | 0 | if (refresh) |
| 695 | { | |
| 696 | 0 | us.buildVamsasStMenu(); |
| 697 | 0 | refresh = false; |
| 698 | } | |
| 699 | } | |
| 700 | }); | |
| 701 | 11 | vamsasStart.setVisible(true); |
| 702 | } | |
| 703 | } | |
| 704 | ||
| 705 | 0 | void showPasteMenu(int x, int y) |
| 706 | { | |
| 707 | 0 | JPopupMenu popup = new JPopupMenu(); |
| 708 | 0 | JMenuItem item = new JMenuItem( |
| 709 | MessageManager.getString("label.paste_new_window")); | |
| 710 | 0 | item.addActionListener(new ActionListener() |
| 711 | { | |
| 712 | 0 | @Override |
| 713 | public void actionPerformed(ActionEvent evt) | |
| 714 | { | |
| 715 | 0 | paste(); |
| 716 | } | |
| 717 | }); | |
| 718 | ||
| 719 | 0 | popup.add(item); |
| 720 | 0 | popup.show(this, x, y); |
| 721 | } | |
| 722 | ||
| 723 | 0 | public void paste() |
| 724 | { | |
| 725 | 0 | try |
| 726 | { | |
| 727 | 0 | Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); |
| 728 | 0 | Transferable contents = c.getContents(this); |
| 729 | ||
| 730 | 0 | if (contents != null) |
| 731 | { | |
| 732 | 0 | String file = (String) contents |
| 733 | .getTransferData(DataFlavor.stringFlavor); | |
| 734 | ||
| 735 | 0 | FileFormatI format = new IdentifyFile().identify(file, |
| 736 | DataSourceType.PASTE); | |
| 737 | ||
| 738 | 0 | new FileLoader().LoadFile(file, DataSourceType.PASTE, format); |
| 739 | ||
| 740 | } | |
| 741 | } catch (Exception ex) | |
| 742 | { | |
| 743 | 0 | System.out.println( |
| 744 | "Unable to paste alignment from system clipboard:\n" + ex); | |
| 745 | } | |
| 746 | } | |
| 747 | ||
| 748 | /** | |
| 749 | * Adds and opens the given frame to the desktop | |
| 750 | * | |
| 751 | * @param frame | |
| 752 | * Frame to show | |
| 753 | * @param title | |
| 754 | * Visible Title | |
| 755 | * @param w | |
| 756 | * width | |
| 757 | * @param h | |
| 758 | * height | |
| 759 | */ | |
| 760 | 157 | public static synchronized void addInternalFrame( |
| 761 | final JInternalFrame frame, String title, int w, int h) | |
| 762 | { | |
| 763 | 157 | addInternalFrame(frame, title, true, w, h, true, false); |
| 764 | } | |
| 765 | ||
| 766 | /** | |
| 767 | * Add an internal frame to the Jalview desktop | |
| 768 | * | |
| 769 | * @param frame | |
| 770 | * Frame to show | |
| 771 | * @param title | |
| 772 | * Visible Title | |
| 773 | * @param makeVisible | |
| 774 | * When true, display frame immediately, otherwise, caller must call | |
| 775 | * setVisible themselves. | |
| 776 | * @param w | |
| 777 | * width | |
| 778 | * @param h | |
| 779 | * height | |
| 780 | */ | |
| 781 | 0 | public static synchronized void addInternalFrame( |
| 782 | final JInternalFrame frame, String title, boolean makeVisible, | |
| 783 | int w, int h) | |
| 784 | { | |
| 785 | 0 | addInternalFrame(frame, title, makeVisible, w, h, true, false); |
| 786 | } | |
| 787 | ||
| 788 | /** | |
| 789 | * Add an internal frame to the Jalview desktop and make it visible | |
| 790 | * | |
| 791 | * @param frame | |
| 792 | * Frame to show | |
| 793 | * @param title | |
| 794 | * Visible Title | |
| 795 | * @param w | |
| 796 | * width | |
| 797 | * @param h | |
| 798 | * height | |
| 799 | * @param resizable | |
| 800 | * Allow resize | |
| 801 | */ | |
| 802 | 17 | public static synchronized void addInternalFrame( |
| 803 | final JInternalFrame frame, String title, int w, int h, | |
| 804 | boolean resizable) | |
| 805 | { | |
| 806 | 17 | addInternalFrame(frame, title, true, w, h, resizable, false); |
| 807 | } | |
| 808 | ||
| 809 | /** | |
| 810 | * Add an internal frame to the Jalview desktop | |
| 811 | * | |
| 812 | * @param frame | |
| 813 | * Frame to show | |
| 814 | * @param title | |
| 815 | * Visible Title | |
| 816 | * @param makeVisible | |
| 817 | * When true, display frame immediately, otherwise, caller must call | |
| 818 | * setVisible themselves. | |
| 819 | * @param w | |
| 820 | * width | |
| 821 | * @param h | |
| 822 | * height | |
| 823 | * @param resizable | |
| 824 | * Allow resize | |
| 825 | * @param ignoreMinSize | |
| 826 | * Do not set the default minimum size for frame | |
| 827 | */ | |
| 828 | 190 | public static synchronized void addInternalFrame( |
| 829 | final JInternalFrame frame, String title, boolean makeVisible, | |
| 830 | int w, int h, boolean resizable, boolean ignoreMinSize) | |
| 831 | { | |
| 832 | ||
| 833 | // TODO: allow callers to determine X and Y position of frame (eg. via | |
| 834 | // bounds object). | |
| 835 | // TODO: consider fixing method to update entries in the window submenu with | |
| 836 | // the current window title | |
| 837 | ||
| 838 | 190 | frame.setTitle(title); |
| 839 | 190 | if (frame.getWidth() < 1 || frame.getHeight() < 1) |
| 840 | { | |
| 841 | 37 | frame.setSize(w, h); |
| 842 | } | |
| 843 | // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN | |
| 844 | // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN | |
| 845 | // IF JALVIEW IS RUNNING HEADLESS | |
| 846 | // /////////////////////////////////////////////// | |
| 847 | 190 | if (instance == null || (System.getProperty("java.awt.headless") != null |
| 848 | && System.getProperty("java.awt.headless").equals("true"))) | |
| 849 | { | |
| 850 | 1 | return; |
| 851 | } | |
| 852 | ||
| 853 | 189 | openFrameCount++; |
| 854 | ||
| 855 | 189 | if (!ignoreMinSize) |
| 856 | { | |
| 857 | 173 | frame.setMinimumSize( |
| 858 | new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); | |
| 859 | ||
| 860 | // Set default dimension for Alignment Frame window. | |
| 861 | // The Alignment Frame window could be added from a number of places, | |
| 862 | // hence, | |
| 863 | // I did this here in order not to miss out on any Alignment frame. | |
| 864 | 173 | if (frame instanceof AlignFrame) |
| 865 | { | |
| 866 | 130 | frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, |
| 867 | ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); | |
| 868 | } | |
| 869 | } | |
| 870 | ||
| 871 | 189 | frame.setVisible(makeVisible); |
| 872 | 189 | frame.setClosable(true); |
| 873 | 189 | frame.setResizable(resizable); |
| 874 | 189 | frame.setMaximizable(resizable); |
| 875 | 189 | frame.setIconifiable(resizable); |
| 876 | 189 | frame.setOpaque(/** @j2sNative true || */ |
| 877 | false); | |
| 878 | ||
| 879 | 189 | if (frame.getX() < 1 && frame.getY() < 1) |
| 880 | { | |
| 881 | 92 | frame.setLocation(xOffset * openFrameCount, |
| 882 | yOffset * ((openFrameCount - 1) % 10) + yOffset); | |
| 883 | } | |
| 884 | ||
| 885 | /* | |
| 886 | * add an entry for the new frame in the Window menu | |
| 887 | * (and remove it when the frame is closed) | |
| 888 | */ | |
| 889 | 189 | final JMenuItem menuItem = new JMenuItem(title); |
| 890 | 189 | frame.addInternalFrameListener(new InternalFrameAdapter() |
| 891 | { | |
| 892 | 274 | @Override |
| 893 | public void internalFrameActivated(InternalFrameEvent evt) | |
| 894 | { | |
| 895 | 274 | JInternalFrame itf = desktop.getSelectedFrame(); |
| 896 | 274 | if (itf != null) |
| 897 | { | |
| 898 | 274 | if (itf instanceof AlignFrame) |
| 899 | { | |
| 900 | 182 | Jalview.setCurrentAlignFrame((AlignFrame) itf); |
| 901 | } | |
| 902 | 274 | itf.requestFocus(); |
| 903 | } | |
| 904 | } | |
| 905 | ||
| 906 | 134 | @Override |
| 907 | public void internalFrameClosed(InternalFrameEvent evt) | |
| 908 | { | |
| 909 | 134 | PaintRefresher.RemoveComponent(frame); |
| 910 | ||
| 911 | /* | |
| 912 | * defensive check to prevent frames being | |
| 913 | * added half off the window | |
| 914 | */ | |
| 915 | 134 | if (openFrameCount > 0) |
| 916 | { | |
| 917 | 134 | openFrameCount--; |
| 918 | } | |
| 919 | ||
| 920 | /* | |
| 921 | * ensure no reference to alignFrame retained by menu item listener | |
| 922 | */ | |
| 923 | 134 | if (menuItem.getActionListeners().length > 0) |
| 924 | { | |
| 925 | 134 | menuItem.removeActionListener(menuItem.getActionListeners()[0]); |
| 926 | } | |
| 927 | 134 | windowMenu.remove(menuItem); |
| 928 | }; | |
| 929 | }); | |
| 930 | ||
| 931 | 189 | menuItem.addActionListener(new ActionListener() |
| 932 | { | |
| 933 | 0 | @Override |
| 934 | public void actionPerformed(ActionEvent e) | |
| 935 | { | |
| 936 | 0 | try |
| 937 | { | |
| 938 | 0 | frame.setSelected(true); |
| 939 | 0 | frame.setIcon(false); |
| 940 | } catch (java.beans.PropertyVetoException ex) | |
| 941 | { | |
| 942 | // System.err.println(ex.toString()); | |
| 943 | } | |
| 944 | } | |
| 945 | }); | |
| 946 | ||
| 947 | 189 | setKeyBindings(frame); |
| 948 | ||
| 949 | 189 | desktop.add(frame); |
| 950 | ||
| 951 | 189 | windowMenu.add(menuItem); |
| 952 | ||
| 953 | 189 | frame.toFront(); |
| 954 | 189 | try |
| 955 | { | |
| 956 | 189 | frame.setSelected(true); |
| 957 | 189 | frame.requestFocus(); |
| 958 | } catch (java.beans.PropertyVetoException ve) | |
| 959 | { | |
| 960 | } catch (java.lang.ClassCastException cex) | |
| 961 | { | |
| 962 | 0 | Cache.log.warn( |
| 963 | "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869", | |
| 964 | cex); | |
| 965 | } | |
| 966 | } | |
| 967 | ||
| 968 | /** | |
| 969 | * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the | |
| 970 | * window | |
| 971 | * | |
| 972 | * @param frame | |
| 973 | */ | |
| 974 | 189 | private static void setKeyBindings(JInternalFrame frame) |
| 975 | { | |
| 976 | 189 | @SuppressWarnings("serial") |
| 977 | final Action closeAction = new AbstractAction() | |
| 978 | { | |
| 979 | 0 | @Override |
| 980 | public void actionPerformed(ActionEvent e) | |
| 981 | { | |
| 982 | 0 | frame.dispose(); |
| 983 | } | |
| 984 | }; | |
| 985 | ||
| 986 | /* | |
| 987 | * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action | |
| 988 | */ | |
| 989 | 189 | KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
| 990 | InputEvent.CTRL_DOWN_MASK); | |
| 991 | 189 | KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
| 992 | Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); | |
| 993 | ||
| 994 | 189 | InputMap inputMap = frame |
| 995 | .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); | |
| 996 | 189 | String ctrlW = ctrlWKey.toString(); |
| 997 | 189 | inputMap.put(ctrlWKey, ctrlW); |
| 998 | 189 | inputMap.put(cmdWKey, ctrlW); |
| 999 | ||
| 1000 | 189 | ActionMap actionMap = frame.getActionMap(); |
| 1001 | 189 | actionMap.put(ctrlW, closeAction); |
| 1002 | } | |
| 1003 | ||
| 1004 | 0 | @Override |
| 1005 | public void lostOwnership(Clipboard clipboard, Transferable contents) | |
| 1006 | { | |
| 1007 | 0 | if (!internalCopy) |
| 1008 | { | |
| 1009 | 0 | Desktop.jalviewClipboard = null; |
| 1010 | } | |
| 1011 | ||
| 1012 | 0 | internalCopy = false; |
| 1013 | } | |
| 1014 | ||
| 1015 | 0 | @Override |
| 1016 | public void dragEnter(DropTargetDragEvent evt) | |
| 1017 | { | |
| 1018 | } | |
| 1019 | ||
| 1020 | 0 | @Override |
| 1021 | public void dragExit(DropTargetEvent evt) | |
| 1022 | { | |
| 1023 | } | |
| 1024 | ||
| 1025 | 0 | @Override |
| 1026 | public void dragOver(DropTargetDragEvent evt) | |
| 1027 | { | |
| 1028 | } | |
| 1029 | ||
| 1030 | 0 | @Override |
| 1031 | public void dropActionChanged(DropTargetDragEvent evt) | |
| 1032 | { | |
| 1033 | } | |
| 1034 | ||
| 1035 | /** | |
| 1036 | * DOCUMENT ME! | |
| 1037 | * | |
| 1038 | * @param evt | |
| 1039 | * DOCUMENT ME! | |
| 1040 | */ | |
| 1041 | 0 | @Override |
| 1042 | public void drop(DropTargetDropEvent evt) | |
| 1043 | { | |
| 1044 | 0 | boolean success = true; |
| 1045 | // JAL-1552 - acceptDrop required before getTransferable call for | |
| 1046 | // Java's Transferable for native dnd | |
| 1047 | 0 | evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); |
| 1048 | 0 | Transferable t = evt.getTransferable(); |
| 1049 | 0 | List<Object> files = new ArrayList<>(); |
| 1050 | 0 | List<DataSourceType> protocols = new ArrayList<>(); |
| 1051 | ||
| 1052 | 0 | try |
| 1053 | { | |
| 1054 | 0 | Desktop.transferFromDropTarget(files, protocols, evt, t); |
| 1055 | } catch (Exception e) | |
| 1056 | { | |
| 1057 | 0 | e.printStackTrace(); |
| 1058 | 0 | success = false; |
| 1059 | } | |
| 1060 | ||
| 1061 | 0 | if (files != null) |
| 1062 | { | |
| 1063 | 0 | try |
| 1064 | { | |
| 1065 | 0 | for (int i = 0; i < files.size(); i++) |
| 1066 | { | |
| 1067 | // BH 2018 File or String | |
| 1068 | 0 | Object file = files.get(i); |
| 1069 | 0 | String fileName = file.toString(); |
| 1070 | 0 | DataSourceType protocol = (protocols == null) |
| 1071 | ? DataSourceType.FILE | |
| 1072 | : protocols.get(i); | |
| 1073 | 0 | FileFormatI format = null; |
| 1074 | ||
| 1075 | 0 | if (fileName.endsWith(".jar")) |
| 1076 | { | |
| 1077 | 0 | format = FileFormat.Jalview; |
| 1078 | ||
| 1079 | } | |
| 1080 | else | |
| 1081 | { | |
| 1082 | 0 | format = new IdentifyFile().identify(file, protocol); |
| 1083 | } | |
| 1084 | ||
| 1085 | 0 | new FileLoader().LoadFile(null, file, protocol, format); |
| 1086 | ||
| 1087 | } | |
| 1088 | } catch (Exception ex) | |
| 1089 | { | |
| 1090 | 0 | success = false; |
| 1091 | } | |
| 1092 | } | |
| 1093 | 0 | evt.dropComplete(success); // need this to ensure input focus is properly |
| 1094 | // transfered to any new windows created | |
| 1095 | } | |
| 1096 | ||
