X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=e13a63e1a4f6791e1e692f77dd00f52016ca6628;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=bdb6de93bd7eaaf1f048828eff84117fb0dd91f8;hpb=5721b73c6d5de84b21a989a8734e4c161f5dc630;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index bdb6de9..e13a63e 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -22,6 +22,9 @@ package jalview.gui; 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; @@ -36,6 +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; @@ -47,6 +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; @@ -133,10 +138,11 @@ import org.stackoverflowusers.file.WindowsShortcut; * @version $Revision: 1.155 $ */ @SuppressWarnings("serial") -public class Desktop extends jalview.jbgui.GDesktop +public class Desktop extends GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator, - jalview.api.StructureSelectionManagerProvider + StructureSelectionManagerProvider, ApplicationSingletonI { + private final static int DEFAULT_MIN_WIDTH = 300; private final static int DEFAULT_MIN_HEIGHT = 250; @@ -191,47 +197,16 @@ public class Desktop extends jalview.jbgui.GDesktop listener); } - /** - * Singleton Desktop instance only in Java; - */ - private static Desktop instance; - - public static Desktop getInstance() - { - Desktop d; - @SuppressWarnings("unused") - ThreadGroup g = Thread.currentThread().getThreadGroup(); - /** - * @j2sNative d = g._jalviewDesktopInstance; - */ - { - d = instance; - } - return d; - } - - private static void setInstance(Desktop d) - { - @SuppressWarnings("unused") - ThreadGroup g = Thread.currentThread().getThreadGroup(); - /** - * @j2sNative g._jalviewDesktopInstance = d; - */ - { - instance = d; - } - } - - private MyDesktopPane desktopPane; - public static MyDesktopPane getDesktopPane() { - return getInstance().desktopPane; + Desktop desktop = Desktop.getInstance(); + return desktop == null ? null : desktop.desktopPane; } - private void setDesktopPane(MyDesktopPane pane) + public static StructureSelectionManager getStructureSelectionManager() { - getInstance().desktopPane = pane; + return StructureSelectionManager + .getStructureSelectionManager(getInstance()); } static int openFrameCount = 0; @@ -240,7 +215,7 @@ public class Desktop extends jalview.jbgui.GDesktop static final int yOffset = 30; - public jalview.ws.jws1.Discoverer discoverer; + public Discoverer discoverer; public Object[] jalviewClipboard; @@ -248,6 +223,10 @@ public class Desktop extends jalview.jbgui.GDesktop private static int fileLoadingCount = 0; + public JInternalFrame conservationSlider; + + public JInternalFrame PIDSlider; + class MyDesktopManager implements DesktopManager { @@ -267,7 +246,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (NullPointerException npe) { Point p = getMousePosition(); - getInstance().showPasteMenu(p.x, p.y); + showPasteMenu(p.x, p.y); } } @@ -315,14 +294,14 @@ public class Desktop extends jalview.jbgui.GDesktop public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); - getDesktopPane().repaint(); + desktopPane.repaint(); } @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); - getDesktopPane().repaint(); + desktopPane.repaint(); } @Override @@ -371,179 +350,212 @@ public class Desktop extends jalview.jbgui.GDesktop } + public MyDesktopPane desktopPane; + /** - * Creates a new Desktop object. + * 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 Desktop() + public static Desktop getInstance() { - 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. - */ - setInstance(this); - if (!Platform.isJS()) - { - doVamsasClientCheck(); - } - - doConfigureStructurePrefs(); - setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); - setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", - false); - boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", - false); - setDesktopPane(new MyDesktopPane(selmemusage)); - - showMemusage.setSelected(selmemusage); - getDesktopPane().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()) + return Jalview.isHeadlessMode() ? null + : (Desktop) ApplicationSingletonProvider + .getInstance(Desktop.class); + } + + /** + * Private constructor enforces singleton pattern. It is called by reflection + * from ApplicationSingletonProvider.getInstance(). + */ + private Desktop() + { + Cache.initLogger(); + try { - getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); - } + /** + * 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. + */ + if (!Platform.isJS()) + { + doVamsasClientCheck(); + } - getContentPane().add(getDesktopPane(), BorderLayout.CENTER); - getDesktopPane().setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); + doConfigureStructurePrefs(); + setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); + setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", + false); + boolean showjconsole = jalview.bin.Cache + .getDefault("SHOW_JAVA_CONSOLE", false); + desktopPane = new MyDesktopPane(selmemusage); - // This line prevents Windows Look&Feel resizing all new windows to maximum - // if previous window was maximised - getDesktopPane().setDesktopManager(new MyDesktopManager( - (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() - : Platform.isAMacAndNotJS() - ? new AquaInternalFrameManager( - getDesktopPane().getDesktopManager()) - : getDesktopPane().getDesktopManager()))); + showMemusage.setSelected(selmemusage); + 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); - Rectangle dims = getLastKnownDimensions(""); - if (dims != null) - { - setBounds(dims); - } - else - { - Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); - int xPos = Math.max(5, (screenSize.width - 900) / 2); - int yPos = Math.max(5, (screenSize.height - 650) / 2); - setBounds(xPos, yPos, 900, 650); - } + // BH 2018 - just an experiment to try unclipped JInternalFrames. + if (Platform.isJS()) + { + getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); + } - if (!Platform.isJS()) - /** - * Java only - * - * @j2sIgnore - */ - { + getContentPane().add(desktopPane, BorderLayout.CENTER); + desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); - jconsole = new Console(this, showjconsole); - // add essential build information - jconsole.setHeader("Jalview Version: " - + jalview.bin.Cache.getProperty("VERSION") + "\n" - + "Jalview Installation: " - + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") - + "\n" + "Build Date: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n" - + "Java version: " + System.getProperty("java.version") + "\n" - + System.getProperty("os.arch") + " " - + System.getProperty("os.name") + " " - + System.getProperty("os.version")); + // This line prevents Windows Look&Feel resizing all new windows to + // maximum + // if previous window was maximised + desktopPane.setDesktopManager(new MyDesktopManager( + (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() + : Platform.isAMacAndNotJS() + ? new AquaInternalFrameManager( + desktopPane.getDesktopManager()) + : desktopPane.getDesktopManager()))); - showConsole(showjconsole); + Rectangle dims = getLastKnownDimensions(""); + if (dims != null) + { + setBounds(dims); + } + else + { + Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); + int xPos = Math.max(5, (screenSize.width - 900) / 2); + int yPos = Math.max(5, (screenSize.height - 650) / 2); + setBounds(xPos, yPos, 900, 650); + } - showNews.setVisible(false); + // Note that this next syntax, checking for Platform.isJS and also + // escaping the code using @j2sIgnore, serves two purposes. It gives + // us an easily findable tag, Platform.isJS(), to places in the code where + // there is something different about the SwingJS implementation. Second, + // it deletes the unneeded Java-only code form the JavaScript version + // completely (@j2sIgnore), since it will never be used there. - experimentalFeatures.setSelected(showExperimental()); + if (!Platform.isJS() && !Jalview.isSynchronous()) + /** + * Java only + * + * @j2sIgnore + */ + { - getIdentifiersOrgData(); + jconsole = new Console(this, showjconsole); + // add essential build information + jconsole.setHeader("Jalview Version: " + + jalview.bin.Cache.getProperty("VERSION") + "\n" + + "Jalview Installation: " + + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") + + "\n" + "Build Date: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + + "\n" + "Java version: " + + System.getProperty("java.version") + "\n" + + System.getProperty("os.arch") + " " + + System.getProperty("os.name") + " " + + System.getProperty("os.version")); - checkURLLinks(); + showConsole(showjconsole); - // Spawn a thread that shows the splashscreen + showNews.setVisible(false); - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - new SplashScreen(); - } - }); + experimentalFeatures.setSelected(showExperimental()); - // Thread off a new instance of the file chooser - this reduces the time - // it - // takes to open it later on. - new Thread(new Runnable() - { - @Override - public void run() + getIdentifiersOrgData(); + + checkURLLinks(); + + // Spawn a thread that shows the splashscreen + + SwingUtilities.invokeLater(new Runnable() { - Cache.log.debug("Filechooser init thread started."); - String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), - fileFormat); - Cache.log.debug("Filechooser init thread finished."); - } - }).start(); - // Add the service change listener - changeSupport.addJalviewPropertyChangeListener("services", - new PropertyChangeListener() - { + @Override + public void run() + { + new SplashScreen(); + } + }); - @Override - public void propertyChange(PropertyChangeEvent evt) + // Thread off a new instance of the file chooser - this reduces the time + // it + // takes to open it later on. + new Thread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Filechooser init thread