X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=c3640a9243e74f8823419f0d29e7790bead3b037;hb=ad16d6cce49a40ea1943431b980b85a6212bb9bf;hp=89499c113a0d389f256776c7492f530bb65149a1;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 89499c1..c3640a9 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,10 +20,11 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.SEQUENCE_ID; - import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.gui.ImageExporter.ImageWriterI; @@ -38,6 +39,7 @@ import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; +import jalview.jbgui.GDesktop; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; import jalview.project.Jalview2XML; @@ -49,6 +51,7 @@ import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.UrlConstants; import jalview.viewmodel.AlignmentViewport; +import jalview.ws.jws1.Discoverer; import jalview.ws.params.ParamManager; import jalview.ws.utils.UrlDownloadClient; @@ -134,26 +137,28 @@ import org.stackoverflowusers.file.WindowsShortcut; * @author $author$ * @version $Revision: 1.155 $ */ -public class Desktop extends jalview.jbgui.GDesktop +@SuppressWarnings("serial") +public class Desktop extends GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator, - jalview.api.StructureSelectionManagerProvider + StructureSelectionManagerProvider, ApplicationSingletonI { - private static int DEFAULT_MIN_WIDTH = 300; - private static int DEFAULT_MIN_HEIGHT = 250; + private final static int DEFAULT_MIN_WIDTH = 300; + + private final static int DEFAULT_MIN_HEIGHT = 250; - private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; + private final static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; - private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; + private final static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; - private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; + private final static String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); /** * news reader - null if it was never started. */ - private BlogReader jvnews = null; + BlogReader jvnews = null; private File projectFile; @@ -192,16 +197,15 @@ public class Desktop extends jalview.jbgui.GDesktop listener); } - /** Singleton Desktop instance */ - public static Desktop instance; - - public static MyDesktopPane desktop; + public static MyDesktopPane getDesktopPane() + { + return Desktop.getInstance().desktopPane; + } - public static MyDesktopPane getDesktop() + public StructureSelectionManager getStructureSelectionManager() { - // BH 2018 could use currentThread() here as a reference to a - // Hashtable in JavaScript - return desktop; + return StructureSelectionManager + .getStructureSelectionManager(this); } static int openFrameCount = 0; @@ -210,13 +214,20 @@ public class Desktop extends jalview.jbgui.GDesktop static final int yOffset = 30; - public static jalview.ws.jws1.Discoverer discoverer; + public Discoverer discoverer; - public static Object[] jalviewClipboard; + public Object[] jalviewClipboard; - public static boolean internalCopy = false; + public boolean internalCopy = false; - static int fileLoadingCount = 0; + private static int fileLoadingCount = 0; + + public JInternalFrame conservationSlider, PIDSlider; + + /** + * just an instance (for testng, probably); no actual frames + */ + private boolean instanceOnly; class MyDesktopManager implements DesktopManager { @@ -237,7 +248,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (NullPointerException npe) { Point p = getMousePosition(); - instance.showPasteMenu(p.x, p.y); + showPasteMenu(p.x, p.y); } } @@ -285,14 +296,14 @@ public class Desktop extends jalview.jbgui.GDesktop public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); - desktop.repaint(); + desktopPane.repaint(); } @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); - desktop.repaint(); + desktopPane.repaint(); } @Override @@ -341,22 +352,48 @@ public class Desktop extends jalview.jbgui.GDesktop } + public MyDesktopPane desktopPane; + + /** + * Answers an 'application scope' singleton instance of this class. Separate + * SwingJS 'applets' running in the same browser page will each have a + * distinct instance of Desktop. + * + * @return + */ + public static Desktop getInstance() + { + return (Desktop) ApplicationSingletonProvider + .getInstance(Desktop.class); + } + /** - * Creates