import jalview.bin.Jalview;
import jalview.bin.Jalview.ExitCode;
import jalview.bin.argparser.Arg;
+import jalview.bin.groovy.JalviewObject;
+import jalview.bin.groovy.JalviewObjectI;
import jalview.datamodel.Alignment;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.urls.IdOrgSettings;
import jalview.util.BrowserLauncher;
import jalview.util.ChannelProperties;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
import jalview.util.ImageMaker.TYPE;
import jalview.util.LaunchUtils;
import jalview.util.MessageManager;
*/
public class Desktop extends jalview.jbgui.GDesktop
implements DropTargetListener, ClipboardOwner, IProgressIndicator,
- jalview.api.StructureSelectionManagerProvider
+ jalview.api.StructureSelectionManagerProvider, JalviewObjectI
{
private static final String CITATION;
static
: " <img alt=\"University of Dundee shield\" src=\""
+ uod_logo_url.toString() + "\">");
sb.append(
- "<br><br>For help, see <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>");
+ "<br><br>For help, see <a href=\"https://www.jalview.org/help/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>");
sb.append("<br><br>If you use Jalview, please cite:"
+ "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
if (LaunchUtils.getJavaVersion() >= 11)
{
/*
- * Send this message to stderr as the warning that follows (due to
- * reflection) also goes to stderr.
+ * Send this message to stderr as the warning that follows (due to reflection)
+ * also goes to stderr.
*/
jalview.bin.Console.errPrintln(
"Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
Platform.isJS() ? desktop.getDesktopManager()
: new DefaultDesktopManager()));
/*
- (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
- : Platform.isAMacAndNotJS()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
- */
+ * (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() :
+ * Platform.isAMacAndNotJS() ? new AquaInternalFrameManager(
+ * desktop.getDesktopManager()) : desktop.getDesktopManager())));
+ */
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
if (Platform.isJS())
{
+ String ns = Jalview.getInstance().getJSNamespace();
+ if (ns != null)
+ {
+
+ String nsc = ns + (ns.length() > 0 ? ":" : "");
+ String splashId = nsc + "jalviewSplash";
+ /**
+ * @j2sNative let splash = document.getElementById(splashId);
+ *
+ * if (splash != null) {
+ *
+ * splash.style.display = "none";
+ *
+ * }
+ */
+ }
// used for jalviewjsTest
jalview.bin.Console.info("JALVIEWJS: CREATED DESKTOP");
}
@Override
public void run()
{
- long now = System.currentTimeMillis();
+ long progressId = IdUtils.newId(IdType.PROGRESS);
Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"), now);
+ MessageManager.getString("status.refreshing_news"),
+ progressId);
jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
+ Desktop.instance.setProgressBar(null, progressId);
jvnews.showNews();
}
}).start();
{
if (itf instanceof AlignFrame)
{
- Jalview.setCurrentAlignFrame((AlignFrame) itf);
+ Jalview.getInstance().setCurrentAlignFrame((AlignFrame) itf);
}
itf.requestFocus();
}
}
}
evt.dropComplete(success); // need this to ensure input focus is properly
- // transfered to any new windows created
+ // transfered to any new windows created
}
/**
desktopQuit(true, false);
}
- public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)
+ /**
+ * close everything, stash window geometries, and shut down all associated
+ * threads/workers
+ *
+ * @param dispose
+ * - sets the dispose on close flag - JVM may terminate when set
+ * @param terminateJvm
+ * - quit with prejudice - stops the JVM.
+ */
+ public void quitTheDesktop(boolean dispose, boolean terminateJvm)
{
- final Runnable doDesktopQuit = () -> {
- Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
- Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x,
- getBounds().y, getWidth(), getHeight()));
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+ getWidth(), getHeight()));
- if (jconsole != null)
- {
- storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
- jconsole.stopConsole();
- }
+ if (jconsole != null)
+ {
+ storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+ jconsole.stopConsole();
+ }
- if (jvnews != null)
- {
- storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
- }
+ if (jvnews != null)
+ {
+ storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+ }
- // Frames should all close automatically. Keeping external
- // viewers open should already be decided by user.