| 1097 | /** | |
| 1098 | * DOCUMENT ME! | |
| 1099 | * | |
| 1100 | * @param e | |
| 1101 | * DOCUMENT ME! | |
| 1102 | */ | |
| 1103 | 0 | @Override |
| 1104 | public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) | |
| 1105 | { | |
| 1106 | 0 | String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); |
| 1107 | 0 | JalviewFileChooser chooser = JalviewFileChooser |
| 1108 | .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); | |
| 1109 | ||
| 1110 | 0 | chooser.setFileView(new JalviewFileView()); |
| 1111 | 0 | chooser.setDialogTitle( |
| 1112 | MessageManager.getString("label.open_local_file")); | |
| 1113 | 0 | chooser.setToolTipText(MessageManager.getString("action.open")); |
| 1114 | ||
| 1115 | 0 | chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) |
| 1116 | { | |
| 1117 | ||
| 1118 | 0 | @Override |
| 1119 | public void run() | |
| 1120 | { | |
| 1121 | 0 | File selectedFile = chooser.getSelectedFile(); |
| 1122 | 0 | Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); |
| 1123 | ||
| 1124 | 0 | FileFormatI format = chooser.getSelectedFormat(); |
| 1125 | ||
| 1126 | /* | |
| 1127 | * Call IdentifyFile to verify the file contains what its extension implies. | |
| 1128 | * Skip this step for dynamically added file formats, because | |
| 1129 | * IdentifyFile does not know how to recognise them. | |
| 1130 | */ | |
| 1131 | 0 | if (FileFormats.getInstance().isIdentifiable(format)) |
| 1132 | { | |
| 1133 | 0 | try |
| 1134 | { | |
| 1135 | 0 | format = new IdentifyFile().identify(selectedFile, |
| 1136 | DataSourceType.FILE); | |
| 1137 | } catch (FileFormatException e) | |
| 1138 | { | |
| 1139 | // format = null; //?? | |
| 1140 | } | |
| 1141 | } | |
| 1142 | ||
| 1143 | 0 | new FileLoader().LoadFile(viewport, selectedFile, |
| 1144 | DataSourceType.FILE, format); | |
| 1145 | } | |
| 1146 | }).openDialog(this); | |
| 1147 | } | |
| 1148 | ||
| 1149 | /** | |
| 1150 | * Shows a dialog for input of a URL at which to retrieve alignment data | |
| 1151 | * | |
| 1152 | * @param viewport | |
| 1153 | */ | |
| 1154 | 0 | @Override |
| 1155 | public void inputURLMenuItem_actionPerformed(AlignViewport viewport) | |
| 1156 | { | |
| 1157 | // This construct allows us to have a wider textfield | |
| 1158 | // for viewing | |
| 1159 | 0 | JLabel label = new JLabel( |
| 1160 | MessageManager.getString("label.input_file_url")); | |
| 1161 | ||
| 1162 | 0 | JPanel panel = new JPanel(new GridLayout(2, 1)); |
| 1163 | 0 | panel.add(label); |
| 1164 | ||
| 1165 | /* | |
| 1166 | * the URL to fetch is | |
| 1167 | * Java: an editable combobox with history | |
| 1168 | * JS: (pending JAL-3038) a plain text field | |
| 1169 | */ | |
| 1170 | 0 | JComponent history; |
| 1171 | 0 | String urlBase = "http://www."; |
| 1172 | 0 | if (Jalview.isJS()) |
| 1173 | { | |
| 1174 | 0 | history = new JTextField(urlBase, 35); |
| 1175 | } | |
| 1176 | else | |
| 1177 | { | |
| 1178 | 0 | JComboBox<String> asCombo = new JComboBox<>(); |
| 1179 | 0 | asCombo.setPreferredSize(new Dimension(400, 20)); |
| 1180 | 0 | asCombo.setEditable(true); |
| 1181 | 0 | asCombo.addItem(urlBase); |
| 1182 | 0 | String historyItems = Cache.getProperty("RECENT_URL"); |
| 1183 | 0 | if (historyItems != null) |
| 1184 | { | |
| 1185 | 0 | for (String token : historyItems.split("\\t")) |
| 1186 | { | |
| 1187 | 0 | asCombo.addItem(token); |
| 1188 | } | |
| 1189 | } | |
| 1190 | 0 | history = asCombo; |
| 1191 | } | |
| 1192 | 0 | panel.add(history); |
| 1193 | ||
| 1194 | 0 | Object[] options = new Object[] { MessageManager.getString("action.ok"), |
| 1195 | MessageManager.getString("action.cancel") }; | |
| 1196 | 0 | RunResponse action = new RunResponse(JvOptionPane.OK_OPTION) { |
| 1197 | 0 | @Override |
| 1198 | public void run() | |
| 1199 | { | |
| 1200 | 0 | String url = Jalview.isJS() ? ((JTextField) history).getText() |
| 1201 | : ((JComboBox<String>) history).getSelectedItem() | |
| 1202 | .toString(); | |
| 1203 | ||
| 1204 | 0 | if (url.toLowerCase().endsWith(".jar")) |
| 1205 | { | |
| 1206 | 0 | if (viewport != null) |
| 1207 | { | |
| 1208 | 0 | new FileLoader().LoadFile(viewport, url, DataSourceType.URL, |
| 1209 | FileFormat.Jalview); | |
| 1210 | } | |
| 1211 | else | |
| 1212 | { | |
| 1213 | 0 | new FileLoader().LoadFile(url, DataSourceType.URL, |
| 1214 | FileFormat.Jalview); | |
| 1215 | } | |
| 1216 | } | |
| 1217 | else | |
| 1218 | { | |
| 1219 | 0 | FileFormatI format = null; |
| 1220 | 0 | try |
| 1221 | { | |
| 1222 | 0 | format = new IdentifyFile().identify(url, DataSourceType.URL); |
| 1223 | } catch (FileFormatException e) | |
| 1224 | { | |
| 1225 | // TODO revise error handling, distinguish between | |
| 1226 | // URL not found and response not valid | |
| 1227 | } | |
| 1228 | ||
| 1229 | 0 | if (format == null) |
| 1230 | { | |
| 1231 | 0 | String msg = MessageManager.formatMessage("label.couldnt_locate", url); |
| 1232 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, |
| 1233 | MessageManager.getString("label.url_not_found"), | |
| 1234 | JvOptionPane.WARNING_MESSAGE); | |
| 1235 | ||
| 1236 | 0 | return; |
| 1237 | } | |
| 1238 | ||
| 1239 | 0 | if (viewport != null) |
| 1240 | { | |
| 1241 | 0 | new FileLoader().LoadFile(viewport, url, DataSourceType.URL, |
| 1242 | format); | |
| 1243 | } | |
| 1244 | else | |
| 1245 | { | |
| 1246 | 0 | new FileLoader().LoadFile(url, DataSourceType.URL, format); |
| 1247 | } | |
| 1248 | } | |
| 1249 | }}; | |
| 1250 | 0 | String dialogOption = MessageManager |
| 1251 | .getString("label.input_alignment_from_url"); | |
| 1252 | 0 | JvOptionPane.newOptionDialog(desktop).response(action) |
| 1253 | .showInternalDialog(panel, dialogOption, | |
| 1254 | JvOptionPane.YES_NO_CANCEL_OPTION, | |
| 1255 | JvOptionPane.PLAIN_MESSAGE, null, options, | |
| 1256 | MessageManager.getString("action.ok")); | |
| 1257 | } | |
| 1258 | ||
| 1259 | /** | |
| 1260 | * Opens the CutAndPaste window for the user to paste an alignment in to | |
| 1261 | * | |
| 1262 | * @param viewPanel | |
| 1263 | * - if not null, the pasted alignment is added to the current | |
| 1264 | * alignment; if null, to a new alignment window | |
| 1265 | */ | |
| 1266 | 0 | @Override |
| 1267 | public void inputTextboxMenuItem_actionPerformed( | |
| 1268 | AlignmentViewPanel viewPanel) | |
| 1269 | { | |
| 1270 | 0 | CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
| 1271 | 0 | cap.setForInput(viewPanel); |
| 1272 | 0 | Desktop.addInternalFrame(cap, |
| 1273 | MessageManager.getString("label.cut_paste_alignmen_file"), true, | |
| 1274 | 600, 500); | |
| 1275 | } | |
| 1276 | ||
| 1277 | /* | |
| 1278 | * Exit the program | |
| 1279 | */ | |
| 1280 | 0 | @Override |
| 1281 | public void quit() | |
| 1282 | { | |
| 1283 | 0 | Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); |
| 1284 | 0 | jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH", |
| 1285 | screen.width + ""); | |
| 1286 | 0 | jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", |
| 1287 | screen.height + ""); | |
| 1288 | 0 | storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, |
| 1289 | getWidth(), getHeight())); | |
| 1290 | ||
| 1291 | 0 | if (jconsole != null) |
| 1292 | { | |
| 1293 | 0 | storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); |
| 1294 | 0 | jconsole.stopConsole(); |
| 1295 | } | |
| 1296 | 0 | if (jvnews != null) |
| 1297 | { | |
| 1298 | 0 | storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); |
| 1299 | ||
| 1300 | } | |
| 1301 | 0 | if (dialogExecutor != null) |
| 1302 | { | |
| 1303 | 0 | dialogExecutor.shutdownNow(); |
| 1304 | } | |
| 1305 | 0 | closeAll_actionPerformed(null); |
| 1306 | ||
| 1307 | 0 | if (groovyConsole != null) |
| 1308 | { | |
| 1309 | // suppress a possible repeat prompt to save script | |
| 1310 | 0 | groovyConsole.setDirty(false); |
| 1311 | 0 | groovyConsole.exit(); |
| 1312 | } | |
| 1313 | 0 | System.exit(0); |
| 1314 | } | |
| 1315 | ||
| 1316 | 0 | private void storeLastKnownDimensions(String string, Rectangle jc) |
| 1317 | { | |
| 1318 | 0 | jalview.bin.Cache.log.debug("Storing last known dimensions for " |
| 1319 | + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width | |
| 1320 | + " height:" + jc.height); | |
| 1321 | ||
| 1322 | 0 | jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + ""); |
| 1323 | 0 | jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + ""); |
| 1324 | 0 | jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + ""); |
| 1325 | 0 | jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + ""); |
| 1326 | } | |
| 1327 | ||
| 1328 | /** | |
| 1329 | * DOCUMENT ME! | |
| 1330 | * | |
| 1331 | * @param e | |
| 1332 | * DOCUMENT ME! | |
| 1333 | */ | |
| 1334 | 0 | @Override |
| 1335 | public void aboutMenuItem_actionPerformed(ActionEvent e) | |
| 1336 | { | |
| 1337 | // StringBuffer message = getAboutMessage(false); | |
| 1338 | // JvOptionPane.showInternalMessageDialog(Desktop.desktop, | |
| 1339 | // | |
| 1340 | // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); | |
| 1341 | 0 | new Thread(new Runnable() |
| 1342 | { | |
| 1343 | 0 | @Override |
| 1344 | public void run() | |
| 1345 | { | |
| 1346 | 0 | new SplashScreen(true); |
| 1347 | } | |
| 1348 | }).start(); | |
| 1349 | } | |
| 1350 | ||
| 1351 | 114 | public StringBuffer getAboutMessage(boolean shortv) |
| 1352 | { | |
| 1353 | 114 | StringBuffer message = new StringBuffer(); |
| 1354 | 114 | message.append("<html>"); |
| 1355 | 114 | if (shortv) |
| 1356 | { | |
| 1357 | 114 | message.append("<h1><strong>Version: " |
| 1358 | + jalview.bin.Cache.getProperty("VERSION") | |
| 1359 | + "</strong></h1>"); | |
| 1360 | 114 | message.append("<strong>Last Updated: <em>" |
| 1361 | + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") | |
| 1362 | + "</em></strong>"); | |
| 1363 | ||
| 1364 | } | |
| 1365 | else | |
| 1366 | { | |
| 1367 | ||
| 1368 | 0 | message.append("<strong>Version " |
| 1369 | + jalview.bin.Cache.getProperty("VERSION") | |
| 1370 | + "; last updated: " | |
| 1371 | + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); | |
| 1372 | } | |
| 1373 | ||
| 1374 | 114 | if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") |
| 1375 | .equals("Checking")) | |
| 1376 | { | |
| 1377 | 0 | message.append("<br>...Checking latest version...</br>"); |
| 1378 | } | |
| 1379 | 114 | else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") |
| 1380 | .equals(jalview.bin.Cache.getProperty("VERSION"))) | |
| 1381 | { | |
| 1382 | 0 | boolean red = false; |
| 1383 | 0 | if (jalview.bin.Cache.getProperty("VERSION").toLowerCase() |
| 1384 | .indexOf("automated build") == -1) | |
| 1385 | { | |
| 1386 | 0 | red = true; |
| 1387 | // Displayed when code version and jnlp version do not match and code | |
| 1388 | // version is not a development build | |
| 1389 | 0 | message.append("<div style=\"color: #FF0000;font-style: bold;\">"); |
| 1390 | } | |
| 1391 | ||
| 1392 | 0 | message.append("<br>!! Version " |
| 1393 | + jalview.bin.Cache.getDefault("LATEST_VERSION", | |
| 1394 | "..Checking..") | |
| 1395 | + " is available for download from " | |
| 1396 | + jalview.bin.Cache.getDefault("www.jalview.org", | |
| 1397 | "http://www.jalview.org") | |
| 1398 | + " !!"); | |
| 1399 | 0 | if (red) |
| 1400 | { | |
| 1401 | 0 | message.append("</div>"); |
| 1402 | } | |
| 1403 | } | |
| 1404 | 114 | message.append("<br>Authors: " + jalview.bin.Cache.getDefault( |
| 1405 | "AUTHORFNAMES", | |
| 1406 | "The Jalview Authors (See AUTHORS file for current list)") | |
| 1407 | + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>" | |
| 1408 | + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list" | |
| 1409 | + "<br><br>If you use Jalview, please cite:" | |
| 1410 | + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" | |
| 1411 | + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" | |
| 1412 | + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033" | |
| 1413 | + "</html>"); | |
| 1414 | 113 | return message; |
| 1415 | } | |
| 1416 | ||
| 1417 | /** | |
| 1418 | * Action on requesting Help documentation | |
| 1419 | */ | |
| 1420 | 0 | @Override |
| 1421 | public void documentationMenuItem_actionPerformed() | |
| 1422 | { | |
| 1423 | 0 | try |
| 1424 | { | |
| 1425 | 0 | if (Jalview.isJS()) |
| 1426 | { | |
| 1427 | 0 | BrowserLauncher.openURL("http://www.jalview.org/help.html"); |
| 1428 | } | |
| 1429 | else | |
| 1430 | { | |
| 1431 | 0 | Help.showHelpWindow(); |
| 1432 | } | |
| 1433 | } catch (Exception ex) | |
| 1434 | { | |
| 1435 | 0 | System.err.println("Error opening help: " + ex.getMessage()); |
| 1436 | } | |
| 1437 | } | |
| 1438 | ||
| 1439 | 20 | @Override |
| 1440 | public void closeAll_actionPerformed(ActionEvent e) | |
| 1441 | { | |
| 1442 | // TODO show a progress bar while closing? | |
| 1443 | 20 | JInternalFrame[] frames = desktop.getAllFrames(); |
| 1444 | 90 | for (int i = 0; i < frames.length; i++) |
| 1445 | { | |
| 1446 | 70 | try |
| 1447 | { | |
| 1448 | 70 | frames[i].setClosed(true); |
| 1449 | } catch (java.beans.PropertyVetoException ex) | |
| 1450 | { | |
| 1451 | } | |
| 1452 | } | |
| 1453 | 20 | Jalview.setCurrentAlignFrame(null); |
