import java.util.logging.ConsoleHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
+import java.util.stream.Collectors;
import javax.swing.JDialog;
import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import jalview.gui.PromptUserConfig;
import jalview.gui.QuitHandler;
import jalview.gui.QuitHandler.QResponse;
+import jalview.gui.StructureViewerBase;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
System.setSecurityManager(null);
}
- if (args == null)
+ if (args == null || args.length == 0 || (args.length == 1
+ && (args[0] == null || args[0].length() == 0)))
+ {
args = new String[] {};
+ }
// get args needed before proper ArgParser
bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
}
}
+ // set individual session preferences
+ if (bootstrapArgs.contains(Arg.P))
+ {
+ for (String kev : bootstrapArgs.getValueList(Arg.P))
+ {
+ if (kev == null)
+ {
+ continue;
+ }
+ int equalsIndex = kev.indexOf(ArgParser.EQUALS);
+ if (equalsIndex > -1)
+ {
+ String key = kev.substring(0, equalsIndex);
+ String val = kev.substring(equalsIndex + 1);
+ Cache.setSessionProperty(key, val);
+ }
+ }
+ }
+
// Move any new getdown-launcher-new.jar into place over old
// getdown-launcher.jar
String appdirString = System.getProperty("getdownappdir");
final File appdir = new File(appdirString);
new Thread()
{
+
@Override
public void run()
{
// get bootstrap properties (mainly for the logger level)
Properties bootstrapProperties = Cache
- .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
+ .bootstrapProperties(bootstrapArgs.getValue(Arg.PROPS));
// report Jalview version
Cache.loadBuildProperties(
public void run()
{
Console.debug("Running shutdown hook");
+ QuitHandler.startForceQuit();
+ boolean closeExternal = Cache
+ .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false)
+ || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false);
+ StructureViewerBase.setQuitClose(closeExternal);
+ if (desktop != null)
+ {
+ for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ ((StructureViewerBase) frame).closeViewer(closeExternal);
+ }
+ }
+ }
+
if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
{
// Got to here by a SIGTERM signal.
// Note we will not actually cancel the quit from here -- it's too
- // late -- but we can wait for saving files.
+ // late -- but we can wait for saving files and close external viewers
+ // if configured.
+ // Close viewers/Leave viewers open
Console.debug("Checking for saving files");
QuitHandler.getQuitResponse(false);
}
});
String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
- ? bootstrapArgs.get(Arg.PROPS)
+ ? bootstrapArgs.getValue(Arg.PROPS)
: aparser.getValue("props");
// if usrPropsFile == null, loadProperties will use the Channel
// preferences.file
* @j2sIgnore
*/
{
- if (bootstrapArgs.containsType(Type.HELP))
+ if (bootstrapArgs.contains(Arg.HELP))
{
- System.out.println("##### HERE");
- System.out
- .println(Arg.usage(bootstrapArgs.getArgsOfType(Type.HELP)));
+ List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
+ .getList(Arg.HELP);
+ System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
+ .collect(Collectors.toList())));
Jalview.exit(null, 0);
}
if (aparser.contains("help") || aparser.contains("h"))
Jalview.exit(null, 0);
}
- if (bootstrapArgs.contains(Arg.HEADLESS))
+ // new CLI
+ headlessArg = bootstrapArgs.isHeadless();
+ if (headlessArg)
{
System.setProperty("java.awt.headless", "true");
- // new
- headlessArg = bootstrapArgs.getBoolean(Arg.HEADLESS);
}
+ // old CLI
if (aparser.contains("nodisplay") || aparser.contains("nogui")
|| aparser.contains("headless"))
{
System.setProperty("java.awt.headless", "true");
- // old
headless = true;
}
// anything else!
