: " <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"
// configure services
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(this);
- if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
- {
- ssm.setAddTempFacAnnot(
- Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(
- Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
- // JAL-3915 - RNAView is no longer an option so this has no effect
- ssm.setSecStructServices(
- Cache.getDefault(Preferences.USE_RNAVIEW, false));
- }
- else
- {
- ssm.setAddTempFacAnnot(false);
- ssm.setProcessSecondaryStructure(false);
- ssm.setSecStructServices(false);
- }
+ StructureSelectionManager.doConfigureStructurePrefs(ssm);
}
public void checkForNews()
}
/**
- * 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.
+ * 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) {
+ public void quitTheDesktop(boolean dispose, boolean terminateJvm)
+ {
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()));
+ storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+ getWidth(), getHeight()));
if (jconsole != null)
{
{
// suppress a possible repeat prompt to save script
groovyConsole.setDirty(false);
- groovyConsole.exit();
+
+ // and tidy up
+ if (((Window) groovyConsole.getFrame()) != null
+ && ((Window) groovyConsole.getFrame()).isVisible())
+ {
+ // console is visible -- FIXME JAL-4327
+ groovyConsole.exit();
+ }
+ else
+ {
+ // console is not, so just let it dispose itself when we shutdown
+ // we don't call groovyConsole.exit() because it calls the shutdown
+ // handler with invokeAndWait() causing deadlock
+ groovyConsole = null;
+ }
}
if (terminateJvm)
// instance.dispose();
}
}
+
public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)
{
final Runnable doDesktopQuit = () -> {
- // FIRST !! check for aborted quit
+ // FIRST !! check for aborted quit
if (QuitHandler.quitCancelled())
{
- jalview.bin.Console.debug("Quit was cancelled - Desktop aborting quit");
+ jalview.bin.Console
+ .debug("Quit was cancelled - Desktop aborting quit");
return;
}
-
+
// Proceed with quitting
- quitTheDesktop(disposeFlag, QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT);
+ quitTheDesktop(disposeFlag,
+ QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT);
// and exit the JVM
instance.quit();
};
}
/**
- * Exits the program and the JVM.
+ * 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
+ * - use closeDesktop() to shutdown Jalview without shutting down the JVM
*
*/
@Override
*/
public static void showUrl(final String url)
{
- if (url!=null && !url.trim().equals("")) {
- jalview.bin.Console.info("Opening URL: "+url);
+ if (url != null && !url.trim().equals(""))
+ {
+ jalview.bin.Console.info("Opening URL: " + url);
showUrl(url, Desktop.instance);
- } else {
+ }
+ else
+ {
jalview.bin.Console.warn("Ignoring attempt to show an empty URL.");
}
-
+
}
/**
}
/**
- * 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.
+ * 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()
{