| 1454 | 20 | System.out.println("ALL CLOSED"); |
| 1455 | 20 | if (v_client != null) |
| 1456 | { | |
| 1457 | // TODO clear binding to vamsas document objects on close_all | |
| 1458 | } | |
| 1459 | ||
| 1460 | /* | |
| 1461 | * reset state of singleton objects as appropriate (clear down session state | |
| 1462 | * when all windows are closed) | |
| 1463 | */ | |
| 1464 | 20 | StructureSelectionManager ssm = StructureSelectionManager |
| 1465 | .getStructureSelectionManager(this); | |
| 1466 | 20 | if (ssm != null) |
| 1467 | { | |
| 1468 | 20 | ssm.resetAll(); |
| 1469 | } | |
| 1470 | } | |
| 1471 | ||
| 1472 | 0 | @Override |
| 1473 | public void raiseRelated_actionPerformed(ActionEvent e) | |
| 1474 | { | |
| 1475 | 0 | reorderAssociatedWindows(false, false); |
| 1476 | } | |
| 1477 | ||
| 1478 | 0 | @Override |
| 1479 | public void minimizeAssociated_actionPerformed(ActionEvent e) | |
| 1480 | { | |
| 1481 | 0 | reorderAssociatedWindows(true, false); |
| 1482 | } | |
| 1483 | ||
| 1484 | 0 | void closeAssociatedWindows() |
| 1485 | { | |
| 1486 | 0 | reorderAssociatedWindows(false, true); |
| 1487 | } | |
| 1488 | ||
| 1489 | /* | |
| 1490 | * (non-Javadoc) | |
| 1491 | * | |
| 1492 | * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event. | |
| 1493 | * ActionEvent) | |
| 1494 | */ | |
| 1495 | 0 | @Override |
| 1496 | protected void garbageCollect_actionPerformed(ActionEvent e) | |
| 1497 | { | |
| 1498 | // We simply collect the garbage | |
| 1499 | 0 | jalview.bin.Cache.log.debug("Collecting garbage..."); |
| 1500 | 0 | System.gc(); |
| 1501 | 0 | jalview.bin.Cache.log.debug("Finished garbage collection."); |
| 1502 | } | |
| 1503 | ||
| 1504 | /* | |
| 1505 | * (non-Javadoc) | |
| 1506 | * | |
| 1507 | * @see | |
| 1508 | * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent | |
| 1509 | * ) | |
| 1510 | */ | |
| 1511 | 0 | @Override |
| 1512 | protected void showMemusage_actionPerformed(ActionEvent e) | |
| 1513 | { | |
| 1514 | 0 | desktop.showMemoryUsage(showMemusage.isSelected()); |
| 1515 | } | |
| 1516 | ||
| 1517 | /* | |
| 1518 | * (non-Javadoc) | |
| 1519 | * | |
| 1520 | * @see | |
| 1521 | * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent | |
| 1522 | * ) | |
| 1523 | */ | |
| 1524 | 0 | @Override |
| 1525 | protected void showConsole_actionPerformed(ActionEvent e) | |
| 1526 | { | |
| 1527 | 0 | showConsole(showConsole.isSelected()); |
| 1528 | } | |
| 1529 | ||
| 1530 | Console jconsole = null; | |
| 1531 | ||
| 1532 | /** | |
| 1533 | * control whether the java console is visible or not | |
| 1534 | * | |
| 1535 | * @param selected | |
| 1536 | */ | |
| 1537 | 11 | void showConsole(boolean selected) |
| 1538 | { | |
| 1539 | // TODO: decide if we should update properties file | |
| 1540 | 11 | if (jconsole != null) // BH 2018 |
| 1541 | { | |
| 1542 | 11 | showConsole.setSelected(selected); |
| 1543 | 11 | Cache.setProperty("SHOW_JAVA_CONSOLE", |
| 1544 | Boolean.valueOf(selected).toString()); | |
| 1545 | 11 | jconsole.setVisible(selected); |
| 1546 | } | |
| 1547 | } | |
| 1548 | ||
| 1549 | 0 | void reorderAssociatedWindows(boolean minimize, boolean close) |
| 1550 | { | |
| 1551 | 0 | JInternalFrame[] frames = desktop.getAllFrames(); |
| 1552 | 0 | if (frames == null || frames.length < 1) |
| 1553 | { | |
| 1554 | 0 | return; |
| 1555 | } | |
| 1556 | ||
| 1557 | 0 | AlignmentViewport source = null, target = null; |
| 1558 | 0 | if (frames[0] instanceof AlignFrame) |
| 1559 | { | |
| 1560 | 0 | source = ((AlignFrame) frames[0]).getCurrentView(); |
| 1561 | } | |
| 1562 | 0 | else if (frames[0] instanceof TreePanel) |
| 1563 | { | |
| 1564 | 0 | source = ((TreePanel) frames[0]).getViewPort(); |
| 1565 | } | |
| 1566 | 0 | else if (frames[0] instanceof PCAPanel) |
| 1567 | { | |
| 1568 | 0 | source = ((PCAPanel) frames[0]).av; |
| 1569 | } | |
| 1570 | 0 | else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) |
| 1571 | { | |
| 1572 | 0 | source = ((PairwiseAlignPanel) frames[0].getContentPane()).av; |
| 1573 | } | |
| 1574 | ||
| 1575 | 0 | if (source != null) |
| 1576 | { | |
| 1577 | 0 | for (int i = 0; i < frames.length; i++) |
| 1578 | { | |
| 1579 | 0 | target = null; |
| 1580 | 0 | if (frames[i] == null) |
| 1581 | { | |
| 1582 | 0 | continue; |
| 1583 | } | |
| 1584 | 0 | if (frames[i] instanceof AlignFrame) |
| 1585 | { | |
| 1586 | 0 | target = ((AlignFrame) frames[i]).getCurrentView(); |
| 1587 | } | |
| 1588 | 0 | else if (frames[i] instanceof TreePanel) |
| 1589 | { | |
| 1590 | 0 | target = ((TreePanel) frames[i]).getViewPort(); |
| 1591 | } | |
| 1592 | 0 | else if (frames[i] instanceof PCAPanel) |
| 1593 | { | |
| 1594 | 0 | target = ((PCAPanel) frames[i]).av; |
| 1595 | } | |
| 1596 | 0 | else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) |
| 1597 | { | |
| 1598 | 0 | target = ((PairwiseAlignPanel) frames[i].getContentPane()).av; |
| 1599 | } | |
| 1600 | ||
| 1601 | 0 | if (source == target) |
| 1602 | { | |
| 1603 | 0 | try |
| 1604 | { | |
| 1605 | 0 | if (close) |
| 1606 | { | |
| 1607 | 0 | frames[i].setClosed(true); |
| 1608 | } | |
| 1609 | else | |
| 1610 | { | |
| 1611 | 0 | frames[i].setIcon(minimize); |
| 1612 | 0 | if (!minimize) |
| 1613 | { | |
| 1614 | 0 | frames[i].toFront(); |
| 1615 | } | |
| 1616 | } | |
| 1617 | ||
| 1618 | } catch (java.beans.PropertyVetoException ex) | |
| 1619 | { | |
| 1620 | } | |
| 1621 | } | |
| 1622 | } | |
| 1623 | } | |
| 1624 | } | |
| 1625 | ||
| 1626 | /** | |
| 1627 | * DOCUMENT ME! | |
| 1628 | * | |
| 1629 | * @param e | |
| 1630 | * DOCUMENT ME! | |
| 1631 | */ | |
| 1632 | 0 | @Override |
| 1633 | protected void preferences_actionPerformed(ActionEvent e) | |
| 1634 | { | |
| 1635 | 0 | new Preferences(); |
| 1636 | } | |
| 1637 | ||
| 1638 | /** | |
| 1639 | * Prompts the user to choose a file and then saves the Jalview state as a | |
| 1640 | * Jalview project file | |
| 1641 | */ | |
| 1642 | 0 | @Override |
| 1643 | public void saveState_actionPerformed() | |
| 1644 | { | |
| 1645 | 0 | JalviewFileChooser chooser = new JalviewFileChooser("jvp", |
| 1646 | "Jalview Project"); | |
| 1647 | ||
| 1648 | 0 | chooser.setFileView(new JalviewFileView()); |
| 1649 | 0 | chooser.setDialogTitle(MessageManager.getString("label.save_state")); |
| 1650 | ||
| 1651 | 0 | int value = chooser.showSaveDialog(this); |
| 1652 | ||
| 1653 | 0 | if (value == JalviewFileChooser.APPROVE_OPTION) |
| 1654 | { | |
| 1655 | 0 | final Desktop me = this; |
| 1656 | 0 | final java.io.File choice = chooser.getSelectedFile(); |
| 1657 | 0 | setProjectFile(choice); |
| 1658 | ||
| 1659 | 0 | new Thread(new Runnable() |
| 1660 | { | |
| 1661 | 0 | @Override |
| 1662 | public void run() | |
| 1663 | { | |
| 1664 | // TODO: refactor to Jalview desktop session controller action. | |
| 1665 | 0 | setProgressBar(MessageManager.formatMessage( |
| 1666 | "label.saving_jalview_project", new Object[] | |
| 1667 | { choice.getName() }), choice.hashCode()); | |
| 1668 | 0 | jalview.bin.Cache.setProperty("LAST_DIRECTORY", |
| 1669 | choice.getParent()); | |
| 1670 | // TODO catch and handle errors for savestate | |
| 1671 | // TODO prevent user from messing with the Desktop whilst we're saving | |
| 1672 | 0 | try |
| 1673 | { | |
| 1674 | 0 | new Jalview2XML().saveState(choice); |
| 1675 | } catch (OutOfMemoryError oom) | |
| 1676 | { | |
| 1677 | 0 | new OOMWarning( |
| 1678 | "Whilst saving current state to " + choice.getName(), | |
| 1679 | oom); | |
| 1680 | } catch (Exception ex) | |
| 1681 | { | |
| 1682 | 0 | Cache.log.error( |
| 1683 | "Problems whilst trying to save to " + choice.getName(), | |
| 1684 | ex); | |
| 1685 | 0 | JvOptionPane.showMessageDialog(me, |
| 1686 | MessageManager.formatMessage( | |
| 1687 | "label.error_whilst_saving_current_state_to", | |
| 1688 | new Object[] | |
| 1689 | { choice.getName() }), | |
| 1690 | MessageManager.getString("label.couldnt_save_project"), | |
| 1691 | JvOptionPane.WARNING_MESSAGE); | |
| 1692 | } | |
| 1693 | 0 | setProgressBar(null, choice.hashCode()); |
| 1694 | } | |
| 1695 | }).start(); | |
| 1696 | } | |
| 1697 | } | |
| 1698 | ||
| 1699 | 0 | private void setProjectFile(File choice) |
| 1700 | { | |
| 1701 | 0 | this.projectFile = choice; |
| 1702 | } | |
| 1703 | ||
| 1704 | 0 | public File getProjectFile() |
| 1705 | { | |
| 1706 | 0 | return this.projectFile; |
| 1707 | } | |
| 1708 | ||
| 1709 | /** | |
| 1710 | * Prompts the user to choose a file and loads in as a Jalview project file | |
| 1711 | */ | |
| 1712 | 0 | @Override |
| 1713 | public void loadState_actionPerformed() | |
| 1714 | { | |
| 1715 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
| 1716 | Cache.getProperty("LAST_DIRECTORY"), new String[] | |
| 1717 | { "jvp", "jar" }, | |
| 1718 | new String[] | |
| 1719 | { "Jalview Project", "Jalview Project (old)" }, | |
| 1720 | "Jalview Project"); | |
| 1721 | 0 | chooser.setFileView(new JalviewFileView()); |
| 1722 | 0 | chooser.setDialogTitle(MessageManager.getString("label.restore_state")); |
| 1723 | ||
| 1724 | 0 | int value = chooser.showOpenDialog(this); |
| 1725 | ||
| 1726 | 0 | if (value == JalviewFileChooser.APPROVE_OPTION) |
| 1727 | { | |
| 1728 | 0 | final File selectedFile = chooser.getSelectedFile(); |
| 1729 | 0 | setProjectFile(selectedFile); |
| 1730 | 0 | final String choice = selectedFile.getAbsolutePath(); |
| 1731 | 0 | Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); |
| 1732 | 0 | new Thread(new Runnable() |
| 1733 | { | |
| 1734 | 0 | @Override |
| 1735 | public void run() | |
| 1736 | { | |
| 1737 | 0 | setProgressBar(MessageManager.formatMessage( |
| 1738 | "label.loading_jalview_project", new Object[] | |
| 1739 | { choice }), choice.hashCode()); | |
| 1740 | 0 | try |
| 1741 | { | |
| 1742 | 0 | new Jalview2XML().loadJalviewAlign(choice); |
| 1743 | } catch (OutOfMemoryError oom) | |
| 1744 | { | |
| 1745 | 0 | new OOMWarning("Whilst loading project from " + choice, oom); |
| 1746 | } catch (Exception ex) | |
| 1747 | { | |
| 1748 | 0 | Cache.log.error( |
| 1749 | "Problems whilst loading project from " + choice, ex); | |
| 1750 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
| 1751 | MessageManager.formatMessage( | |
| 1752 | "label.error_whilst_loading_project_from", | |
| 1753 | new Object[] | |
| 1754 | { choice }), | |
| 1755 | MessageManager.getString("label.couldnt_load_project"), | |
| 1756 | JvOptionPane.WARNING_MESSAGE); | |
| 1757 | } | |
| 1758 | 0 | setProgressBar(null, choice.hashCode()); |
| 1759 | } | |
| 1760 | }).start(); | |
| 1761 | } | |
| 1762 | } | |
| 1763 | ||
| 1764 | 0 | @Override |
| 1765 | public void inputSequence_actionPerformed(ActionEvent e) | |
| 1766 | { | |
| 1767 | 0 | new SequenceFetcher(this); |
| 1768 | } | |
| 1769 | ||
| 1770 | JPanel progressPanel; | |
| 1771 | ||
| 1772 | ArrayList<JPanel> fileLoadingPanels = new ArrayList<>(); | |
| 1773 | ||
| 1774 | 89 | public void startLoading(final Object fileName) |
| 1775 | { | |
| 1776 | 89 | if (fileLoadingCount == 0) |
| 1777 | { | |
| 1778 | 89 | fileLoadingPanels.add(addProgressPanel(MessageManager |
| 1779 | .formatMessage("label.loading_file", new Object[] | |
| 1780 | { fileName }))); | |
| 1781 | } | |
| 1782 | 89 | fileLoadingCount++; |
| 1783 | } | |
| 1784 | ||
| 1785 | 89 | private JPanel addProgressPanel(String string) |
| 1786 | { | |
| 1787 | 89 | if (progressPanel == null) |
| 1788 | { | |
| 1789 | 89 | progressPanel = new JPanel(new GridLayout(1, 1)); |
| 1790 | 89 | totalProgressCount = 0; |
| 1791 | 89 | instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); |
| 1792 | } | |
| 1793 | 89 | JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); |
| 1794 | 89 | JProgressBar progressBar = new JProgressBar(); |
| 1795 | 89 | progressBar.setIndeterminate(true); |
| 1796 | ||
| 1797 | 89 | thisprogress.add(new JLabel(string), BorderLayout.WEST); |
| 1798 | ||
| 1799 | 89 | thisprogress.add(progressBar, BorderLayout.CENTER); |
| 1800 | 89 | progressPanel.add(thisprogress); |
| 1801 | 89 | ((GridLayout) progressPanel.getLayout()).setRows( |
| 1802 | ((GridLayout) progressPanel.getLayout()).getRows() + 1); | |
| 1803 | 89 | ++totalProgressCount; |
| 1804 | 89 | instance.validate(); |
| 1805 | 89 | return thisprogress; |
| 1806 | } | |
| 1807 | ||
| 1808 | int totalProgressCount = 0; | |
| 1809 | ||
| 1810 | 89 | private void removeProgressPanel(JPanel progbar) |
| 1811 | { | |
| 1812 | 89 | if (progressPanel != null) |
| 1813 | { | |
| 1814 | 89 | synchronized (progressPanel) |
| 1815 | { | |
| 1816 | 89 | progressPanel.remove(progbar); |
| 1817 | 89 | GridLayout gl = (GridLayout) progressPanel.getLayout(); |
| 1818 | 89 | gl.setRows(gl.getRows() - 1); |
| 1819 | 89 | if (--totalProgressCount < 1) |
| 1820 | { | |
| 1821 | 89 | this.getContentPane().remove(progressPanel); |
| 1822 | 89 | progressPanel = null; |
| 1823 | } | |
| 1824 | } | |
| 1825 | } | |
| 1826 | 89 | validate(); |
| 1827 | } | |
| 1828 | ||
| 1829 | 109 | public void stopLoading() |
| 1830 | { | |
| 1831 | 109 | fileLoadingCount--; |
| 1832 | 109 | if (fileLoadingCount < 1) |
| 1833 | { | |
| 1834 | 198 | while (fileLoadingPanels.size() > 0) |
| 1835 | { | |