started."); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), + fileFormat); + Cache.log.debug("Filechooser init thread finished."); + } + }).start(); + // Add the service change listener + changeSupport.addJalviewPropertyChangeListener("services", + new PropertyChangeListener() { - Cache.log.debug("Firing service changed event for " - + evt.getNewValue()); - JalviewServicesChanged(evt); - } - }); - - } + @Override + public void propertyChange(PropertyChangeEvent evt) + { + Cache.log.debug("Firing service changed event for " + + evt.getNewValue()); + JalviewServicesChanged(evt); + } - this.setDropTarget(new java.awt.dnd.DropTarget(getDesktopPane(), this)); + }); - this.addWindowListener(new WindowAdapter() - { - @Override - public void windowClosing(WindowEvent evt) - { - quit(); } - }); - MouseAdapter ma; - this.addMouseListener(ma = new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) + if (!Jalview.isSynchronous()) { - if (evt.isPopupTrigger()) // Mac + this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this)); + + this.addWindowListener(new WindowAdapter() { - showPasteMenu(evt.getX(), evt.getY()); - } - } + @Override + public void windowClosing(WindowEvent evt) + { + quit(); + } + }); - @Override - public void mouseReleased(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Windows + MouseAdapter ma; + this.addMouseListener(ma = new MouseAdapter() { - showPasteMenu(evt.getX(), evt.getY()); - } - } - }); - getDesktopPane().addMouseListener(ma); + @Override + public void mousePressed(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + }); + desktopPane.addMouseListener(ma); + } + } catch (Throwable t) + { + t.printStackTrace(); + } } /** @@ -619,7 +631,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } }).start(); - ; + } @Override @@ -640,10 +652,10 @@ public class Desktop extends jalview.jbgui.GDesktop public void run() { long now = System.currentTimeMillis(); - Desktop.getInstance().setProgressBar( + setProgressBar( MessageManager.getString("status.refreshing_news"), now); jvnews.refreshNews(); - Desktop.getInstance().setProgressBar(null, now); + setProgressBar(null, now); jvnews.showNews(); } }).start(); @@ -781,7 +793,7 @@ public class Desktop extends jalview.jbgui.GDesktop FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE); - new FileLoader().LoadFile(file, DataSourceType.PASTE, format); + new FileLoader().loadFile(file, DataSourceType.PASTE, format); } } catch (Exception ex) @@ -876,13 +888,14 @@ public class Desktop extends jalview.jbgui.GDesktop int w, int h, boolean resizable, boolean ignoreMinSize) { + // TODO: allow callers to determine X and Y position of frame (eg. via // bounds object). // TODO: consider fixing method to update entries in the window submenu with // the current window title frame.setTitle(title); - if (frame.getWidth() < 1 || frame.getHeight() < 1) + if (w > 0 && (frame.getWidth() < 1 || frame.getHeight() < 1)) { frame.setSize(w, h); } @@ -890,7 +903,7 @@ public class Desktop extends jalview.jbgui.GDesktop // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN // IF JALVIEW IS RUNNING HEADLESS // /////////////////////////////////////////////// - if (getInstance() == null || Jalview.isHeadlessMode()) + if (Jalview.isHeadlessMode()) { return; } @@ -920,7 +933,8 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setIconifiable(resizable); frame.setOpaque(Platform.isJS()); - if (frame.getX() < 1 && frame.getY() < 1) + boolean isEmbedded = (Platform.getDimIfEmbedded(frame, -1, -1) != null); + if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset); @@ -968,8 +982,8 @@ public class Desktop extends jalview.jbgui.GDesktop { menuItem.removeActionListener(menuItem.getActionListeners()[0]); } - getInstance().windowMenu.remove(menuItem); - }; + Desktop.getInstance().windowMenu.remove(menuItem); + } }); menuItem.addActionListener(new ActionListener() @@ -992,7 +1006,7 @@ public class Desktop extends jalview.jbgui.GDesktop getDesktopPane().add(frame); - getInstance().windowMenu.add(menuItem); + Desktop.getInstance().windowMenu.add(menuItem); frame.toFront(); try @@ -1128,7 +1142,7 @@ public class Desktop extends jalview.jbgui.GDesktop { Platform.cacheFileData((File) file); } - new FileLoader().LoadFile(null, file, protocol, format); + new FileLoader().loadFile(null, file, protocol, format); } } catch (Exception ex) @@ -1185,7 +1199,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - new FileLoader().LoadFile(viewport, selectedFile, + new FileLoader().loadFile(viewport, selectedFile, DataSourceType.FILE, format); } }); @@ -1259,12 +1273,12 @@ public class Desktop extends jalview.jbgui.GDesktop { if (viewport != null) { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + new FileLoader().loadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview); } else { - new FileLoader().LoadFile(url, DataSourceType.URL, + new