- closeAll_actionPerformed(null);
+ // Frames should all close automatically. Keeping external
+ // viewers open should already be decided by user.
+ closeAll_actionPerformed(null);
- // check for aborted quit
- if (QuitHandler.quitCancelled())
- {
- jalview.bin.Console.debug("Desktop aborting quit");
- return;
- }
+ if (dialogExecutor != null)
+ {
+ dialogExecutor.shutdownNow();
+ }
- if (dialogExecutor != null)
- {
- dialogExecutor.shutdownNow();
- }
+ if (groovyConsole != null)
+ {
+ // suppress a possible repeat prompt to save script
+ groovyConsole.setDirty(false);
+ groovyConsole.exit();
+ }
- if (groovyConsole != null)
- {
- // suppress a possible repeat prompt to save script
- groovyConsole.setDirty(false);
- groovyConsole.exit();
- }
+ if (terminateJvm)
+ {
+ // note that shutdown hook will not be run
+ jalview.bin.Console.debug("Force Quit selected by user");
+ Runtime.getRuntime().halt(0);
+ }
- if (QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT)
- {
- // note that shutdown hook will not be run
- jalview.bin.Console.debug("Force Quit selected by user");
- Runtime.getRuntime().halt(0);
- }
+ jalview.bin.Console.debug("Quit selected by user");
+ if (dispose)
+ {
+ instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ // instance.dispose();
+ }
+ }
+
+ public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)
+ {
+ final Runnable doDesktopQuit = () -> {
- jalview.bin.Console.debug("Quit selected by user");
- if (disposeFlag)
+ // FIRST !! check for aborted quit
+ if (QuitHandler.quitCancelled())
{
- instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- // instance.dispose();
+ jalview.bin.Console
+ .debug("Quit was cancelled - Desktop aborting quit");
+ return;
}
+
+ // Proceed with quitting
+ quitTheDesktop(disposeFlag,
+ QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT);
+ // and exit the JVM
instance.quit();
};
}
/**
- * Don't call this directly, use desktopQuit() above. Exits the program.
+ * Exits the program and the JVM.
+ *
+ * Don't call this directly
+ *
+ * - use desktopQuit() above to tidy up first.
+ *
+ * - use closeDesktop() to shutdown Jalview without shutting down the JVM
+ *
*/
@Override
public void quit()
{
}
}
- Jalview.setCurrentAlignFrame(null);
+ Jalview.getInstance().setCurrentAlignFrame(null);
jalview.bin.Console.info("ALL CLOSED");
/*
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
- { chosenFile.getName() }), chosenFile.hashCode());
+ { chosenFile.getName() }),
+ IdUtils.newId(IdType.PROGRESS, chosenFile));
Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
MessageManager.getString("label.couldnt_save_project"),
JvOptionPane.WARNING_MESSAGE);
}
- setProgressBar(null, chosenFile.hashCode());
+ setProgressBar(null, IdUtils.newId(IdType.PROGRESS, chosenFile));
}
}).start();
}
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
"Jalview Project", true, BackupFiles.getEnabled()); // last two
- // booleans:
- // allFiles,
+ // booleans:
+ // allFiles,
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
return null;
}
List<AlignmentPanel> aps = new ArrayList<>();
- AlignFrame[] frames = getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
if (frames == null)
{
return null;
List<AlignmentViewport> viewp = new ArrayList<>();
if (desktop != null)
{
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
for (AlignFrame afr : frames)
{
*
* @return an array of AlignFrame, or null if none found
*/
- public static AlignFrame[] getAlignFrames()
+ @Override
+ public AlignFrame[] getAlignFrames()
{
- if (Jalview.isHeadlessMode())
+ if (desktop == null)
{
- // Desktop.desktop is null in headless mode
- return new AlignFrame[] { Jalview.currentAlignFrame };
+ return null;
}
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
}
/**
+ * static version
+ */
+ public static AlignFrame[] getDesktopAlignFrames()
+ {
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return Jalview.getInstance().getAlignFrames();
+ }
+
+ if (instance != null && desktop != null)
+ {
+ return instance.getAlignFrames();
+ }
+
+ return null;
+ }
+
+ /**
* Returns an array of any AppJmol frames in the Desktop (or null if none).