| 1836 | 89 | removeProgressPanel(fileLoadingPanels.remove(0)); |
| 1837 | } | |
| 1838 | 109 | fileLoadingPanels.clear(); |
| 1839 | 109 | fileLoadingCount = 0; |
| 1840 | } | |
| 1841 | 109 | validate(); |
| 1842 | } | |
| 1843 | ||
| 1844 | 3 | public static int getViewCount(String alignmentId) |
| 1845 | { | |
| 1846 | 3 | AlignmentViewport[] aps = getViewports(alignmentId); |
| 1847 | 3 | return (aps == null) ? 0 : aps.length; |
| 1848 | } | |
| 1849 | ||
| 1850 | /** | |
| 1851 | * | |
| 1852 | * @param alignmentId | |
| 1853 | * - if null, all sets are returned | |
| 1854 | * @return all AlignmentPanels concerning the alignmentId sequence set | |
| 1855 | */ | |
| 1856 | 79 | public static AlignmentPanel[] getAlignmentPanels(String alignmentId) |
| 1857 | { | |
| 1858 | 79 | if (Desktop.desktop == null) |
| 1859 | { | |
| 1860 | // no frames created and in headless mode | |
| 1861 | // TODO: verify that frames are recoverable when in headless mode | |
| 1862 | 0 | return null; |
| 1863 | } | |
| 1864 | 79 | List<AlignmentPanel> aps = new ArrayList<>(); |
| 1865 | 79 | AlignFrame[] frames = getAlignFrames(); |
| 1866 | 79 | if (frames == null) |
| 1867 | { | |
| 1868 | 12 | return null; |
| 1869 | } | |
| 1870 | 67 | for (AlignFrame af : frames) |
| 1871 | { | |
| 1872 | 203 | for (AlignmentPanel ap : af.alignPanels) |
| 1873 | { | |
| 1874 | 405 | if (alignmentId == null |
| 1875 | || alignmentId.equals(ap.av.getSequenceSetId())) | |
| 1876 | { | |
| 1877 | 157 | aps.add(ap); |
| 1878 | } | |
| 1879 | } | |
| 1880 | } | |
| 1881 | 67 | if (aps.size() == 0) |
| 1882 | { | |
| 1883 | 8 | return null; |
| 1884 | } | |
| 1885 | 59 | AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); |
| 1886 | 59 | return vap; |
| 1887 | } | |
| 1888 | ||
| 1889 | /** | |
| 1890 | * get all the viewports on an alignment. | |
| 1891 | * | |
| 1892 | * @param sequenceSetId | |
| 1893 | * unique alignment id (may be null - all viewports returned in that | |
| 1894 | * case) | |
| 1895 | * @return all viewports on the alignment bound to sequenceSetId | |
| 1896 | */ | |
| 1897 | 3 | public static AlignmentViewport[] getViewports(String sequenceSetId) |
| 1898 | { | |
| 1899 | 3 | List<AlignmentViewport> viewp = new ArrayList<>(); |
| 1900 | 3 | if (desktop != null) |
| 1901 | { | |
| 1902 | 3 | AlignFrame[] frames = Desktop.getAlignFrames(); |
| 1903 | ||
| 1904 | 3 | for (AlignFrame afr : frames) |
| 1905 | { | |
| 1906 | 3 | if (sequenceSetId == null || afr.getViewport().getSequenceSetId() |
| 1907 | .equals(sequenceSetId)) | |
| 1908 | { | |
| 1909 | 3 | if (afr.alignPanels != null) |
| 1910 | { | |
| 1911 | 3 | for (AlignmentPanel ap : afr.alignPanels) |
| 1912 | { | |
| 1913 | 3 | if (sequenceSetId == null |
| 1914 | || sequenceSetId.equals(ap.av.getSequenceSetId())) | |
| 1915 | { | |
| 1916 | 3 | viewp.add(ap.av); |
| 1917 | } | |
| 1918 | } | |
| 1919 | } | |
| 1920 | else | |
| 1921 | { | |
| 1922 | 0 | viewp.add(afr.getViewport()); |
| 1923 | } | |
| 1924 | } | |
| 1925 | } | |
| 1926 | 3 | if (viewp.size() > 0) |
| 1927 | { | |
| 1928 | 3 | return viewp.toArray(new AlignmentViewport[viewp.size()]); |
| 1929 | } | |
| 1930 | } | |
| 1931 | 0 | return null; |
| 1932 | } | |
| 1933 | ||
| 1934 | /** | |
| 1935 | * Explode the views in the given frame into separate AlignFrame | |
| 1936 | * | |
| 1937 | * @param af | |
| 1938 | */ | |
| 1939 | 1 | public static void explodeViews(AlignFrame af) |
| 1940 | { | |
| 1941 | 1 | int size = af.alignPanels.size(); |
| 1942 | 1 | if (size < 2) |
| 1943 | { | |
| 1944 | 0 | return; |
| 1945 | } | |
| 1946 | ||
| 1947 | 6 | for (int i = 0; i < size; i++) |
| 1948 | { | |
| 1949 | 5 | AlignmentPanel ap = af.alignPanels.get(i); |
| 1950 | 5 | AlignFrame newaf = new AlignFrame(ap); |
| 1951 | ||
| 1952 | /* | |
| 1953 | * Restore the view's last exploded frame geometry if known. Multiple | |
| 1954 | * views from one exploded frame share and restore the same (frame) | |
| 1955 | * position and size. | |
| 1956 | */ | |
| 1957 | 5 | Rectangle geometry = ap.av.getExplodedGeometry(); |
| 1958 | 5 | if (geometry != null) |
| 1959 | { | |
| 1960 | 5 | newaf.setBounds(geometry); |
| 1961 | } | |
| 1962 | ||
| 1963 | 5 | ap.av.setGatherViewsHere(false); |
| 1964 | ||
| 1965 | 5 | addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, |
| 1966 | AlignFrame.DEFAULT_HEIGHT); | |
| 1967 | } | |
| 1968 | ||
| 1969 | 1 | af.alignPanels.clear(); |
| 1970 | 1 | af.closeMenuItem_actionPerformed(true); |
| 1971 | ||
| 1972 | } | |
| 1973 | ||
| 1974 | /** | |
| 1975 | * Gather expanded views (separate AlignFrame's) with the same sequence set | |
| 1976 | * identifier back in to this frame as additional views, and close the expanded | |
| 1977 | * views. Note the expanded frames may themselves have multiple views. We take | |
| 1978 | * the lot. | |
| 1979 | * | |
| 1980 | * @param source | |
| 1981 | */ | |
| 1982 | 12 | public void gatherViews(AlignFrame source) |
| 1983 | { | |
| 1984 | 12 | source.viewport.setGatherViewsHere(true); |
| 1985 | 12 | source.viewport.setExplodedGeometry(source.getBounds()); |
| 1986 | 12 | JInternalFrame[] frames = desktop.getAllFrames(); |
| 1987 | 12 | String viewId = source.viewport.getSequenceSetId(); |
| 1988 | ||
| 1989 | 112 | for (int t = 0; t < frames.length; t++) |
| 1990 | { | |
| 1991 | 100 | if (frames[t] instanceof AlignFrame && frames[t] != source) |
| 1992 | { | |
| 1993 | 54 | AlignFrame af = (AlignFrame) frames[t]; |
| 1994 | 54 | boolean gatherThis = false; |
| 1995 | 136 | for (int a = 0; a < af.alignPanels.size(); a++) |
| 1996 | { | |
| 1997 | 82 | AlignmentPanel ap = af.alignPanels.get(a); |
| 1998 | 82 | if (viewId.equals(ap.av.getSequenceSetId())) |
| 1999 | { | |
| 2000 | 45 | gatherThis = true; |
| 2001 | 45 | ap.av.setGatherViewsHere(false); |
| 2002 | 45 | ap.av.setExplodedGeometry(af.getBounds()); |
| 2003 | 45 | source.addAlignmentPanel(ap, false); |
| 2004 | } | |
| 2005 | } | |
| 2006 | ||
| 2007 | 54 | if (gatherThis) |
| 2008 | { | |
| 2009 | 45 | af.alignPanels.clear(); |
| 2010 | 45 | af.closeMenuItem_actionPerformed(true); |
| 2011 | } | |
| 2012 | } | |
| 2013 | } | |
| 2014 | ||
| 2015 | } | |
| 2016 | ||
| 2017 | jalview.gui.VamsasApplication v_client = null; | |
| 2018 | ||
| 2019 | 0 | @Override |
| 2020 | public void vamsasImport_actionPerformed(ActionEvent e) | |
| 2021 | { | |
| 2022 | // TODO: JAL-3048 not needed for Jalview-JS | |
| 2023 | ||
| 2024 | 0 | if (v_client == null) |
| 2025 | { | |
| 2026 | // Load and try to start a session. | |
| 2027 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
| 2028 | jalview.bin.Cache.getProperty("LAST_DIRECTORY")); | |
| 2029 | ||
| 2030 | 0 | chooser.setFileView(new JalviewFileView()); |
| 2031 | 0 | chooser.setDialogTitle( |
| 2032 | MessageManager.getString("label.open_saved_vamsas_session")); | |
| 2033 | 0 | chooser.setToolTipText(MessageManager.getString( |
| 2034 | "label.select_vamsas_session_opened_as_new_vamsas_session")); | |
| 2035 | ||
| 2036 | 0 | int value = chooser.showOpenDialog(this); |
| 2037 | ||
| 2038 | 0 | if (value == JalviewFileChooser.APPROVE_OPTION) |
| 2039 | { | |
| 2040 | 0 | String fle = chooser.getSelectedFile().toString(); |
| 2041 | 0 | if (!vamsasImport(chooser.getSelectedFile())) |
| 2042 | { | |
| 2043 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
| 2044 | MessageManager.formatMessage( | |
| 2045 | "label.couldnt_import_as_vamsas_session", | |
| 2046 | new Object[] | |
| 2047 | { fle }), | |
| 2048 | MessageManager | |
| 2049 | .getString("label.vamsas_document_import_failed"), | |
| 2050 | JvOptionPane.ERROR_MESSAGE); | |
| 2051 | } | |
| 2052 | } | |
| 2053 | } | |
| 2054 | else | |
| 2055 | { | |
| 2056 | 0 | jalview.bin.Cache.log.error( |
| 2057 | "Implementation error - load session from a running session is not supported."); | |
| 2058 | } | |
| 2059 | } | |
| 2060 | ||
| 2061 | /** | |
| 2062 | * import file into a new vamsas session (uses jalview.gui.VamsasApplication) | |
| 2063 | * | |
| 2064 | * @param file | |
| 2065 | * @return true if import was a success and a session was started. | |
| 2066 | */ | |
| 2067 | 0 | public boolean vamsasImport(URL url) |
| 2068 | { | |
| 2069 | // TODO: create progress bar | |
| 2070 | 0 | if (v_client != null) |
| 2071 | { | |
| 2072 | ||
| 2073 | 0 | jalview.bin.Cache.log.error( |
| 2074 | "Implementation error - load session from a running session is not supported."); | |
| 2075 | 0 | return false; |
| 2076 | } | |
| 2077 | ||
| 2078 | 0 | try |
| 2079 | { | |
| 2080 | // copy the URL content to a temporary local file | |
| 2081 | // TODO: be a bit cleverer here with nio (?!) | |
| 2082 | 0 | File file = File.createTempFile("vdocfromurl", ".vdj"); |
| 2083 | 0 | FileOutputStream fos = new FileOutputStream(file); |
| 2084 | 0 | BufferedInputStream bis = new BufferedInputStream(url.openStream()); |
| 2085 | 0 | byte[] buffer = new byte[2048]; |
| 2086 | 0 | int ln; |
| 2087 | 0 | while ((ln = bis.read(buffer)) > -1) |
| 2088 | { | |
| 2089 | 0 | fos.write(buffer, 0, ln); |
| 2090 | } | |
| 2091 | 0 | bis.close(); |
| 2092 | 0 | fos.close(); |
| 2093 | 0 | v_client = new jalview.gui.VamsasApplication(this, file, |
| 2094 | url.toExternalForm()); | |
| 2095 | } catch (Exception ex) | |
| 2096 | { | |
| 2097 | 0 | jalview.bin.Cache.log.error( |
| 2098 | "Failed to create new vamsas session from contents of URL " | |
| 2099 | + url, | |
| 2100 | ex); | |
| 2101 | 0 | return false; |
| 2102 | } | |
| 2103 | 0 | setupVamsasConnectedGui(); |
| 2104 | 0 | v_client.initial_update(); // TODO: thread ? |
| 2105 | 0 | return v_client.inSession(); |
| 2106 | } | |
| 2107 | ||
| 2108 | /** | |
| 2109 | * import file into a new vamsas session (uses jalview.gui.VamsasApplication) | |
| 2110 | * | |
| 2111 | * @param file | |
| 2112 | * @return true if import was a success and a session was started. | |
| 2113 | */ | |
| 2114 | 0 | public boolean vamsasImport(File file) |
| 2115 | { | |
| 2116 | 0 | if (v_client != null) |
| 2117 | { | |
| 2118 | ||
| 2119 | 0 | jalview.bin.Cache.log.error( |
| 2120 | "Implementation error - load session from a running session is not supported."); | |
| 2121 | 0 | return false; |
| 2122 | } | |
| 2123 | ||
| 2124 | 0 | setProgressBar(MessageManager.formatMessage( |
| 2125 | "status.importing_vamsas_session_from", new Object[] | |
| 2126 | { file.getName() }), file.hashCode()); | |
| 2127 | 0 | try |
| 2128 | { | |
| 2129 | 0 | v_client = new jalview.gui.VamsasApplication(this, file, null); |
| 2130 | } catch (Exception ex) | |
| 2131 | { | |
| 2132 | 0 | setProgressBar(MessageManager.formatMessage( |
| 2133 | "status.importing_vamsas_session_from", new Object[] | |
| 2134 | { file.getName() }), file.hashCode()); | |
| 2135 | 0 | jalview.bin.Cache.log.error( |
| 2136 | "New vamsas session from existing session file failed:", ex); | |
| 2137 | 0 | return false; |
| 2138 | } | |
| 2139 | 0 | setupVamsasConnectedGui(); |
| 2140 | 0 | v_client.initial_update(); // TODO: thread ? |
| 2141 | 0 | setProgressBar(MessageManager.formatMessage( |
| 2142 | "status.importing_vamsas_session_from", new Object[] | |
| 2143 | { file.getName() }), file.hashCode()); | |
| 2144 | 0 | return v_client.inSession(); |
| 2145 | } | |
| 2146 | ||
| 2147 | 0 | public boolean joinVamsasSession(String mysesid) |
| 2148 | { | |
| 2149 | 0 | if (v_client != null) |
| 2150 | { | |
| 2151 | 0 | throw new Error(MessageManager |
| 2152 | .getString("error.try_join_vamsas_session_another")); | |
| 2153 | } | |
| 2154 | 0 | if (mysesid == null) |
| 2155 | { | |
| 2156 | 0 | throw new Error( |
| 2157 | MessageManager.getString("error.invalid_vamsas_session_id")); | |
| 2158 | } | |
| 2159 | 0 | v_client = new VamsasApplication(this, mysesid); |
| 2160 | 0 | setupVamsasConnectedGui(); |
| 2161 | 0 | v_client.initial_update(); |
| 2162 | 0 | return (v_client.inSession()); |
| 2163 | } | |
| 2164 | ||
| 2165 | 0 | @Override |
| 2166 | public void vamsasStart_actionPerformed(ActionEvent e) | |
| 2167 | { | |
| 2168 | 0 | if (v_client == null) |
| 2169 | { | |
| 2170 | // Start a session. | |
| 2171 | // we just start a default session for moment. | |
| 2172 | /* | |
| 2173 | * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. | |
| 2174 | * getProperty("LAST_DIRECTORY")); | |
| 2175 | * | |
| 2176 | * chooser.setFileView(new JalviewFileView()); | |
| 2177 | * chooser.setDialogTitle("Load Vamsas file"); | |
| 2178 | * chooser.setToolTipText("Import"); | |
| 2179 | * | |
| 2180 | * int value = chooser.showOpenDialog(this); | |
| 2181 | * | |
| 2182 | * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new | |
| 2183 | * jalview.gui.VamsasApplication(this, chooser.getSelectedFile()); | |
| 2184 | */ | |
| 2185 | 0 | v_client = new VamsasApplication(this); |
| 2186 | 0 | setupVamsasConnectedGui(); |
| 2187 | 0 | v_client.initial_update(); // TODO: thread ? |
| 2188 | } | |
| 2189 | else | |
| 2190 | { | |
| 2191 | // store current data in session. | |
| 2192 | 0 | v_client.push_update(); // TODO: thread |
| 2193 | } | |
| 2194 | } | |
| 2195 | ||
| 2196 | 0 | protected void setupVamsasConnectedGui() |
| 2197 | { | |