a new Desktop object. + * For testing. + * + * @param forInstance + */ + public Desktop(boolean forInstance) + { + instanceOnly = true; + } + + /** + * Private constructor enforces singleton pattern. It is called by reflection + * from ApplicationSingletonProvider.getInstance(). */ - public Desktop() + @SuppressWarnings("unused") + private Desktop() { - super(); /** - * A note to implementors. It is ESSENTIAL that any activities that might block - * are spawned off as threads rather than waited for during this constructor. + * A note to implementors. It is ESSENTIAL that any activities that might + * block are spawned off as threads rather than waited for during this + * constructor. */ - instance = this; if (!Platform.isJS()) { doVamsasClientCheck(); } - + doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); @@ -364,35 +401,34 @@ public class Desktop extends jalview.jbgui.GDesktop false); boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", false); - desktop = new MyDesktopPane(selmemusage); - + desktopPane = new MyDesktopPane(selmemusage); showMemusage.setSelected(selmemusage); - desktop.setBackground(Color.white); + desktopPane.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); // alternate config - have scrollbars - see notes in JAL-153 // JScrollPane sp = new JScrollPane(); // sp.getViewport().setView(desktop); // getContentPane().add(sp, BorderLayout.CENTER); - // BH 2018 - just an experiment to try unclipped JInternalFrames. - if (Platform.isJS()) - { - getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); - } + // BH 2018 - just an experiment to try unclipped JInternalFrames. + if (Platform.isJS()) + { + getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); + } - getContentPane().add(desktop, BorderLayout.CENTER); - desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); + getContentPane().add(desktopPane, BorderLayout.CENTER); + desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised - desktop.setDesktopManager(new MyDesktopManager( + desktopPane.setDesktopManager(new MyDesktopManager( (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager( - desktop.getDesktopManager()) - : desktop.getDesktopManager()))); - + desktopPane.getDesktopManager()) + : desktopPane.getDesktopManager()))); + Rectangle dims = getLastKnownDimensions(""); if (dims != null) { @@ -406,10 +442,14 @@ public class Desktop extends jalview.jbgui.GDesktop setBounds(xPos, yPos, 900, 650); } - boolean doFullLoad = /** @j2sNative ! */true; + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { - if (doFullLoad) { - jconsole = new Console(this, showjconsole); // add essential build information jconsole.setHeader("Jalview Version: " @@ -422,19 +462,19 @@ public class Desktop extends jalview.jbgui.GDesktop + System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); - + showConsole(showjconsole); - + showNews.setVisible(false); - + experimentalFeatures.setSelected(showExperimental()); - + getIdentifiersOrgData(); - + checkURLLinks(); - + // Spawn a thread that shows the splashscreen - + SwingUtilities.invokeLater(new Runnable() { @Override @@ -443,8 +483,9 @@ public class Desktop extends jalview.jbgui.GDesktop new SplashScreen(); } }); - - // Thread off a new instance of the file chooser - this reduces the time it + + // Thread off a new instance of the file chooser - this reduces the time + // it // takes to open it later on. new Thread(new Runnable() { @@ -462,7 +503,7 @@ public class Desktop extends jalview.jbgui.GDesktop changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() { - + @Override public void propertyChange(PropertyChangeEvent evt) { @@ -470,13 +511,13 @@ public class Desktop extends jalview.jbgui.GDesktop + evt.getNewValue()); JalviewServicesChanged(evt); } - + }); - - } - - this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - + + } + + this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this)); + this.addWindowListener(new WindowAdapter() { @Override @@ -485,7 +526,7 @@ public class Desktop extends jalview.jbgui.GDesktop quit(); } }); - + MouseAdapter ma; this.addMouseListener(ma = new MouseAdapter() { @@ -497,7 +538,7 @@ public class Desktop extends jalview.jbgui.GDesktop showPasteMenu(evt.getX(), evt.getY()); } } - + @Override public void mouseReleased(MouseEvent evt) { @@ -507,8 +548,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } }); - desktop.addMouseListener(ma); - + desktopPane.addMouseListener(ma); } /** @@ -527,8 +567,7 @@ public class Desktop extends jalview.jbgui.GDesktop public void doConfigureStructurePrefs() { // configure services - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(this); + StructureSelectionManager ssm = getStructureSelectionManager(); if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true)) { ssm.setAddTempFacAnnot(jalview.bin.Cache @@ -572,10 +611,10 @@ public class Desktop extends jalview.jbgui.GDesktop public void run() { Cache.log.debug("Downloading data from identifiers.org"); - UrlDownloadClient client = new UrlDownloadClient(); + // UrlDownloadClient client = new UrlDownloadClient(); try { - client.download(IdOrgSettings.getUrl(), + UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation()); } catch (IOException e) { @@ -584,7 +623,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } }).start(); - ; + } @Override @@ -593,7 +632,7 @@ public class Desktop extends jalview.jbgui.GDesktop showNews(showNews.isSelected()); } - void showNews(boolean visible) + protected void showNews(boolean visible) { Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); showNews.setSelected(visible); @@ -605,10 +644,10 @@ public class Desktop extends jalview.jbgui.GDesktop public void run() { long now = System.currentTimeMillis(); - Desktop.instance.setProgressBar( + setProgressBar( MessageManager.getString("status.refreshing_news"), now); jvnews.refreshNews(); - Desktop.instance.setProgressBar(null, now); + setProgressBar(null, now); jvnews.showNews(); } }).start(); @@ -713,7 +752,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - void showPasteMenu(int x, int y) + protected void showPasteMenu(int x, int y) { JPopupMenu popup = new JPopupMenu(); JMenuItem item = new JMenuItem( @@ -855,8 +894,7 @@ public class Desktop extends jalview.jbgui.GDesktop // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN // IF JALVIEW IS RUNNING HEADLESS // /////////////////////////////////////////////// - if (instance == null || (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true"))) + if (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode()) { return; } @@ -884,8 +922,7 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); - frame.setOpaque(/** @j2sNative true || */ - false); + frame.setOpaque(Platform.isJS()); if (frame.getX() < 1 && frame.getY() < 1) { @@ -897,13 +934,13 @@ public class Desktop extends jalview.jbgui.GDesktop * add an entry for the new frame in the Window menu * (and remove it when the frame is closed) */ - final JMenuItem menuItem = new JMenuItem(title); + JMenuItem menuItem = new JMenuItem(title); frame.addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameActivated(InternalFrameEvent evt) { - JInternalFrame itf = desktop.getSelectedFrame(); + JInternalFrame itf = getDesktopPane().getSelectedFrame(); if (itf != null) { if (itf instanceof AlignFrame) @@ -935,8 +972,8 @@ public class Desktop extends jalview.jbgui.GDesktop { menuItem.removeActionListener(menuItem.getActionListeners()[0]); } - windowMenu.remove(menuItem); - }; + Desktop.getInstance().windowMenu.remove(menuItem); + } }); menuItem.addActionListener(new ActionListener() @@ -957,9 +994,9 @@ public class Desktop extends jalview.jbgui.GDesktop setKeyBindings(frame); - desktop.add(frame); + getDesktopPane().add(frame); - windowMenu.add(menuItem); + Desktop.getInstance().windowMenu.add(menuItem); frame.toFront(); try @@ -984,7 +1021,6 @@ public class Desktop extends jalview.jbgui.GDesktop */ private static void setKeyBindings(JInternalFrame frame) { - @SuppressWarnings("serial") final Action closeAction = new AbstractAction() { @Override @@ -1017,7 +1053,7 @@ public class Desktop extends jalview.jbgui.GDesktop { if (!internalCopy) { - Desktop.jalviewClipboard = null; + Desktop.getInstance().jalviewClipboard = null; } internalCopy = false; @@ -1092,7 +1128,10 @@ public class Desktop extends jalview.jbgui.GDesktop { format = new IdentifyFile().identify(file, protocol); } - + if (file instanceof File) + { + Platform.cacheFileData((File) file); + } new FileLoader().LoadFile(null, file, protocol, format); } @@ -1172,7 +1211,7 @@ public class Desktop extends jalview.jbgui.GDesktop JPanel panel = new JPanel(new GridLayout(2, 1)); panel.add(label); - + /* * the URL to fetch is * Java: an editable combobox with history @@ -1185,6 +1224,11 @@ public class Desktop extends jalview.jbgui.GDesktop history = new JTextField(urlBase, 35); } else + /** + * Java only + * + * @j2sIgnore + */ { JComboBox asCombo = new JComboBox<>(); asCombo.setPreferredSize(new Dimension(400, 20)); @@ -1204,13 +1248,16 @@ public class Desktop extends jalview.jbgui.GDesktop Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; - Runnable action = new Runnable() { + Runnable action = new Runnable() + { @Override public void run() { - String url = Platform.isJS() ? ((JTextField) history).getText() + @SuppressWarnings("unchecked") + String url = (history instanceof JTextField + ? ((JTextField) history).getText() : ((JComboBox) history).getSelectedItem() - .toString(); + .toString()); if (url.toLowerCase().endsWith(".jar")) { @@ -1239,8 +1286,10 @@ public class Desktop extends jalview.jbgui.GDesktop if (format == null) { - String msg = MessageManager.formatMessage("label.couldnt_locate", url); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, + String msg = MessageManager + .formatMessage("label.couldnt_locate", url); + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + msg, MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE); @@ -1257,10 +1306,12 @@ public class Desktop extends jalview.jbgui.GDesktop new FileLoader().LoadFile(url, DataSourceType.URL, format); } } - }}; + } + }; String dialogOption = MessageManager .getString("label.input_alignment_from_url"); - JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action) + JvOptionPane.newOptionDialog(getDesktopPane()) + .setResponseHandler(0, action) .showInternalDialog(panel, dialogOption, JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, @@ -1346,7 +1397,7 @@ public class Desktop extends jalview.jbgui.GDesktop public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); - // JvOptionPane.showInternalMessageDialog(Desktop.desktop, + // JvOptionPane.showInternalMessageDialog(Desktop.getDesktop(), // // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() @@ -1438,6 +1489,11 @@ public class Desktop extends jalview.jbgui.GDesktop BrowserLauncher.openURL("http://www.jalview.org/help.html"); } else + /** + * Java only + * + * @j2sIgnore + */ { Help.showHelpWindow(); } @@ -1450,8 +1506,12 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void closeAll_actionPerformed(ActionEvent e) { + if (desktopPane == null) + { + return; + } // TODO show a progress bar while closing? - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); for (int i = 0; i < frames.length; i++) { try @@ -1472,12 +1532,7 @@ public class Desktop extends jalview.jbgui.GDesktop * reset state of singleton objects as appropriate (clear down session state * when all windows are closed) */ - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(this); - if (ssm != null) - { - ssm.resetAll(); - } + getStructureSelectionManager().resetAll(); } @Override @@ -1522,7 +1577,7 @@ public class Desktop extends jalview.jbgui.GDesktop @Override protected void showMemusage_actionPerformed(ActionEvent e) { - desktop.showMemoryUsage(showMemusage.isSelected()); + getDesktopPane().showMemoryUsage(showMemusage.isSelected()); } /* @@ -1559,7 +1614,7 @@ public class Desktop extends jalview.jbgui.GDesktop void reorderAssociatedWindows(boolean minimize, boolean close) { - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = getDesktopPane().getAllFrames(); if (frames == null || frames.length < 1) { return; @@ -1705,12 +1760,16 @@ public class Desktop extends jalview.jbgui.GDesktop // TODO prevent user from messing with the Desktop whilst we're saving try { - BackupFiles backupfiles = new BackupFiles(chosenFile); + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null; - new Jalview2XML().saveState(backupfiles.getTempFile()); + new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile); - backupfiles.setWriteSuccess(true); - backupfiles.rollBackupsAndRenameTempFile(); + if (doBackup) + { + backupfiles.setWriteSuccess(true); + backupfiles.rollBackupsAndRenameTempFile(); + } } catch (OutOfMemoryError oom) { new OOMWarning("Whilst saving current state to " @@ -1739,7 +1798,7 @@ public class Desktop extends jalview.jbgui.GDesktop saveState_actionPerformed(true); } - private void setProjectFile(File choice) + protected void setProjectFile(File choice) { this.projectFile = choice; } @@ -1789,7 +1848,7 @@ public class Desktop extends jalview.jbgui.GDesktop { Cache.log.error( "Problems whilst loading project from " + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "label.error_whilst_loading_project_from", new Object[] @@ -1832,7 +1891,7 @@ public class Desktop extends jalview.jbgui.GDesktop { progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; - instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); + getContentPane().add(progressPanel, BorderLayout.SOUTH); } JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); @@ -1845,7 +1904,7 @@ public class Desktop extends jalview.jbgui.GDesktop ((GridLayout) progressPanel.getLayout()).setRows( ((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; - instance.validate(); + validate(); return thisprogress; } @@ -1899,7 +1958,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { - if (Desktop.desktop == null) + if (Desktop.getDesktopPane() == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode @@ -1941,7 +2000,7 @@ public class Desktop extends jalview.jbgui.GDesktop public static AlignmentViewport[] getViewports(String sequenceSetId) { List viewp = new ArrayList<>(); - if (desktop != null) + if (getDesktopPane() != null) { AlignFrame[] frames = Desktop.getAlignFrames(); @@ -2027,7 +2086,7 @@ public class Desktop extends jalview.jbgui.GDesktop { source.viewport.setGatherViewsHere(true); source.viewport.setExplodedGeometry(source.getBounds()); - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = getAllFrames(); String viewId = source.viewport.getSequenceSetId(); for (int t = 0; t < frames.length; t++) @@ -2084,7 +2143,7 @@ public class Desktop extends jalview.jbgui.GDesktop String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", new Object[] @@ -2316,7 +2375,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); rthr.start(); } - }; + } }); VamsasStMenu.add(sessit); } @@ -2385,7 +2444,7 @@ public class Desktop extends jalview.jbgui.GDesktop removeProgressPanel(progpanel); if (warnmsg != null) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } @@ -2422,7 +2481,7 @@ public class Desktop extends jalview.jbgui.GDesktop public JInternalFrame[] getAllFrames() { - return desktop.getAllFrames(); + return desktopPane.getAllFrames(); } /** @@ -2461,7 +2520,7 @@ public class Desktop extends jalview.jbgui.GDesktop while (li.hasNext()) { String link = li.next(); - if (link.contains(SEQUENCE_ID) + if (link.contains(UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) { check = true; @@ -2508,7 +2567,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); msgPanel.add(jcb); - JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + JvOptionPane.showMessageDialog(desktopPane, msgPanel, MessageManager .getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE); @@ -2623,11 +2682,11 @@ public class Desktop extends jalview.jbgui.GDesktop { if (Jalview.isHeadlessMode()) { - // Desktop.desktop is null in headless mode - return new AlignFrame[] { Jalview.currentAlignFrame }; + // Desktop.getDesktop() is null in headless mode + return new AlignFrame[] { Jalview.getCurrentAlignFrame() }; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); if (frames == null) { @@ -2672,7 +2731,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public GStructureViewer[] getJmols() { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); if (frames == null) { @@ -2708,7 +2767,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(desktopPane, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), @@ -2719,7 +2778,7 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Open the Groovy console */ - void openGroovyConsole() + private void openGroovyConsole() { if (groovyConsole == null) { @@ -2905,7 +2964,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { - if (desktop != null) + if (getDesktopPane() != null) { AlignmentPanel[] aps = getAlignmentPanels( viewport.getSequenceSetId()); @@ -2966,8 +3025,8 @@ public class Desktop extends jalview.jbgui.GDesktop // todo: changesupport handlers need to be transferred if (discoverer == null) { - discoverer = new jalview.ws.jws1.Discoverer(); - // register PCS handler for desktop. + discoverer = Discoverer.getInstance(); + // register PCS handler for getDesktop(). discoverer.addPropertyChangeListener(changeSupport); } // JAL-940 - disabled JWS1 service configuration - always start discoverer @@ -2977,7 +3036,7 @@ public class Desktop extends jalview.jbgui.GDesktop if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + t2 = jalview.ws.jws2.Jws2Discoverer.getInstance() .startDiscoverer(changeSupport); } Thread t3 = null; @@ -3010,7 +3069,7 @@ public class Desktop extends jalview.jbgui.GDesktop { if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) { - final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance() .getErrorMessages(); if (ermsg != null) { @@ -3049,7 +3108,7 @@ public class Desktop extends jalview.jbgui.GDesktop * * jd.waitForInput(); */ - JvOptionPane.showConfirmDialog(Desktop.desktop, + JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(), new JLabel("
" + ermsg + "
" + "

It may be that you have invalid JABA URLs
in your web service preferences," @@ -3075,7 +3134,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - private Runnable serviceChangedDialog = null; + Runnable serviceChangedDialog = null; /** * start a thread to open a URL in the configured browser. Pops up a warning @@ -3086,7 +3145,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static void showUrl(final String url) { - showUrl(url, Desktop.instance); + showUrl(url, Desktop.getInstance()); } /** @@ -3112,10 +3171,10 @@ public class Desktop extends jalview.jbgui.GDesktop .formatMessage("status.opening_params", new Object[] { url }), this.hashCode()); } - jalview.util.BrowserLauncher.openURL(url); + BrowserLauncher.openURL(url); } catch (Exception ex) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), @@ -3131,15 +3190,16 @@ public class Desktop extends jalview.jbgui.GDesktop }).start(); } - public static WsParamSetManager wsparamManager = null; + private WsParamSetManager wsparamManager = null; public static ParamManager getUserParameterStore() { - if (wsparamManager == null) + Desktop d = Desktop.getInstance(); + if (d.wsparamManager == null) { - wsparamManager = new WsParamSetManager(); + d.wsparamManager = new WsParamSetManager(); } - return wsparamManager; + return d.wsparamManager; } /** @@ -3184,14 +3244,16 @@ public class Desktop extends jalview.jbgui.GDesktop /** * flag indicating if dialogExecutor should try to acquire a permit */ - private volatile boolean dialogPause = true; + volatile boolean dialogPause = true; /** * pause the queue */ - private java.util.concurrent.Semaphore block = new Semaphore(0); + java.util.concurrent.Semaphore block = new Semaphore(0); - private static groovy.ui.Console groovyConsole; + private groovy.ui.Console groovyConsole; + + public StructureViewer lastTargetedView; /** * add another dialog thread to the queue @@ -3213,9 +3275,8 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (InterruptedException x) { } - ; } - if (instance == null) + if (instanceOnly) { return; } @@ -3379,7 +3440,7 @@ public class Desktop extends jalview.jbgui.GDesktop String topViewId = myTopFrame.viewport.getSequenceSetId(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof SplitFrame && frame != source) @@ -3424,7 +3485,7 @@ public class Desktop extends jalview.jbgui.GDesktop public static groovy.ui.Console getGroovyConsole() { - return groovyConsole; + return Desktop.getInstance().groovyConsole; } /** @@ -3442,6 +3503,7 @@ public class Desktop extends jalview.jbgui.GDesktop * - the payload from the drop event * @throws Exception */ + @SuppressWarnings("unchecked") public static void transferFromDropTarget(List files, List protocols, DropTargetDropEvent evt, Transferable t) throws Exception @@ -3501,7 +3563,6 @@ public class Desktop extends jalview.jbgui.GDesktop System.err.println( "Please ignore plist error - occurs due to problem with java 8 on OSX"); } - ; } } catch (Throwable ex) { @@ -3512,7 +3573,7 @@ public class Desktop extends jalview.jbgui.GDesktop { // Works on Windows and MacOSX Cache.log.debug("Drop handled as javaFileListFlavor"); - for (Object file : (List) t + for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { files.add(file); @@ -3676,7 +3737,7 @@ public class Desktop extends jalview.jbgui.GDesktop Class structureViewerClass) { List result = new ArrayList<>(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); + JInternalFrame[] frames = getAllFrames(); for (JInternalFrame frame : frames) { @@ -3695,4 +3756,5 @@ public class Desktop extends jalview.jbgui.GDesktop } return result; } + }