*
* @return
openGroovyConsole();
} catch (Exception ex)
{
- jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
+ jalview.bin.Console.error("Groovy Console creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
{
if (groovyConsole == null)
{
- groovyConsole = new groovy.ui.Console();
- groovyConsole.setVariable("Jalview", this);
+ JalviewObjectI j = new JalviewObject(this);
+ groovyConsole = new groovy.console.ui.Console();
+ groovyConsole.setVariable(JalviewObjectI.jalviewObjectName, j);
+ groovyConsole.setVariable(JalviewObjectI.currentAlFrameName,
+ getCurrentAlignFrame());
groovyConsole.run();
/*
*/
groovyShell.setEnabled(!enabled);
- AlignFrame[] alignFrames = getAlignFrames();
+ AlignFrame[] alignFrames = getDesktopAlignFrames();
if (alignFrames != null)
{
for (AlignFrame af : alignFrames)
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ if (url != null && !url.trim().equals(""))
+ {
+ jalview.bin.Console.info("Opening URL: " + url);
+ showUrl(url, Desktop.instance);
+ }
+ else
+ {
+ jalview.bin.Console.warn("Ignoring attempt to show an empty URL.");
+ }
+
}
/**
{
progress.setProgressBar(MessageManager
.formatMessage("status.opening_params", new Object[]
- { url }), this.hashCode());
+ { url }), IdUtils.newId(IdType.PROGRESS, this));
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
}
if (progress != null)
{
- progress.setProgressBar(null, this.hashCode());
+ progress.setProgressBar(null,
+ IdUtils.newId(IdType.PROGRESS, this));
}
}
}).start();
*/
private Semaphore block = new Semaphore(0);
- private static groovy.ui.Console groovyConsole;
+ private static groovy.console.ui.Console groovyConsole;
/**
* add another dialog thread to the queue
myTopFrame.setDisplayedView(myTopFrame.alignPanel);
}
- public static groovy.ui.Console getGroovyConsole()
+ public static groovy.console.ui.Console getGroovyConsole()
{
return groovyConsole;
}
}
/**
- * closes the current instance window, disposes and forgets about it.
+ * closes the current instance window, but leaves the JVM running. Bypasses
+ * any shutdown prompts, but does not set window dispose on close in case JVM
+ * terminates.
*/
public static void closeDesktop()
{
if (Desktop.instance != null)
{
- Desktop.instance.closeAll_actionPerformed(null);
- Desktop.instance.setVisible(false);
Desktop us = Desktop.instance;
- Desktop.instance = null;
+ Desktop.instance.quitTheDesktop(false, false);
// call dispose in a separate thread - try to avoid indirect deadlocks
- new Thread(new Runnable()
+ if (us != null)
{
- @Override
- public void run()
+ new Thread(new Runnable()
{
- ExecutorService dex = us.dialogExecutor;
- if (dex != null)
+ @Override
+ public void run()
{
- dex.shutdownNow();
- us.dialogExecutor = null;
- us.block.drainPermits();
+ ExecutorService dex = us.dialogExecutor;
+ if (dex != null)
+ {
+ dex.shutdownNow();
+ us.dialogExecutor = null;
+ us.block.drainPermits();
+ }
+ us.dispose();
}
- us.dispose();
- }
- }).start();
+ }).start();
+ }
}
}
boolean html, boolean modal, int timeout)
{
nonBlockingDialog(32, 2, title, message, boxtext, button, type,
- scrollable, false, modal, timeout);
+ scrollable, html, modal, timeout);
}
public void nonBlockingDialog(int width, int height, String title,
{ button }, button, modal, new JButton[] { jb }, false);
}
+ @Override
+ public AlignFrame getCurrentAlignFrame()
+ {
+ return Jalview.getInstance().getCurrentAlignFrame();
+ }
}
git://source.jalview.org / jalview.git / blobdiff