| 2198 | 0 | vamsasStart.setText(MessageManager.getString("label.session_update")); |
| 2199 | 0 | vamsasSave.setVisible(true); |
| 2200 | 0 | vamsasStop.setVisible(true); |
| 2201 | 0 | vamsasImport.setVisible(false); // Document import to existing session is |
| 2202 | // not possible for vamsas-client-1.0. | |
| 2203 | } | |
| 2204 | ||
| 2205 | 11 | protected void setupVamsasDisconnectedGui() |
| 2206 | { | |
| 2207 | 11 | vamsasSave.setVisible(false); |
| 2208 | 11 | vamsasStop.setVisible(false); |
| 2209 | 11 | vamsasImport.setVisible(true); |
| 2210 | 11 | vamsasStart |
| 2211 | .setText(MessageManager.getString("label.new_vamsas_session")); | |
| 2212 | } | |
| 2213 | ||
| 2214 | 0 | @Override |
| 2215 | public void vamsasStop_actionPerformed(ActionEvent e) | |
| 2216 | { | |
| 2217 | 0 | if (v_client != null) |
| 2218 | { | |
| 2219 | 0 | v_client.end_session(); |
| 2220 | 0 | v_client = null; |
| 2221 | 0 | setupVamsasDisconnectedGui(); |
| 2222 | } | |
| 2223 | } | |
| 2224 | ||
| 2225 | 0 | protected void buildVamsasStMenu() |
| 2226 | { | |
| 2227 | 0 | if (v_client == null) |
| 2228 | { | |
| 2229 | 0 | String[] sess = null; |
| 2230 | 0 | try |
| 2231 | { | |
| 2232 | 0 | sess = VamsasApplication.getSessionList(); |
| 2233 | } catch (Exception e) | |
| 2234 | { | |
| 2235 | 0 | jalview.bin.Cache.log.warn("Problem getting current sessions list.", |
| 2236 | e); | |
| 2237 | 0 | sess = null; |
| 2238 | } | |
| 2239 | 0 | if (sess != null) |
| 2240 | { | |
| 2241 | 0 | jalview.bin.Cache.log.debug( |
| 2242 | "Got current sessions list: " + sess.length + " entries."); | |
| 2243 | 0 | VamsasStMenu.removeAll(); |
| 2244 | 0 | for (int i = 0; i < sess.length; i++) |
| 2245 | { | |
| 2246 | 0 | JMenuItem sessit = new JMenuItem(); |
| 2247 | 0 | sessit.setText(sess[i]); |
| 2248 | 0 | sessit.setToolTipText(MessageManager |
| 2249 | .formatMessage("label.connect_to_session", new Object[] | |
| 2250 | { sess[i] })); | |
| 2251 | 0 | final Desktop dsktp = this; |
| 2252 | 0 | final String mysesid = sess[i]; |
| 2253 | 0 | sessit.addActionListener(new ActionListener() |
| 2254 | { | |
| 2255 | ||
| 2256 | 0 | @Override |
| 2257 | public void actionPerformed(ActionEvent e) | |
| 2258 | { | |
| 2259 | 0 | if (dsktp.v_client == null) |
| 2260 | { | |
| 2261 | 0 | Thread rthr = new Thread(new Runnable() |
| 2262 | { | |
| 2263 | ||
| 2264 | 0 | @Override |
| 2265 | public void run() | |
| 2266 | { | |
| 2267 | 0 | dsktp.v_client = new VamsasApplication(dsktp, mysesid); |
| 2268 | 0 | dsktp.setupVamsasConnectedGui(); |
| 2269 | 0 | dsktp.v_client.initial_update(); |
| 2270 | } | |
| 2271 | ||
| 2272 | }); | |
| 2273 | 0 | rthr.start(); |
| 2274 | } | |
| 2275 | }; | |
| 2276 | }); | |
| 2277 | 0 | VamsasStMenu.add(sessit); |
| 2278 | } | |
| 2279 | // don't show an empty menu. | |
| 2280 | 0 | VamsasStMenu.setVisible(sess.length > 0); |
| 2281 | ||
| 2282 | } | |
| 2283 | else | |
| 2284 | { | |
| 2285 | 0 | jalview.bin.Cache.log.debug("No current vamsas sessions."); |
| 2286 | 0 | VamsasStMenu.removeAll(); |
| 2287 | 0 | VamsasStMenu.setVisible(false); |
| 2288 | } | |
| 2289 | } | |
| 2290 | else | |
| 2291 | { | |
| 2292 | // Not interested in the content. Just hide ourselves. | |
| 2293 | 0 | VamsasStMenu.setVisible(false); |
| 2294 | } | |
| 2295 | } | |
| 2296 | ||
| 2297 | 0 | @Override |
| 2298 | public void vamsasSave_actionPerformed(ActionEvent e) | |
| 2299 | { | |
| 2300 | // TODO: JAL-3048 not needed for Jalview-JS | |
| 2301 | ||
| 2302 | 0 | if (v_client != null) |
| 2303 | { | |
| 2304 | // TODO: VAMSAS DOCUMENT EXTENSION is VDJ | |
| 2305 | 0 | JalviewFileChooser chooser = new JalviewFileChooser("vdj", |
| 2306 | "Vamsas Document"); | |
| 2307 | ||
| 2308 | 0 | chooser.setFileView(new JalviewFileView()); |
| 2309 | 0 | chooser.setDialogTitle(MessageManager |
| 2310 | .getString("label.save_vamsas_document_archive")); | |
| 2311 | ||
| 2312 | 0 | int value = chooser.showSaveDialog(this); |
| 2313 | ||
| 2314 | 0 | if (value == JalviewFileChooser.APPROVE_OPTION) |
| 2315 | { | |
| 2316 | 0 | java.io.File choice = chooser.getSelectedFile(); |
| 2317 | 0 | JPanel progpanel = addProgressPanel(MessageManager |
| 2318 | .formatMessage("label.saving_vamsas_doc", new Object[] | |
| 2319 | { choice.getName() })); | |
| 2320 | 0 | Cache.setProperty("LAST_DIRECTORY", choice.getParent()); |
| 2321 | 0 | String warnmsg = null; |
| 2322 | 0 | String warnttl = null; |
| 2323 | 0 | try |
| 2324 | { | |
| 2325 | 0 | v_client.vclient.storeDocument(choice); |
| 2326 | } catch (Error ex) | |
| 2327 | { | |
| 2328 | 0 | warnttl = "Serious Problem saving Vamsas Document"; |
| 2329 | 0 | warnmsg = ex.toString(); |
| 2330 | 0 | jalview.bin.Cache.log |
| 2331 | .error("Error Whilst saving document to " + choice, ex); | |
| 2332 | ||
| 2333 | } catch (Exception ex) | |
| 2334 | { | |
| 2335 | 0 | warnttl = "Problem saving Vamsas Document."; |
| 2336 | 0 | warnmsg = ex.toString(); |
| 2337 | 0 | jalview.bin.Cache.log.warn( |
| 2338 | "Exception Whilst saving document to " + choice, ex); | |
| 2339 | ||
| 2340 | } | |
| 2341 | 0 | removeProgressPanel(progpanel); |
| 2342 | 0 | if (warnmsg != null) |
| 2343 | { | |
| 2344 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
| 2345 | ||
| 2346 | warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); | |
| 2347 | } | |
| 2348 | } | |
| 2349 | } | |
| 2350 | } | |
| 2351 | ||
| 2352 | JPanel vamUpdate = null; | |
| 2353 | ||
| 2354 | /** | |
| 2355 | * hide vamsas user gui bits when a vamsas document event is being handled. | |
| 2356 | * | |
| 2357 | * @param b | |
| 2358 | * true to hide gui, false to reveal gui | |
| 2359 | */ | |
| 2360 | 0 | public void setVamsasUpdate(boolean b) |
| 2361 | { | |
| 2362 | 0 | Cache.log.debug("Setting gui for Vamsas update " |
| 2363 | 0 | + (b ? "in progress" : "finished")); |
| 2364 | ||
| 2365 | 0 | if (vamUpdate != null) |
| 2366 | { | |
| 2367 | 0 | this.removeProgressPanel(vamUpdate); |
| 2368 | } | |
| 2369 | 0 | if (b) |
| 2370 | { | |
| 2371 | 0 | vamUpdate = this.addProgressPanel( |
| 2372 | MessageManager.getString("label.updating_vamsas_session")); | |
| 2373 | } | |
| 2374 | 0 | vamsasStart.setVisible(!b); |
| 2375 | 0 | vamsasStop.setVisible(!b); |
| 2376 | 0 | vamsasSave.setVisible(!b); |
| 2377 | } | |
| 2378 | ||
| 2379 | 1 | public JInternalFrame[] getAllFrames() |
| 2380 | { | |
| 2381 | 1 | return desktop.getAllFrames(); |
| 2382 | } | |
| 2383 | ||
| 2384 | /** | |
| 2385 | * Checks the given url to see if it gives a response indicating that the user | |
| 2386 | * should be informed of a new questionnaire. | |
| 2387 | * | |
| 2388 | * @param url | |
| 2389 | */ | |
| 2390 | 4 | public void checkForQuestionnaire(String url) |
| 2391 | { | |
| 2392 | 4 | UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url); |
| 2393 | // javax.swing.SwingUtilities.invokeLater(jvq); | |
| 2394 | 4 | new Thread(jvq).start(); |
| 2395 | } | |
| 2396 | ||
| 2397 | 11 | public void checkURLLinks() |
| 2398 | { | |
| 2399 | // Thread off the URL link checker | |
| 2400 | 11 | addDialogThread(new Runnable() |
| 2401 | { | |
| 2402 | 5 | @Override |
| 2403 | public void run() | |
| 2404 | { | |
| 2405 | 5 | if (Cache.getDefault("CHECKURLLINKS", true)) |
| 2406 | { | |
| 2407 | // check what the actual links are - if it's just the default don't | |
| 2408 | // bother with the warning | |
| 2409 | 5 | List<String> links = Preferences.sequenceUrlLinks |
| 2410 | .getLinksForMenu(); | |
| 2411 | ||
| 2412 | // only need to check links if there is one with a | |
| 2413 | // SEQUENCE_ID which is not the default EMBL_EBI link | |
| 2414 | 5 | ListIterator<String> li = links.listIterator(); |
| 2415 | 5 | boolean check = false; |
| 2416 | 5 | List<JLabel> urls = new ArrayList<>(); |
| 2417 | 14 | while (li.hasNext()) |
| 2418 | { | |
| 2419 | 9 | String link = li.next(); |
| 2420 | 9 | if (link.contains(SEQUENCE_ID) |
| 2421 | && !UrlConstants.isDefaultString(link)) | |
| 2422 | { | |
| 2423 | 0 | check = true; |
| 2424 | 0 | int barPos = link.indexOf("|"); |
| 2425 | 0 | String urlMsg = barPos == -1 ? link |
| 2426 | : link.substring(0, barPos) + ": " | |
| 2427 | + link.substring(barPos + 1); | |
| 2428 | 0 | urls.add(new JLabel(urlMsg)); |
| 2429 | } | |
| 2430 | } | |
| 2431 | 5 | if (!check) |
| 2432 | { | |
| 2433 | 5 | return; |
| 2434 | } | |
| 2435 | ||
| 2436 | // ask user to check in case URL links use old style tokens | |
| 2437 | // ($SEQUENCE_ID$ for sequence id _or_ accession id) | |
| 2438 | 0 | JPanel msgPanel = new JPanel(); |
| 2439 | 0 | msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); |
| 2440 | 0 | msgPanel.add(Box.createVerticalGlue()); |
| 2441 | 0 | JLabel msg = new JLabel(MessageManager |
| 2442 | .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); | |
| 2443 | 0 | JLabel msg2 = new JLabel(MessageManager |
| 2444 | .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); | |
| 2445 | 0 | msgPanel.add(msg); |
| 2446 | 0 | for (JLabel url : urls) |
| 2447 | { | |
| 2448 | 0 | msgPanel.add(url); |
| 2449 | } | |
| 2450 | 0 | msgPanel.add(msg2); |
| 2451 | ||
| 2452 | 0 | final JCheckBox jcb = new JCheckBox( |
| 2453 | MessageManager.getString("label.do_not_display_again")); | |
| 2454 | 0 | jcb.addActionListener(new ActionListener() |
| 2455 | { | |
| 2456 | 0 | @Override |
| 2457 | public void actionPerformed(ActionEvent e) | |
| 2458 | { | |
| 2459 | // update Cache settings for "don't show this again" | |
| 2460 | 0 | boolean showWarningAgain = !jcb.isSelected(); |
| 2461 | 0 | Cache.setProperty("CHECKURLLINKS", |
| 2462 | Boolean.valueOf(showWarningAgain).toString()); | |
| 2463 | } | |
| 2464 | }); | |
| 2465 | 0 | msgPanel.add(jcb); |
| 2466 | ||
| 2467 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, |
| 2468 | MessageManager | |
| 2469 | .getString("label.SEQUENCE_ID_no_longer_used"), | |
| 2470 | JvOptionPane.WARNING_MESSAGE); | |
| 2471 | } | |
| 2472 | } | |
| 2473 | }); | |
| 2474 | } | |
| 2475 | ||
| 2476 | /** | |
| 2477 | * Proxy class for JDesktopPane which optionally displays the current memory | |
| 2478 | * usage and highlights the desktop area with a red bar if free memory runs low. | |
| 2479 | * | |
| 2480 | * @author AMW | |
| 2481 | */ | |
| 2482 | public class MyDesktopPane extends JDesktopPane | |
| 2483 | implements Runnable | |
| 2484 | { | |
| 2485 | private static final float ONE_MB = 1048576f; | |
| 2486 | ||
| 2487 | boolean showMemoryUsage = false; | |
| 2488 | ||
| 2489 | Runtime runtime; | |
| 2490 | ||
| 2491 | java.text.NumberFormat df; | |
| 2492 | ||
| 2493 | float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, | |
| 2494 | percentUsage; | |
| 2495 | ||
| 2496 | 11 | public MyDesktopPane(boolean showMemoryUsage) |
| 2497 | { | |
| 2498 | 11 | showMemoryUsage(showMemoryUsage); |
| 2499 | } | |
| 2500 | ||
| 2501 | 11 | public void showMemoryUsage(boolean showMemory) |
| 2502 | { | |
| 2503 | 11 | this.showMemoryUsage = showMemory; |
| 2504 | 11 | if (showMemory) |
| 2505 | { | |
| 2506 | 0 | Thread worker = new Thread(this); |
| 2507 | 0 | worker.start(); |
| 2508 | } | |
| 2509 | 11 | repaint(); |
| 2510 | } | |
| 2511 | ||
| 2512 | 177 | public boolean isShowMemoryUsage() |
| 2513 | { | |
| 2514 | 177 | return showMemoryUsage; |
| 2515 | } | |
| 2516 | ||
| 2517 | 0 | @Override |
| 2518 | public void run() | |
| 2519 | { | |
| 2520 | 0 | df = java.text.NumberFormat.getNumberInstance(); |
| 2521 | 0 | df.setMaximumFractionDigits(2); |
| 2522 | 0 | runtime = Runtime.getRuntime(); |
| 2523 | ||
| 2524 | 0 | while (showMemoryUsage) |
| 2525 | { | |
| 2526 | 0 | try |
| 2527 | { | |
| 2528 | 0 | maxMemory = runtime.maxMemory() / ONE_MB; |
| 2529 | 0 | allocatedMemory = runtime.totalMemory() / ONE_MB; |
| 2530 | 0 | freeMemory = runtime.freeMemory() / ONE_MB; |
| 2531 | 0 | totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); |
| 2532 | ||
| 2533 | 0 | percentUsage = (totalFreeMemory / maxMemory) * 100; |
| 2534 | ||
| 2535 | // if (percentUsage < 20) | |
| 2536 | { | |
| 2537 | // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, | |
| 2538 | // Color.red); | |
| 2539 | // instance.set.setBorder(border1); | |
| 2540 | } | |
| 2541 | 0 | repaint(); |
| 2542 | // sleep after showing usage | |
| 2543 | 0 | Thread.sleep(3000); |
| 2544 | } catch (Exception ex) | |
| 2545 | { | |
| 2546 | 0 | ex.printStackTrace(); |
| 2547 | } | |
| 2548 | } | |
| 2549 | } | |
| 2550 | ||
| 2551 | 480 | @Override |
| 2552 | public void paintComponent(Graphics g) | |
| 2553 | { | |
| 2554 | 480 | if (showMemoryUsage && g != null && df != null) |
| 2555 | { | |
| 2556 | 0 | if (percentUsage < 20) |
| 2557 | { | |
| 2558 | 0 | g.setColor(Color.red); |
| 2559 | } | |
| 2560 | 0 | FontMetrics fm = g.getFontMetrics(); |
| 2561 | 0 | if (fm != null) |
| 2562 | { | |
| 2563 | 0 | g.drawString(MessageManager.formatMessage("label.memory_stats", |
| 2564 | new Object[] | |
| 2565 | { df.format(totalFreeMemory), df.format(maxMemory), | |
| 2566 | df.format(percentUsage) }), | |
| 2567 | 10, getHeight() - fm.getHeight()); | |
| 2568 | } | |
| 2569 | } | |
| 2570 | } | |
| 2571 | } | |
| 2572 | ||
| 2573 | /** | |