FileLoader().loadFile(url, DataSourceType.URL, FileFormat.Jalview); } } @@ -1294,12 +1308,12 @@ public class Desktop extends jalview.jbgui.GDesktop if (viewport != null) { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + new FileLoader().loadFile(viewport, url, DataSourceType.URL, format); } else { - new FileLoader().LoadFile(url, DataSourceType.URL, format); + new FileLoader().loadFile(url, DataSourceType.URL, format); } } } @@ -1502,8 +1516,12 @@ 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 = getDesktopPane().getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); for (int i = 0; i < frames.length; i++) { try @@ -1524,12 +1542,7 @@ 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 @@ -1837,7 +1850,7 @@ public class Desktop extends jalview.jbgui.GDesktop { try { - new Jalview2XML().loadJalviewAlign(choice); + new Jalview2XML().loadJalviewAlign(selectedFile); } catch (OutOfMemoryError oom) { new OOMWarning("Whilst loading project from " + choice, oom); @@ -1888,7 +1901,7 @@ public class Desktop extends jalview.jbgui.GDesktop { progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; - getInstance().getContentPane().add(progressPanel, BorderLayout.SOUTH); + getContentPane().add(progressPanel, BorderLayout.SOUTH); } JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); @@ -1901,7 +1914,7 @@ public class Desktop extends jalview.jbgui.GDesktop ((GridLayout) progressPanel.getLayout()).setRows( ((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; - getInstance().validate(); + validate(); return thisprogress; } @@ -2083,7 +2096,7 @@ public class Desktop extends jalview.jbgui.GDesktop { source.viewport.setGatherViewsHere(true); source.viewport.setExplodedGeometry(source.getBounds()); - JInternalFrame[] frames = getDesktopPane().getAllFrames(); + JInternalFrame[] frames = getAllFrames(); String viewId = source.viewport.getSequenceSetId(); for (int t = 0; t < frames.length; t++) @@ -2372,7 +2385,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); rthr.start(); } - }; + } }); VamsasStMenu.add(sessit); } @@ -2478,7 +2491,7 @@ public class Desktop extends jalview.jbgui.GDesktop public JInternalFrame[] getAllFrames() { - return getDesktopPane().getAllFrames(); + return desktopPane.getAllFrames(); } /** @@ -2564,7 +2577,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); msgPanel.add(jcb); - JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msgPanel, + JvOptionPane.showMessageDialog(desktopPane, msgPanel, MessageManager .getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE); @@ -2764,7 +2777,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + JvOptionPane.showInternalMessageDialog(desktopPane, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), @@ -3022,7 +3035,7 @@ public class Desktop extends jalview.jbgui.GDesktop // todo: changesupport handlers need to be transferred if (discoverer == null) { - discoverer = new jalview.ws.jws1.Discoverer(); + discoverer = Discoverer.getInstance(); // register PCS handler for getDesktop(). discoverer.addPropertyChangeListener(changeSupport); } @@ -3033,7 +3046,7 @@ 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; @@ -3066,7 +3079,7 @@ 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) { @@ -3168,7 +3181,7 @@ 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.getDesktopPane(), @@ -3191,7 +3204,7 @@ public class Desktop extends jalview.jbgui.GDesktop public static ParamManager getUserParameterStore() { - Desktop d = getInstance(); + Desktop d = Desktop.getInstance(); if (d.wsparamManager == null) { d.wsparamManager = new WsParamSetManager(); @@ -3250,6 +3263,8 @@ public class Desktop extends jalview.jbgui.GDesktop private groovy.ui.Console groovyConsole; + public StructureViewer lastTargetedView; + /** * add another dialog thread to the queue * @@ -3270,9 +3285,8 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (InterruptedException x) { } - ; } - if (getInstance() == null) + if (Jalview.isHeadlessMode()) { return; } @@ -3436,7 +3450,7 @@ public class Desktop extends jalview.jbgui.GDesktop String topViewId = myTopFrame.viewport.getSequenceSetId(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); - JInternalFrame[] frames = getDesktopPane().getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof SplitFrame && frame != source) @@ -3481,7 +3495,8 @@ public class Desktop extends jalview.jbgui.GDesktop public static groovy.ui.Console getGroovyConsole() { - return getInstance().groovyConsole; + Desktop desktop = Desktop.getInstance(); + return desktop == null ? null : desktop.groovyConsole; } /** @@ -3559,7 +3574,6 @@ 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) { @@ -3734,7 +3748,7 @@ public class Desktop extends jalview.jbgui.GDesktop Class structureViewerClass) { List result = new ArrayList<>(); - JInternalFrame[] frames = Desktop.getInstance().getAllFrames(); + JInternalFrame[] frames = getAllFrames(); for (JInternalFrame frame : frames) {