X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=85ec3aecf2c5b616c88a8e7e80522f6a69f42be2;hb=cb51e62fe2166b236ef488e0a8f35081fcd71388;hp=b7e11178fea37712dbf83d0fca0d3cf469f4092b;hpb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index b7e1117..85ec3aecf 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 +197,16 @@ public class Desktop extends jalview.jbgui.GDesktop listener); } - /** Singleton Desktop instance */ - public static Desktop instance; - - public static MyDesktopPane desktop; + public static MyDesktopPane getDesktopPane() + { + Desktop desktop = Desktop.getInstance(); + return desktop == null ? null : desktop.desktopPane; + } - public static MyDesktopPane getDesktop() + public static StructureSelectionManager getStructureSelectionManager() { - // BH 2018 could use currentThread() here as a reference to a - // Hashtable in JavaScript - return desktop; + return StructureSelectionManager + .getStructureSelectionManager(getInstance()); } static int openFrameCount = 0; @@ -210,13 +215,34 @@ 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; + + public JInternalFrame PIDSlider; + + /** + * just an instance (for testng, probably); no actual frames + * + * This flag, when set true, allows a headless-like operation, with a Desktop + * object but no actual frames. The issue has to do with the mess-up of the + * Windows JInternalFrame implementation, which surreptitiously and + * unforgivingly accesses a native peer class, preventing headless operation. + * + * It is set by invoking the Desktop(true) constructor. + * + * It is possible that we can remove this option now, since headless mode is + * finally working on Windows through careful attention to not creating any + * JInternalFrame objects when in that mode. + * + */ + private boolean instanceOnly; class MyDesktopManager implements DesktopManager { @@ -237,7 +263,7 @@ 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 +311,14 @@ 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 @@ -341,179 +367,226 @@ 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 Jalview.isHeadlessMode() ? null + : (Desktop) ApplicationSingletonProvider + .getInstance(Desktop.class); + } + /** - * Creates a new Desktop object. + * For testing purposes, this constructor can be utilized to allow the creation + * of a singleton Desktop instance without the formation of frames. The Cache is + * initialized, but that is all. + * + * It is not currently used. + * + * @param forInstance */ - public Desktop() + public Desktop(boolean forInstance) { - 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. - */ - instance = 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); - desktop = new MyDesktopPane(selmemusage); - - showMemusage.setSelected(selmemusage); - desktop.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()) + + Cache.initLogger(); + instanceOnly = true; + } + + /** + * Private constructor enforces singleton pattern. It is called by reflection + * from ApplicationSingletonProvider.getInstance(). + */ + @SuppressWarnings("unused") + 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(desktop, BorderLayout.CENTER); - desktop.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 - desktop.setDesktopManager(new MyDesktopManager( - (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() - : Platform.isAMacAndNotJS() - ? new AquaInternalFrameManager( - desktop.getDesktopManager()) - : desktop.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 - * - * @j2sNative - */ - { + 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()) + /** + * 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(desktop, 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) + this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this)); + + this.addWindowListener(new WindowAdapter() { - if (evt.isPopupTrigger()) // Mac + @Override + public void windowClosing(WindowEvent evt) { - showPasteMenu(evt.getX(), evt.getY()); + quit(); } - } + }); - @Override - public void mouseReleased(MouseEvent evt) + MouseAdapter ma; + this.addMouseListener(ma = new MouseAdapter() { - if (evt.isPopupTrigger()) // Windows + @Override + public void mousePressed(MouseEvent evt) { - showPasteMenu(evt.getX(), evt.getY()); + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } } - } - }); - desktop.addMouseListener(ma); + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + }); + desktopPane.addMouseListener(ma); + } catch (Throwable t) + { + t.printStackTrace(); + } } /** @@ -577,10 +650,10 @@ 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) { @@ -589,7 +662,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } }).start(); - ; + } @Override @@ -598,7 +671,7 @@ 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); @@ -610,10 +683,10 @@ 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(); @@ -718,7 +791,7 @@ 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( @@ -751,7 +824,7 @@ 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) @@ -846,13 +919,14 @@ 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); } @@ -860,8 +934,7 @@ 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 (Jalview.isHeadlessMode() || Desktop.getInstance().instanceOnly) { return; } @@ -891,7 +964,8 @@ 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); @@ -901,13 +975,13 @@ 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) @@ -939,8 +1013,8 @@ public class Desktop extends jalview.jbgui.GDesktop { menuItem.removeActionListener(menuItem.getActionListeners()[0]); } - windowMenu.remove(menuItem); - }; + Desktop.getInstance().windowMenu.remove(menuItem); + } }); menuItem.addActionListener(new ActionListener() @@ -961,9 +1035,9 @@ 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 @@ -988,7 +1062,6 @@ public class Desktop extends jalview.jbgui.GDesktop */ private static void setKeyBindings(JInternalFrame frame) { - @SuppressWarnings("serial") final Action closeAction = new AbstractAction() { @Override @@ -1021,7 +1094,7 @@ public class Desktop extends jalview.jbgui.GDesktop { if (!internalCopy) { - Desktop.jalviewClipboard = null; + Desktop.getInstance().jalviewClipboard = null; } internalCopy = false; @@ -1096,8 +1169,11 @@ public class Desktop extends jalview.jbgui.GDesktop { format = new IdentifyFile().identify(file, protocol); } - - new FileLoader().LoadFile(null, file, protocol, format); + if (file instanceof File) + { + Platform.cacheFileData((File) file); + } + new FileLoader().loadFile(null, file, protocol, format); } } catch (Exception ex) @@ -1154,7 +1230,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - new FileLoader().LoadFile(viewport, selectedFile, + new FileLoader().loadFile(viewport, selectedFile, DataSourceType.FILE, format); } }); @@ -1192,7 +1268,7 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Java only * - * @j2sNative + * @j2sIgnore */ { JComboBox asCombo = new JComboBox<>(); @@ -1228,12 +1304,12 @@ 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); } } @@ -1253,7 +1329,8 @@ public class Desktop extends jalview.jbgui.GDesktop { String msg = MessageManager .formatMessage("label.couldnt_locate", url); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + msg, MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE); @@ -1262,19 +1339,20 @@ 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); } } } }; 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, @@ -1360,7 +1438,7 @@ 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() @@ -1455,7 +1533,7 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Java only * - * @j2sNative + * @j2sIgnore */ { Help.showHelpWindow(); @@ -1469,8 +1547,12 @@ 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 @@ -1491,12 +1573,7 @@ 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 @@ -1541,7 +1618,7 @@ public class Desktop extends jalview.jbgui.GDesktop @Override protected void showMemusage_actionPerformed(ActionEvent e) { - desktop.showMemoryUsage(showMemusage.isSelected()); + getDesktopPane().showMemoryUsage(showMemusage.isSelected()); } /* @@ -1578,7 +1655,7 @@ 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; @@ -1762,7 +1839,7 @@ public class Desktop extends jalview.jbgui.GDesktop saveState_actionPerformed(true); } - private void setProjectFile(File choice) + protected void setProjectFile(File choice) { this.projectFile = choice; } @@ -1812,7 +1889,7 @@ 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[] @@ -1855,7 +1932,7 @@ 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(); @@ -1868,7 +1945,7 @@ public class Desktop extends jalview.jbgui.GDesktop ((GridLayout) progressPanel.getLayout()).setRows( ((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; - instance.validate(); + validate(); return thisprogress; } @@ -1922,7 +1999,7 @@ 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 @@ -1964,7 +2041,7 @@ 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(); @@ -2050,7 +2127,7 @@ 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++) @@ -2107,7 +2184,7 @@ 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[] @@ -2339,7 +2416,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); rthr.start(); } - }; + } }); VamsasStMenu.add(sessit); } @@ -2408,7 +2485,7 @@ 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); } @@ -2445,7 +2522,7 @@ public class Desktop extends jalview.jbgui.GDesktop public JInternalFrame[] getAllFrames() { - return desktop.getAllFrames(); + return desktopPane.getAllFrames(); } /** @@ -2484,7 +2561,7 @@ 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; @@ -2531,7 +2608,7 @@ 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); @@ -2646,11 +2723,11 @@ 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) { @@ -2695,7 +2772,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public GStructureViewer[] getJmols() { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); if (frames == null) { @@ -2731,7 +2808,7 @@ 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"), @@ -2742,7 +2819,7 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Open the Groovy console */ - void openGroovyConsole() + private void openGroovyConsole() { if (groovyConsole == null) { @@ -2928,7 +3005,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { - if (desktop != null) + if (getDesktopPane() != null) { AlignmentPanel[] aps = getAlignmentPanels( viewport.getSequenceSetId()); @@ -2989,8 +3066,8 @@ 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 @@ -3000,7 +3077,7 @@ 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; @@ -3033,7 +3110,7 @@ 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) { @@ -3072,7 +3149,7 @@ 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," @@ -3098,7 +3175,7 @@ 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 @@ -3109,7 +3186,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static void showUrl(final String url) { - showUrl(url, Desktop.instance); + showUrl(url, Desktop.getInstance()); } /** @@ -3135,10 +3212,10 @@ 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"), @@ -3154,15 +3231,16 @@ 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; } /** @@ -3207,14 +3285,16 @@ 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 @@ -3236,9 +3316,8 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (InterruptedException x) { } - ; } - if (instance == null) + if (instanceOnly) { return; } @@ -3402,7 +3481,7 @@ 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) @@ -3447,7 +3526,8 @@ public class Desktop extends jalview.jbgui.GDesktop public static groovy.ui.Console getGroovyConsole() { - return groovyConsole; + Desktop desktop = Desktop.getInstance(); + return desktop == null ? null : desktop.groovyConsole; } /** @@ -3465,6 +3545,7 @@ 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 @@ -3524,7 +3605,6 @@ 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) { @@ -3535,7 +3615,7 @@ 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); @@ -3699,7 +3779,7 @@ 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) { @@ -3718,4 +3798,5 @@ public class Desktop extends jalview.jbgui.GDesktop } return result; } + }