| 2574 | * Accessor method to quickly get all the AlignmentFrames loaded. | |
| 2575 | * | |
| 2576 | * @return an array of AlignFrame, or null if none found | |
| 2577 | */ | |
| 2578 | 104 | public static AlignFrame[] getAlignFrames() |
| 2579 | { | |
| 2580 | 104 | if (Jalview.isHeadlessMode()) |
| 2581 | { | |
| 2582 | // Desktop.desktop is null in headless mode | |
| 2583 | 0 | return new AlignFrame[] { Jalview.currentAlignFrame }; |
| 2584 | } | |
| 2585 | ||
| 2586 | 104 | JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
| 2587 | ||
| 2588 | 104 | if (frames == null) |
| 2589 | { | |
| 2590 | 0 | return null; |
| 2591 | } | |
| 2592 | 104 | List<AlignFrame> avp = new ArrayList<>(); |
| 2593 | // REVERSE ORDER | |
| 2594 | 550 | for (int i = frames.length - 1; i > -1; i--) |
| 2595 | { | |
| 2596 | 446 | if (frames[i] instanceof AlignFrame) |
| 2597 | { | |
| 2598 | 247 | avp.add((AlignFrame) frames[i]); |
| 2599 | } | |
| 2600 | 199 | else if (frames[i] instanceof SplitFrame) |
| 2601 | { | |
| 2602 | /* | |
| 2603 | * Also check for a split frame containing an AlignFrame | |
| 2604 | */ | |
| 2605 | 0 | GSplitFrame sf = (GSplitFrame) frames[i]; |
| 2606 | 0 | if (sf.getTopFrame() instanceof AlignFrame) |
| 2607 | { | |
| 2608 | 0 | avp.add((AlignFrame) sf.getTopFrame()); |
| 2609 | } | |
| 2610 | 0 | if (sf.getBottomFrame() instanceof AlignFrame) |
| 2611 | { | |
| 2612 | 0 | avp.add((AlignFrame) sf.getBottomFrame()); |
| 2613 | } | |
| 2614 | } | |
| 2615 | } | |
| 2616 | 104 | if (avp.size() == 0) |
| 2617 | { | |
| 2618 | 16 | return null; |
| 2619 | } | |
| 2620 | 88 | AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]); |
| 2621 | 88 | return afs; |
| 2622 | } | |
| 2623 | ||
| 2624 | /** | |
| 2625 | * Returns an array of any AppJmol frames in the Desktop (or null if none). | |
| 2626 | * | |
| 2627 | * @return | |
| 2628 | */ | |
| 2629 | 0 | public GStructureViewer[] getJmols() |
| 2630 | { | |
| 2631 | 0 | JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
| 2632 | ||
| 2633 | 0 | if (frames == null) |
| 2634 | { | |
| 2635 | 0 | return null; |
| 2636 | } | |
| 2637 | 0 | List<GStructureViewer> avp = new ArrayList<>(); |
| 2638 | // REVERSE ORDER | |
| 2639 | 0 | for (int i = frames.length - 1; i > -1; i--) |
| 2640 | { | |
| 2641 | 0 | if (frames[i] instanceof AppJmol) |
| 2642 | { | |
| 2643 | 0 | GStructureViewer af = (GStructureViewer) frames[i]; |
| 2644 | 0 | avp.add(af); |
| 2645 | } | |
| 2646 | } | |
| 2647 | 0 | if (avp.size() == 0) |
| 2648 | { | |
| 2649 | 0 | return null; |
| 2650 | } | |
| 2651 | 0 | GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]); |
| 2652 | 0 | return afs; |
| 2653 | } | |
| 2654 | ||
| 2655 | /** | |
| 2656 | * Add Groovy Support to Jalview | |
| 2657 | */ | |
| 2658 | 0 | @Override |
| 2659 | public void groovyShell_actionPerformed() | |
| 2660 | { | |
| 2661 | 0 | try |
| 2662 | { | |
| 2663 | 0 | openGroovyConsole(); |
| 2664 | } catch (Exception ex) | |
| 2665 | { | |
| 2666 | 0 | jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); |
| 2667 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
| 2668 | ||
| 2669 | MessageManager.getString("label.couldnt_create_groovy_shell"), | |
| 2670 | MessageManager.getString("label.groovy_support_failed"), | |
| 2671 | JvOptionPane.ERROR_MESSAGE); | |
| 2672 | } | |
| 2673 | } | |
| 2674 | ||
| 2675 | /** | |
| 2676 | * Open the Groovy console | |
| 2677 | */ | |
| 2678 | 0 | void openGroovyConsole() |
| 2679 | { | |
| 2680 | 0 | if (groovyConsole == null) |
| 2681 | { | |
| 2682 | 0 | groovyConsole = new groovy.ui.Console(); |
| 2683 | 0 | groovyConsole.setVariable("Jalview", this); |
| 2684 | 0 | groovyConsole.run(); |
| 2685 | ||
| 2686 | /* | |
| 2687 | * We allow only one console at a time, so that AlignFrame menu option | |
| 2688 | * 'Calculate | Run Groovy script' is unambiguous. | |
| 2689 | * Disable 'Groovy Console', and enable 'Run script', when the console is | |
| 2690 | * opened, and the reverse when it is closed | |
| 2691 | */ | |
| 2692 | 0 | Window window = (Window) groovyConsole.getFrame(); |
| 2693 | 0 | window.addWindowListener(new WindowAdapter() |
| 2694 | { | |
| 2695 | 0 | @Override |
| 2696 | public void windowClosed(WindowEvent e) | |
| 2697 | { | |
| 2698 | /* | |
| 2699 | * rebind CMD-Q from Groovy Console to Jalview Quit | |
| 2700 | */ | |
| 2701 | 0 | addQuitHandler(); |
| 2702 | 0 | enableExecuteGroovy(false); |
| 2703 | } | |
| 2704 | }); | |
| 2705 | } | |
| 2706 | ||
| 2707 | /* | |
| 2708 | * show Groovy console window (after close and reopen) | |
| 2709 | */ | |
| 2710 | 0 | ((Window) groovyConsole.getFrame()).setVisible(true); |
| 2711 | ||
| 2712 | /* | |
| 2713 | * if we got this far, enable 'Run Groovy' in AlignFrame menus | |
| 2714 | * and disable opening a second console | |
| 2715 | */ | |
| 2716 | 0 | enableExecuteGroovy(true); |
| 2717 | } | |
| 2718 | ||
| 2719 | /** | |
| 2720 | * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding | |
| 2721 | * when opened | |
| 2722 | */ | |
| 2723 | 0 | protected void addQuitHandler() |
| 2724 | { | |
| 2725 | 0 | getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) |
| 2726 | .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, | |
| 2727 | Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()), | |
| 2728 | "Quit"); | |
| 2729 | 0 | getRootPane().getActionMap().put("Quit", new AbstractAction() |
| 2730 | { | |
| 2731 | 0 | @Override |
| 2732 | public void actionPerformed(ActionEvent e) | |
| 2733 | { | |
| 2734 | 0 | quit(); |
| 2735 | } | |
| 2736 | }); | |
| 2737 | } | |
| 2738 | ||
| 2739 | /** | |
| 2740 | * Enable or disable 'Run Groovy script' in AlignFrame calculate menus | |
| 2741 | * | |
| 2742 | * @param enabled | |
| 2743 | * true if Groovy console is open | |
| 2744 | */ | |
| 2745 | 0 | public void enableExecuteGroovy(boolean enabled) |
| 2746 | { | |
| 2747 | /* | |
| 2748 | * disable opening a second Groovy console | |
| 2749 | * (or re-enable when the console is closed) | |
| 2750 | */ | |
| 2751 | 0 | groovyShell.setEnabled(!enabled); |
| 2752 | ||
| 2753 | 0 | AlignFrame[] alignFrames = getAlignFrames(); |
| 2754 | 0 | if (alignFrames != null) |
| 2755 | { | |
| 2756 | 0 | for (AlignFrame af : alignFrames) |
| 2757 | { | |
| 2758 | 0 | af.setGroovyEnabled(enabled); |
| 2759 | } | |
| 2760 | } | |
| 2761 | } | |
| 2762 | ||
| 2763 | /** | |
| 2764 | * Progress bars managed by the IProgressIndicator method. | |
| 2765 | */ | |
| 2766 | private Hashtable<Long, JPanel> progressBars; | |
| 2767 | ||
| 2768 | private Hashtable<Long, IProgressIndicatorHandler> progressBarHandlers; | |
| 2769 | ||
| 2770 | /* | |
| 2771 | * (non-Javadoc) | |
| 2772 | * | |
| 2773 | * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) | |
| 2774 | */ | |
| 2775 | 0 | @Override |
| 2776 | public void setProgressBar(String message, long id) | |
| 2777 | { | |
| 2778 | 0 | if (progressBars == null) |
| 2779 | { | |
| 2780 | 0 | progressBars = new Hashtable<>(); |
| 2781 | 0 | progressBarHandlers = new Hashtable<>(); |
| 2782 | } | |
| 2783 | ||
| 2784 | 0 | if (progressBars.get(new Long(id)) != null) |
| 2785 | { | |
| 2786 | 0 | JPanel panel = progressBars.remove(new Long(id)); |
| 2787 | 0 | if (progressBarHandlers.contains(new Long(id))) |
| 2788 | { | |
| 2789 | 0 | progressBarHandlers.remove(new Long(id)); |
| 2790 | } | |
| 2791 | 0 | removeProgressPanel(panel); |
| 2792 | } | |
| 2793 | else | |
| 2794 | { | |
| 2795 | 0 | progressBars.put(new Long(id), addProgressPanel(message)); |
| 2796 | } | |
| 2797 | } | |
| 2798 | ||
| 2799 | /* | |
| 2800 | * (non-Javadoc) | |
| 2801 | * | |
| 2802 | * @see jalview.gui.IProgressIndicator#registerHandler(long, | |
| 2803 | * jalview.gui.IProgressIndicatorHandler) | |
| 2804 | */ | |
| 2805 | 0 | @Override |
| 2806 | public void registerHandler(final long id, | |
| 2807 | final IProgressIndicatorHandler handler) | |
| 2808 | { | |
| 2809 | 0 | if (progressBarHandlers == null |
| 2810 | || !progressBars.containsKey(new Long(id))) | |
| 2811 | { | |
| 2812 | 0 | throw new Error(MessageManager.getString( |
| 2813 | "error.call_setprogressbar_before_registering_handler")); | |
| 2814 | } | |
| 2815 | 0 | progressBarHandlers.put(new Long(id), handler); |
| 2816 | 0 | final JPanel progressPanel = progressBars.get(new Long(id)); |
| 2817 | 0 | if (handler.canCancel()) |
| 2818 | { | |
| 2819 | 0 | JButton cancel = new JButton( |
| 2820 | MessageManager.getString("action.cancel")); | |
| 2821 | 0 | final IProgressIndicator us = this; |
| 2822 | 0 | cancel.addActionListener(new ActionListener() |
| 2823 | { | |
| 2824 | ||
| 2825 | 0 | @Override |
| 2826 | public void actionPerformed(ActionEvent e) | |
| 2827 | { | |
| 2828 | 0 | handler.cancelActivity(id); |
| 2829 | 0 | us.setProgressBar(MessageManager |
| 2830 | .formatMessage("label.cancelled_params", new Object[] | |
| 2831 | { ((JLabel) progressPanel.getComponent(0)).getText() }), | |
| 2832 | id); | |
| 2833 | } | |
| 2834 | }); | |
| 2835 | 0 | progressPanel.add(cancel, BorderLayout.EAST); |
| 2836 | } | |
| 2837 | } | |
| 2838 | ||
| 2839 | /** | |
| 2840 | * | |
| 2841 | * @return true if any progress bars are still active | |
| 2842 | */ | |
| 2843 | 0 | @Override |
| 2844 | public boolean operationInProgress() | |
| 2845 | { | |
| 2846 | 0 | if (progressBars != null && progressBars.size() > 0) |
| 2847 | { | |
| 2848 | 0 | return true; |
| 2849 | } | |
| 2850 | 0 | return false; |
| 2851 | } | |
| 2852 | ||
| 2853 | /** | |
| 2854 | * This will return the first AlignFrame holding the given viewport instance. It | |
| 2855 | * will break if there are more than one AlignFrames viewing a particular av. | |
| 2856 | * | |
| 2857 | * @param viewport | |
| 2858 | * @return alignFrame for viewport | |
| 2859 | */ | |
| 2860 | 1 | public static AlignFrame getAlignFrameFor(AlignViewportI viewport) |
| 2861 | { | |
| 2862 | 1 | if (desktop != null) |
| 2863 | { | |
| 2864 | 1 | AlignmentPanel[] aps = getAlignmentPanels( |
| 2865 | viewport.getSequenceSetId()); | |
| 2866 | 1 | for (int panel = 0; aps != null && panel < aps.length; panel++) |
| 2867 | { | |
| 2868 | 1 | if (aps[panel] != null && aps[panel].av == viewport) |
| 2869 | { | |
| 2870 | 1 | return aps[panel].alignFrame; |
| 2871 | } | |
| 2872 | } | |
| 2873 | } | |
| 2874 | 0 | return null; |
| 2875 | } | |
| 2876 | ||
| 2877 | 0 | public VamsasApplication getVamsasApplication() |
| 2878 | { | |
| 2879 | 0 | return v_client; |
| 2880 | ||
| 2881 | } | |
| 2882 | ||
| 2883 | /** | |
| 2884 | * flag set if jalview GUI is being operated programmatically | |
| 2885 | */ | |
| 2886 | private boolean inBatchMode = false; | |
| 2887 | ||
| 2888 | /** | |
| 2889 | * check if jalview GUI is being operated programmatically | |
| 2890 | * | |
| 2891 | * @return inBatchMode | |
| 2892 | */ | |
| 2893 | 0 | public boolean isInBatchMode() |
| 2894 | { | |
| 2895 | 0 | return inBatchMode; |
| 2896 | } | |
| 2897 | ||
| 2898 | /** | |
| 2899 | * set flag if jalview GUI is being operated programmatically | |
| 2900 | * | |
| 2901 | * @param inBatchMode | |
| 2902 | */ | |
| 2903 | 22 | public void setInBatchMode(boolean inBatchMode) |
| 2904 | { | |
| 2905 | 22 | this.inBatchMode = inBatchMode; |
| 2906 | } | |
| 2907 | ||
| 2908 | 11 | public void startServiceDiscovery() |
| 2909 | { | |
| 2910 | 11 | startServiceDiscovery(false); |
| 2911 | } | |
| 2912 | ||
| 2913 | 11 | public void startServiceDiscovery(boolean blocking) |
| 2914 | { | |
| 2915 | 11 | boolean alive = true; |
| 2916 | 11 | Thread t0 = null, t1 = null, t2 = null; |
| 2917 | // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release | |
| 2918 | 11 | if (true) |
| 2919 | { | |
| 2920 | // todo: changesupport handlers need to be transferred | |
| 2921 | 11 | if (discoverer == null) |
| 2922 | { | |
| 2923 | 1 | discoverer = new jalview.ws.jws1.Discoverer(); |
| 2924 | // register PCS handler for desktop. | |
| 2925 | 1 | discoverer.addPropertyChangeListener(changeSupport); |
| 2926 | } | |
| 2927 | // JAL-940 - disabled JWS1 service configuration - always start discoverer | |
| 2928 | // until we phase out completely | |
| 2929 | 11 | (t0 = new Thread(discoverer)).start(); |
| 2930 | } | |
| 2931 | ||
| 2932 | 11 | if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) |
| 2933 | { | |
| 2934 | 11 | t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() |
| 2935 | .startDiscoverer(changeSupport); | |
| 2936 | } | |
| 2937 | 11 | Thread t3 = null; |
| 2938 | { | |
| 2939 | // TODO: do rest service discovery | |
| 2940 | } | |
| 2941 | 11 | if (blocking) |
| 2942 | { | |
| 2943 | 0 | while (alive) |
| 2944 | { | |
| 2945 | 0 | try |
| 2946 | { | |
| 2947 | 0 | Thread.sleep(15); |
| 2948 | } catch (Exception e) | |
| 2949 | { | |
| 2950 | } | |
| 2951 | 0 | alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) |
| 2952 | || (t3 != null && t3.isAlive()) | |
| 2953 | || (t0 != null && t0.isAlive()); | |
| 2954 | } | |
| 2955 | } | |
| 2956 | } | |
| 2957 | ||
| 2958 | /** | |
| 2959 | * called to check if the service discovery process completed successfully. | |
| 2960 | * | |
| 2961 | * @param evt | |
| 2962 | */ | |
| 2963 | 131 | protected void JalviewServicesChanged(PropertyChangeEvent evt) |
| 2964 | { | |
| 2965 | 131 | if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) |
| 2966 | { | |
| 2967 | 131 | final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() |
| 2968 | .getErrorMessages(); | |
| 2969 | 131 | if (ermsg != null) |
| 2970 | { | |
| 2971 | 0 | if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) |
| 2972 | { | |
| 2973 | 0 | if (serviceChangedDialog == null) |
| 2974 | { | |
| 2975 | // only run if we aren't already displaying one of these. | |
| 2976 | 0 | addDialogThread(serviceChangedDialog = new Runnable() |
| 2977 | { | |
| 2978 | 0 | @Override |
| 2979 | public void run() | |
| 2980 | { | |
| 2981 | ||
| 2982 | /* | |
| 2983 | * JalviewDialog jd =new JalviewDialog() { | |
| 2984 | * | |
| 2985 | * @Override protected void cancelPressed() { // TODO | |
| 2986 | * Auto-generated method stub | |
| 2987 | * | |
| 2988 | * }@Override protected void okPressed() { // TODO | |
| 2989 | * Auto-generated method stub | |
| 2990 | * | |
| 2991 | * }@Override protected void raiseClosed() { // TODO | |
| 2992 | * Auto-generated method stub | |
| 2993 | * | |
| 2994 | * } }; jd.initDialogFrame(new | |
| 2995 | * JLabel("<html><table width=\"450\"><tr><td>" + ermsg + | |
| 2996 | * "<br/>It may be that you have invalid JABA URLs in your web service preferences," | |
| 2997 | * + " or mis-configured HTTP proxy settings.<br/>" + | |
| 2998 | * "Check the <em>Connections</em> and <em>Web services</em> tab of the" | |
| 2999 | * + | |
| 3000 | * " Tools->Preferences dialog box to change them.</td></tr></table></html>" | |
| 3001 | * ), true, true, "Web Service Configuration Problem", 450, | |
| 3002 | * 400); | |
| 3003 | * | |
| 3004 | * jd.waitForInput(); | |
| 3005 | */ | |
| 3006 | 0 | JvOptionPane.showConfirmDialog(Desktop.desktop, |
| 3007 | new JLabel("<html><table width=\"450\"><tr><td>" | |
| 3008 | + ermsg + "</td></tr></table>" | |
| 3009 | + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences," | |
| 3010 | + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>" | |
| 3011 | + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the" | |
| 3012 | + " Tools->Preferences dialog box to change them.</p></html>"), | |
| 3013 | "Web Service Configuration Problem", | |
| 3014 | JvOptionPane.DEFAULT_OPTION, | |
| 3015 | JvOptionPane.ERROR_MESSAGE); | |
| 3016 | 0 | serviceChangedDialog = null; |
| 3017 | ||
| 3018 | } | |
| 3019 | }); | |
| 3020 | } | |
| 3021 | } | |
| 3022 | else | |
| 3023 | { | |
| 3024 | 0 | Cache.log.error( |
| 3025 | "Errors reported by JABA discovery service. Check web services preferences.\n" | |
| 3026 | + ermsg); | |
| 3027 | } | |
| 3028 | } | |
| 3029 | } | |
| 3030 | } | |
| 3031 | ||
| 3032 | private Runnable serviceChangedDialog = null; | |
| 3033 | ||
| 3034 | /** | |
| 3035 | * start a thread to open a URL in the configured browser. Pops up a warning | |
| 3036 | * dialog to the user if there is an exception when calling out to the browser | |
| 3037 | * to open the URL. | |
| 3038 | * | |
| 3039 | * @param url | |
| 3040 | */ | |
| 3041 | 0 | public static void showUrl(final String url) |
| 3042 | { | |
| 3043 | 0 | showUrl(url, Desktop.instance); |
| 3044 | } | |
| 3045 | ||
| 3046 | /** | |
| 3047 | * Like showUrl but allows progress handler to be specified | |
| 3048 | * | |
| 3049 | * @param url | |
| 3050 | * @param progress | |
| 3051 | * (null) or object implementing IProgressIndicator | |
| 3052 | */ | |
| 3053 | 0 | public static void showUrl(final String url, |
| 3054 | final IProgressIndicator progress) | |
| 3055 | { | |
| 3056 | 0 | new Thread(new Runnable() |
| 3057 | { | |
| 3058 | 0 | @Override |
| 3059 | public void run() | |
| 3060 | { | |
| 3061 | 0 | try |
| 3062 | { | |
| 3063 | 0 | if (progress != null) |
| 3064 | { | |
| 3065 | 0 | progress.setProgressBar(MessageManager |
| 3066 | .formatMessage("status.opening_params", new Object[] | |
| 3067 | { url }), this.hashCode()); | |
| 3068 | } | |
| 3069 | 0 | jalview.util.BrowserLauncher.openURL(url); |
| 3070 | } catch (Exception ex) | |
| 3071 | { | |
| 3072 | 0 | JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
| 3073 | MessageManager | |
| 3074 | .getString("label.web_browser_not_found_unix"), | |
| 3075 | MessageManager.getString("label.web_browser_not_found"), | |
| 3076 | JvOptionPane.WARNING_MESSAGE); | |
| 3077 | ||
| 3078 | 0 | ex.printStackTrace(); |
| 3079 | } | |
| 3080 | 0 | if (progress != null) |
| 3081 | { | |
| 3082 | 0 | progress.setProgressBar(null, this.hashCode()); |
| 3083 | } | |
| 3084 | } | |
| 3085 | }).start(); | |
| 3086 | } | |
| 3087 | ||
| 3088 | public static WsParamSetManager wsparamManager = null; | |
| 3089 | ||
| 3090 | 132 | public static ParamManager getUserParameterStore() |
| 3091 | { | |
| 3092 | 132 | if (wsparamManager == null) |
| 3093 | { | |
| 3094 | 1 | wsparamManager = new WsParamSetManager(); |
| 3095 | } | |
| 3096 | 132 | return wsparamManager; |
| 3097 | } | |
| 3098 | ||
| 3099 | /** | |
| 3100 | * static hyperlink handler proxy method for use by Jalview's internal windows | |
| 3101 | * | |
| 3102 | * @param e | |
| 3103 | */ | |
| 3104 | 0 | public static void hyperlinkUpdate(HyperlinkEvent e) |
| 3105 | { | |
| 3106 | 0 | if (e.getEventType() == EventType.ACTIVATED) |
| 3107 | { | |
| 3108 | 0 | String url = null; |
| 3109 | 0 | try |
| 3110 | { | |
| 3111 | 0 | url = e.getURL().toString(); |
| 3112 | 0 | Desktop.showUrl(url); |
| 3113 | } catch (Exception x) | |
| 3114 | { | |
| 3115 | 0 | if (url != null) |
| 3116 | { | |
| 3117 | 0 | if (Cache.log != null) |
| 3118 | { | |
| 3119 | 0 | Cache.log.error("Couldn't handle string " + url + " as a URL."); |
| 3120 | } | |
| 3121 | else | |
| 3122 | { | |
| 3123 | 0 | System.err.println( |
| 3124 | "Couldn't handle string " + url + " as a URL."); | |
| 3125 | } | |
| 3126 | } | |
| 3127 | // ignore any exceptions due to dud links. | |
| 3128 | } | |
| 3129 | ||
| 3130 | } | |
| 3131 | } | |
| 3132 | ||
| 3133 | /** | |
| 3134 | * single thread that handles display of dialogs to user. | |
| 3135 | */ | |
| 3136 | ExecutorService dialogExecutor = Executors.newSingleThreadExecutor(); | |
| 3137 | ||
| 3138 | /** | |
| 3139 | * flag indicating if dialogExecutor should try to acquire a permit | |
| 3140 | */ | |
| 3141 | private volatile boolean dialogPause = true; | |
| 3142 | ||
| 3143 | /** | |
| 3144 | * pause the queue | |
| 3145 | */ | |
| 3146 | private java.util.concurrent.Semaphore block = new Semaphore(0); | |
| 3147 | ||
| 3148 | private static groovy.ui.Console groovyConsole; | |
| 3149 | ||
| 3150 | /** | |
| 3151 | * add another dialog thread to the queue | |
| 3152 | * | |
| 3153 | * @param prompter | |
| 3154 | */ | |
| 3155 | 37 | public void addDialogThread(final Runnable prompter) |
| 3156 | { | |
| 3157 | 37 | dialogExecutor.submit(new Runnable() |
| 3158 | { | |
| 3159 | 24 | @Override |
| 3160 | public void run() | |
| 3161 | { | |
| 3162 | 24 | if (dialogPause) |
| 3163 | { | |
| 3164 | 11 | try |
| 3165 | { | |
| 3166 | 11 | block.acquire(); |
| 3167 | } catch (InterruptedException x) | |
| 3168 | { | |
| 3169 | } | |
| 3170 | 5 | ; |
| 3171 | } | |
| 3172 | 18 | if (instance == null) |
| 3173 | { | |
| 3174 | 0 | return; |
| 3175 | } | |
| 3176 | 18 | try |
| 3177 | { | |
| 3178 | 18 | SwingUtilities.invokeAndWait(prompter); |
| 3179 | } catch (Exception q) | |
| 3180 | { | |
| 3181 | 0 | Cache.log.warn("Unexpected Exception in dialog thread.", q); |
| 3182 | } | |
| 3183 | } | |
| 3184 | }); | |
| 3185 | } | |
| 3186 | ||
| 3187 | 10 | public void startDialogQueue() |
| 3188 | { | |
| 3189 | // set the flag so we don't pause waiting for another permit and semaphore | |
| 3190 | // the current task to begin | |
| 3191 | 10 | dialogPause = false; |
| 3192 | 10 | block.release(); |
| 3193 | } | |
| 3194 | ||
| 3195 | /** | |
| 3196 | * Outputs an image of the desktop to file in EPS format, after prompting the | |
| 3197 | * user for choice of Text or Lineart character rendering (unless a preference | |
| 3198 | * has been set). The file name is generated as | |
| 3199 | * | |
| 3200 | * <pre> | |
| 3201 | * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds | |
| 3202 | * </pre> | |
| 3203 | */ | |
| 3204 | 0 | @Override |
| 3205 | protected void snapShotWindow_actionPerformed(ActionEvent e) | |
| 3206 | { | |
| 3207 | // currently the menu option to do this is not shown | |
| 3208 | 0 | invalidate(); |
| 3209 | ||
| 3210 | 0 | int width = getWidth(); |
| 3211 | 0 | int height = getHeight(); |
| 3212 | 0 | File of = new File( |
| 3213 | "Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); | |
| 3214 | 0 | ImageWriterI writer = new ImageWriterI() |
| 3215 | { | |
| 3216 | 0 | @Override |
| 3217 | public void exportImage(Graphics g) throws Exception | |
| 3218 | { | |
| 3219 | 0 | paintAll(g); |
| 3220 | 0 | Cache.log.info("Successfully written snapshot to file " |
| 3221 | + of.getAbsolutePath()); | |
| 3222 | } | |
| 3223 | }; | |
| 3224 | 0 | String title = "View of desktop"; |
| 3225 | 0 | ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, |
| 3226 | title); | |
| 3227 | 0 | exporter.doExport(of, this, width, height, title); |
| 3228 | } | |
| 3229 | ||
| 3230 | /** | |
| 3231 | * Explode the views in the given SplitFrame into separate SplitFrame windows. | |
| 3232 | * This respects (remembers) any previous 'exploded geometry' i.e. the size and | |
| 3233 | * location last time the view was expanded (if any). However it does not | |
| 3234 | * remember the split pane divider location - this is set to match the | |
| 3235 | * 'exploding' frame. | |
| 3236 | * | |
| 3237 | * @param sf | |
| 3238 | */ | |
| 3239 | 0 | public void explodeViews(SplitFrame sf) |
| 3240 | { | |
| 3241 | 0 | AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame(); |
| 3242 | 0 | AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame(); |
| 3243 | 0 | List<? extends AlignmentViewPanel> topPanels = oldTopFrame |
| 3244 | .getAlignPanels(); | |
| 3245 | 0 | List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame |
| 3246 | .getAlignPanels(); | |
| 3247 | 0 | int viewCount = topPanels.size(); |
| 3248 | 0 | if (viewCount < 2) |
| 3249 | { | |
| 3250 | 0 | return; |
| 3251 | } | |
| 3252 | ||
| 3253 | /* | |
| 3254 | * Processing in reverse order works, forwards order leaves the first panels | |
| 3255 | * not visible. I don't know why! | |
| 3256 | */ | |
| 3257 | 0 | for (int i = viewCount - 1; i >= 0; i--) |
| 3258 | { | |
| 3259 | /* | |
| 3260 | * Make new top and bottom frames. These take over the respective | |
| 3261 | * AlignmentPanel objects, including their AlignmentViewports, so the | |
| 3262 | * cdna/protein relationships between the viewports is carried over to the | |
| 3263 | * new split frames. | |
| 3264 | * | |
| 3265 | * explodedGeometry holds the (x, y) position of the previously exploded | |
| 3266 | * SplitFrame, and the (width, height) of the AlignFrame component | |
| 3267 | */ | |
| 3268 | 0 | AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); |
| 3269 | 0 | AlignFrame newTopFrame = new AlignFrame(topPanel); |
| 3270 | 0 | newTopFrame.setSize(oldTopFrame.getSize()); |
| 3271 | 0 | newTopFrame.setVisible(true); |
| 3272 | 0 | Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) |
| 3273 | .getExplodedGeometry(); | |
| 3274 | 0 | if (geometry != null) |
| 3275 | { | |
| 3276 | 0 | newTopFrame.setSize(geometry.getSize()); |
| 3277 | } | |
| 3278 | ||
| 3279 | 0 | AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); |
| 3280 | 0 | AlignFrame newBottomFrame = new AlignFrame(bottomPanel); |
| 3281 | 0 | newBottomFrame.setSize(oldBottomFrame.getSize()); |
| 3282 | 0 | newBottomFrame.setVisible(true); |
| 3283 | 0 | geometry = ((AlignViewport) bottomPanel.getAlignViewport()) |
| 3284 | .getExplodedGeometry(); | |
| 3285 | 0 | if (geometry != null) |
| 3286 | { | |
| 3287 | 0 | newBottomFrame.setSize(geometry.getSize()); |
| 3288 | } | |
| 3289 | ||
| 3290 | 0 | topPanel.av.setGatherViewsHere(false); |
| 3291 | 0 | bottomPanel.av.setGatherViewsHere(false); |
| 3292 | 0 | JInternalFrame splitFrame = new SplitFrame(newTopFrame, |
| 3293 | newBottomFrame); | |
| 3294 | 0 | if (geometry != null) |
| 3295 | { | |
| 3296 | 0 | splitFrame.setLocation(geometry.getLocation()); |
| 3297 | } | |
| 3298 | 0 | Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); |
| 3299 | } | |
| 3300 | ||
| 3301 | /* | |
| 3302 | * Clear references to the panels (now relocated in the new SplitFrames) | |
| 3303 | * before closing the old SplitFrame. | |
| 3304 | */ | |
| 3305 | 0 | topPanels.clear(); |
| 3306 | 0 | bottomPanels.clear(); |
| 3307 | 0 | sf.close(); |
| 3308 | } | |
| 3309 | ||
| 3310 | /** | |
| 3311 | * Gather expanded split frames, sharing the same pairs of sequence set ids, | |
| 3312 | * back into the given SplitFrame as additional views. Note that the gathered | |
| 3313 | * frames may themselves have multiple views. | |
| 3314 | * | |
| 3315 | * @param source | |
| 3316 | */ | |
| 3317 | 0 | public void gatherViews(GSplitFrame source) |
| 3318 | { | |
| 3319 | /* | |
| 3320 | * special handling of explodedGeometry for a view within a SplitFrame: - it | |
| 3321 | * holds the (x, y) position of the enclosing SplitFrame, and the (width, | |
| 3322 | * height) of the AlignFrame component | |
| 3323 | */ | |
| 3324 | 0 | AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); |
| 3325 | 0 | AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); |
| 3326 | 0 | myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), |
| 3327 | source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); | |
| 3328 | 0 | myBottomFrame.viewport |
| 3329 | .setExplodedGeometry(new Rectangle(source.getX(), source.getY(), | |
| 3330 | myBottomFrame.getWidth(), myBottomFrame.getHeight())); | |
| 3331 | 0 | myTopFrame.viewport.setGatherViewsHere(true); |
| 3332 | 0 | myBottomFrame.viewport.setGatherViewsHere(true); |
| 3333 | 0 | String topViewId = myTopFrame.viewport.getSequenceSetId(); |
| 3334 | 0 | String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); |
| 3335 | ||
| 3336 | 0 | JInternalFrame[] frames = desktop.getAllFrames(); |
| 3337 | 0 | for (JInternalFrame frame : frames) |
| 3338 | { | |
| 3339 | 0 | if (frame instanceof SplitFrame && frame != source) |
| 3340 | { | |
| 3341 | 0 | SplitFrame sf = (SplitFrame) frame; |
| 3342 | 0 | AlignFrame topFrame = (AlignFrame) sf.getTopFrame(); |
| 3343 | 0 | AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame(); |
| 3344 | 0 | boolean gatherThis = false; |
| 3345 | 0 | for (int a = 0; a < topFrame.alignPanels.size(); a++) |
| 3346 | { | |
| 3347 | 0 | AlignmentPanel topPanel = topFrame.alignPanels.get(a); |
| 3348 | 0 | AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a); |
| 3349 | 0 | if (topViewId.equals(topPanel.av.getSequenceSetId()) |
| 3350 | && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) | |
| 3351 | { | |
| 3352 | 0 | gatherThis = true; |
| 3353 | 0 | topPanel.av.setGatherViewsHere(false); |
| 3354 | 0 | bottomPanel.av.setGatherViewsHere(false); |
| 3355 | 0 | topPanel.av.setExplodedGeometry( |
| 3356 | new Rectangle(sf.getLocation(), topFrame.getSize())); | |
| 3357 | 0 | bottomPanel.av.setExplodedGeometry( |
| 3358 | new Rectangle(sf.getLocation(), bottomFrame.getSize())); | |
| 3359 | 0 | myTopFrame.addAlignmentPanel(topPanel, false); |
| 3360 | 0 | myBottomFrame.addAlignmentPanel(bottomPanel, false); |
| 3361 | } | |
| 3362 | } | |
| 3363 | ||
| 3364 | 0 | if (gatherThis) |
| 3365 | { | |
| 3366 | 0 | topFrame.getAlignPanels().clear(); |
| 3367 | 0 | bottomFrame.getAlignPanels().clear(); |
| 3368 | 0 | sf.close(); |
| 3369 | } | |
| 3370 | } | |
| 3371 | } | |
| 3372 | ||
| 3373 | /* | |
| 3374 | * The dust settles...give focus to the tab we did this from. | |
| 3375 | */ | |
| 3376 | 0 | myTopFrame.setDisplayedView(myTopFrame.alignPanel); |
| 3377 | } | |
| 3378 | ||
| 3379 | 376 | public static groovy.ui.Console getGroovyConsole() |
| 3380 | { | |
| 3381 | 376 | return groovyConsole; |
| 3382 | } | |
| 3383 | ||
| 3384 | /** | |
| 3385 | * handles the payload of a drag and drop event. | |
| 3386 | * | |
| 3387 | * TODO refactor to desktop utilities class | |
| 3388 | * | |
| 3389 | * @param files | |
| 3390 | * - Data source strings extracted from the drop event | |
| 3391 | * @param protocols | |
| 3392 | * - protocol for each data source extracted from the drop event | |
| 3393 | * @param evt | |
| 3394 | * - the drop event | |
| 3395 | * @param t | |
| 3396 | * - the payload from the drop event | |
| 3397 | * @throws Exception | |
| 3398 | */ | |
| 3399 | 0 | public static void transferFromDropTarget(List<Object> files, |
| 3400 | List<DataSourceType> protocols, DropTargetDropEvent evt, | |
| 3401 | Transferable t) throws Exception | |
| 3402 | { | |
| 3403 | ||
| 3404 | // BH 2018 changed List<String> to List<Object> to allow for File from SwingJS | |
| 3405 | ||
| 3406 | // DataFlavor[] flavors = t.getTransferDataFlavors(); | |
| 3407 | // for (int i = 0; i < flavors.length; i++) { | |
| 3408 | // if (flavors[i].isFlavorJavaFileListType()) { | |
| 3409 | // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); | |
| 3410 | // List<File> list = (List<File>) t.getTransferData(flavors[i]); | |
| 3411 | // for (int j = 0; j < list.size(); j++) { | |
| 3412 | // File file = (File) list.get(j); | |
| 3413 | // byte[] data = getDroppedFileBytes(file); | |
| 3414 | // fileName.setText(file.getName() + " - " + data.length + " " + | |
| 3415 | // evt.getLocation()); | |
| 3416 | // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent(); | |
| 3417 | // target.setText(new String(data)); | |
| 3418 | // } | |
| 3419 | // dtde.dropComplete(true); | |
| 3420 | // return; | |
| 3421 | // } | |
| 3422 | // | |
| 3423 | ||
| 3424 | 0 | DataFlavor uriListFlavor = new DataFlavor( |
| 3425 | "text/uri-list;class=java.lang.String"), urlFlavour = null; | |
| 3426 | 0 | try |
| 3427 | { | |
| 3428 | 0 | urlFlavour = new DataFlavor( |
| 3429 | "application/x-java-url; class=java.net.URL"); | |
| 3430 | } catch (ClassNotFoundException cfe) | |
| 3431 | { | |
| 3432 | 0 | Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe); |
| 3433 | } | |
| 3434 | ||
| 3435 | 0 | if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) |
| 3436 | { | |
| 3437 | ||
| 3438 | 0 | try |
| 3439 | { | |
| 3440 | 0 | java.net.URL url = (URL) t.getTransferData(urlFlavour); |
| 3441 | // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099 | |
| 3442 | // means url may be null. | |
| 3443 | 0 | if (url != null) |
| 3444 | { | |
| 3445 | 0 | protocols.add(DataSourceType.URL); |
| 3446 | 0 | files.add(url.toString()); |
| 3447 | 0 | Cache.log.debug("Drop handled as URL dataflavor " |
| 3448 | + files.get(files.size() - 1)); | |
| 3449 | 0 | return; |
| 3450 | } | |
| 3451 | else | |
| 3452 | { | |
| 3453 | 0 | if (Platform.isAMac()) |
| 3454 | { | |
| 3455 | 0 | System.err.println( |
| 3456 | "Please ignore plist error - occurs due to problem with java 8 on OSX"); | |
| 3457 | } | |
| 3458 | 0 | ; |
| 3459 | } | |
| 3460 | } catch (Throwable ex) | |
| 3461 | { | |
| 3462 | 0 | Cache.log.debug("URL drop handler failed.", ex); |
| 3463 | } | |
| 3464 | } | |
| 3465 | 0 | if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) |
| 3466 | { | |
| 3467 | // Works on Windows and MacOSX | |
| 3468 | 0 | Cache.log.debug("Drop handled as javaFileListFlavor"); |
| 3469 | 0 | for (Object file : (List) t |
| 3470 | .getTransferData(DataFlavor.javaFileListFlavor)) | |
| 3471 | { | |
| 3472 | 0 | files.add(file); |
| 3473 | 0 | protocols.add(DataSourceType.FILE); |
| 3474 | } | |
| 3475 | } | |
| 3476 | else | |
| 3477 | { | |
| 3478 | // Unix like behaviour | |
| 3479 | 0 | boolean added = false; |
| 3480 | 0 | String data = null; |
| 3481 | 0 | if (t.isDataFlavorSupported(uriListFlavor)) |
| 3482 | { | |
| 3483 | 0 | Cache.log.debug("Drop handled as uriListFlavor"); |
| 3484 | // This is used by Unix drag system | |
| 3485 | 0 | data = (String) t.getTransferData(uriListFlavor); |
| 3486 | } | |
| 3487 | 0 | if (data == null) |
| 3488 | { | |
| 3489 | // fallback to text: workaround - on OSX where there's a JVM bug | |
| 3490 | 0 | Cache.log.debug("standard URIListFlavor failed. Trying text"); |
| 3491 | // try text fallback | |
| 3492 | 0 | DataFlavor textDf = new DataFlavor( |
| 3493 | "text/plain;class=java.lang.String"); | |
| 3494 | 0 | if (t.isDataFlavorSupported(textDf)) |
| 3495 | { | |
| 3496 | 0 | data = (String) t.getTransferData(textDf); |
| 3497 | } | |
| 3498 | ||
| 3499 | 0 | Cache.log.debug("Plain text drop content returned " |
| 3500 | 0 | + (data == null ? "Null - failed" : data)); |
| 3501 | ||
| 3502 | } | |
| 3503 | 0 | if (data != null) |
| 3504 | { | |
| 3505 | 0 | while (protocols.size() < files.size()) |
| 3506 | { | |
| 3507 | 0 | Cache.log.debug("Adding missing FILE protocol for " |
| 3508 | + files.get(protocols.size())); | |
| 3509 | 0 | protocols.add(DataSourceType.FILE); |
| 3510 | } | |
| 3511 | 0 | for (java.util.StringTokenizer st = new java.util.StringTokenizer( |
| 3512 | 0 | data, "\r\n"); st.hasMoreTokens();) |
| 3513 | { | |
| 3514 | 0 | added = true; |
| 3515 | 0 | String s = st.nextToken(); |
| 3516 | 0 | if (s.startsWith("#")) |
| 3517 | { | |
| 3518 | // the line is a comment (as per the RFC 2483) | |
| 3519 | 0 | continue; |
| 3520 | } | |
| 3521 | 0 | java.net.URI uri = new java.net.URI(s); |
| 3522 | 0 | if (uri.getScheme().toLowerCase().startsWith("http")) |
| 3523 | { | |
| 3524 | 0 | protocols.add(DataSourceType.URL); |
| 3525 | 0 | files.add(uri.toString()); |
| 3526 | } | |
| 3527 | else | |
| 3528 | { | |
| 3529 | // otherwise preserve old behaviour: catch all for file objects | |
| 3530 | 0 | java.io.File file = new java.io.File(uri); |
| 3531 | 0 | protocols.add(DataSourceType.FILE); |
| 3532 | 0 | files.add(file.toString()); |
| 3533 | } | |
| 3534 | } | |
| 3535 | } | |
| 3536 | ||
| 3537 | 0 | if (Cache.log.isDebugEnabled()) |
| 3538 | { | |
| 3539 | 0 | if (data == null || !added) |
| 3540 | { | |
| 3541 | ||
| 3542 | 0 | if (t.getTransferDataFlavors() != null |
| 3543 | && t.getTransferDataFlavors().length > 0) | |
| 3544 | { | |
| 3545 | 0 | Cache.log.debug( |
| 3546 | "Couldn't resolve drop data. Here are the supported flavors:"); | |
| 3547 | 0 | for (DataFlavor fl : t.getTransferDataFlavors()) |
| 3548 | { | |
| 3549 | 0 | Cache.log.debug( |
| 3550 | "Supported transfer dataflavor: " + fl.toString()); | |
| 3551 | 0 | Object df = t.getTransferData(fl); |
| 3552 | 0 | if (df != null) |
| 3553 | { | |
| 3554 | 0 | Cache.log.debug("Retrieves: " + df); |
| 3555 | } | |
| 3556 | else | |
| 3557 | { | |
| 3558 | 0 | Cache.log.debug("Retrieved nothing"); |
| 3559 | } | |
| 3560 | } | |
| 3561 | } | |
| 3562 | else | |
| 3563 | { | |
| 3564 | 0 | Cache.log.debug("Couldn't resolve dataflavor for drop: " |
| 3565 | + t.toString()); | |
| 3566 | } | |
| 3567 | } | |
| 3568 | } | |
| 3569 | } | |
| 3570 | 0 | if (Platform.isWindows()) |
| 3571 | ||
| 3572 | { | |
| 3573 | 0 | Cache.log.debug("Scanning dropped content for Windows Link Files"); |
| 3574 | ||
| 3575 | // resolve any .lnk files in the file drop | |
| 3576 | 0 | for (int f = 0; f < files.size(); f++) |
| 3577 | { | |
| 3578 | 0 | String source = files.get(f).toString().toLowerCase(); |
| 3579 | 0 | if (protocols.get(f).equals(DataSourceType.FILE) |
| 3580 | && (source.endsWith(".lnk") || source.endsWith(".url") | |
| 3581 | || source.endsWith(".site"))) | |
| 3582 | { | |
| 3583 | 0 | try |
| 3584 | { | |
| 3585 | 0 | Object obj = files.get(f); |
| 3586 | 0 | File lf = (obj instanceof File ? (File) obj |
| 3587 | : new File((String) obj)); | |
| 3588 | // process link file to get a URL | |
| 3589 | 0 | Cache.log.debug("Found potential link file: " + lf); |
| 3590 | 0 | WindowsShortcut wscfile = new WindowsShortcut(lf); |
| 3591 | 0 | String fullname = wscfile.getRealFilename(); |
| 3592 | 0 | protocols.set(f, FormatAdapter.checkProtocol(fullname)); |
| 3593 | 0 | files.set(f, fullname); |
| 3594 | 0 | Cache.log.debug("Parsed real filename " + fullname |
| 3595 | + " to extract protocol: " + protocols.get(f)); | |
| 3596 | } catch (Exception ex) | |
| 3597 | { | |
| 3598 | 0 | Cache.log.error( |
| 3599 | "Couldn't parse " + files.get(f) + " as a link file.", | |
| 3600 | ex); | |
| 3601 | } | |
| 3602 | } | |
| 3603 | } | |
| 3604 | } | |
| 3605 | } | |
| 3606 | ||
| 3607 | /** | |
| 3608 | * Sets the Preferences property for experimental features to True or False | |
| 3609 | * depending on the state of the controlling menu item | |
| 3610 | */ | |
| 3611 | 0 | @Override |
| 3612 | protected void showExperimental_actionPerformed(boolean selected) | |
| 3613 | { | |
| 3614 | 0 | Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); |
| 3615 | } | |
| 3616 | ||
| 3617 | /** | |
| 3618 | * Answers a (possibly empty) list of any structure viewer frames (currently for | |
| 3619 | * either Jmol or Chimera) which are currently open. This may optionally be | |
| 3620 | * restricted to viewers of a specified class, or viewers linked to a specified | |
| 3621 | * alignment panel. | |
| 3622 | * | |
| 3623 | * @param apanel | |
| 3624 | * if not null, only return viewers linked to this panel | |
| 3625 | * @param structureViewerClass | |
| 3626 | * if not null, only return viewers of this class | |
| 3627 | * @return | |
| 3628 | */ | |
| 3629 | 1 | public List<StructureViewerBase> getStructureViewers( |
| 3630 | AlignmentPanel apanel, | |
| 3631 | Class<? extends StructureViewerBase> structureViewerClass) | |
| 3632 | { | |
| 3633 | 1 | List<StructureViewerBase> result = new ArrayList<>(); |
| 3634 | 1 | JInternalFrame[] frames = Desktop.instance.getAllFrames(); |
| 3635 | ||
| 3636 | 1 | for (JInternalFrame frame : frames) |
| 3637 | { | |
| 3638 | 3 | if (frame instanceof StructureViewerBase) |
| 3639 | { | |
| 3640 | 1 | if (structureViewerClass == null |
| 3641 | || structureViewerClass.isInstance(frame)) | |
| 3642 | { | |
| 3643 | 1 | if (apanel == null |
| 3644 | || ((StructureViewerBase) frame).isLinkedWith(apanel)) | |
| 3645 | { | |
| 3646 | 1 | result.add((StructureViewerBase) frame); |
| 3647 | } | |
| 3648 | } | |
| 3649 | } | |
| 3650 | } | |
| 3651 | 1 | return result; |
| 3652 | } | |
| 3653 | } |