// allow https handshakes to download intermediate certs if necessary
System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
- String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+ String jabawsUrl = bootstrapArgs.getValue(Arg.JABAWS);
if (jabawsUrl == null)
jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
if (!(headless || headlessArg))
{
- Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+ Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
|| aparser.contains("nosplash")
|| Cache.getDefault("SPLASH", "true").equals("false");
desktop = new Desktop();
testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
}
- boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+ boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
if (aparser.contains("nousagestats"))
usagestats = false;
if (usagestats)
{
startUsageStats(desktop);
- testoutput(argparser, Arg.USAGESTATS);
+ testoutput(argparser, Arg.NOUSAGESTATS);
}
else
{
System.out.println("CMD [-nousagestats] executed successfully!");
- testoutput(argparser, Arg.USAGESTATS);
+ testoutput(argparser, Arg.NOUSAGESTATS);
}
boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
if ((!aparser.contains("nonews")
&& Cache.getProperty("NONEWS") == null
- && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
- || "true".equals(bootstrapArgs.get(Arg.NEWS)))
+ && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
+ || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
{
desktop.checkForNews();
}
{
if (headlessArg)
{
- Jalview.exit("Successfully completed commands in headless mode", 0);
+ if (argparser.getBoolean(Arg.NOQUIT))
+ {
+ Console.warn(
+ "Completed " + Arg.HEADLESS.getName() + " commands, but "
+ + Arg.NOQUIT + " is set so not quitting!");
+ }
+ else
+ {
+ Jalview.exit("Successfully completed commands in headless mode",
+ 0);
+ }
}
Console.info("Successfully completed commands");
}
if (!Platform.isJS() && !headless && file == null
&& Cache.getDefault("SHOW_STARTUP_FILE", true)
- && !cmds.commandArgsProvided())
+ && !cmds.commandArgsProvided()
+ && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
// don't open the startup file if command line args have been processed
// (&& !Commands.commandArgsProvided())
/**
}
if (!lafSet)
{
- setSystemLookAndFeel();
+ // Flatlaf default for everyone!
+ lafSet = setFlatLookAndFeel();
+ if (!lafSet)
+ {
+ setSystemLookAndFeel();
+ }
if (Platform.isLinux())
{
setLinuxLookAndFeel();
UIManager.put("TabbedPane.smoothScrolling", true);
UIManager.put("TabbedPane.tabWidthMode", "compact");
UIManager.put("TabbedPane.selectedBackground", Color.white);
+ UIManager.put("TabbedPane.background", new Color(236, 236, 236));
+ UIManager.put("TabbedPane.hoverColor", Color.lightGray);
}
Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
return set;
}
+ /*
private static void showUsage()
{
System.out.println(
+ "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
}
+ */
private static void startUsageStats(final Desktop desktop)
{
public static void exit(String message, int exitcode)
{
- Console.debug("Using Jalview.exit");
- if (message != null)
- if (exitcode == 0)
- Console.info(message);
- else
- Console.error(message);
+ if (Console.log == null)
+ {
+ // Don't start the logger just to exit!
+ if (message != null)
+ {
+ if (exitcode == 0)
+ {
+ System.out.println(message);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+ }
+ }
+ else
+ {
+ Console.debug("Using Jalview.exit");
+ if (message != null)
+ {
+ if (exitcode == 0)
+ {
+ Console.info(message);
+ }
+ else
+ {
+ Console.error(message);
+ }
+ }
+ }
if (exitcode > -1)
+ {
System.exit(exitcode);
+ }
}
/*
}
/*
- * testoutput for boolean values
+ * testoutput for boolean and unary values
*/
protected static void testoutput(ArgParser ap, Arg a)
{
private static void testoutput(boolean yes, Arg a)
{
- System.out.println("[TESTOUTPUT] arg "
- + (yes ? a.argString() : a.negateArgString()) + " was set");
+ String message = null;
+ if (a.hasOption(Opt.BOOLEAN))
+ {
+ message = (yes ? a.argString() : a.negateArgString()) + " was set";
+ }
+ else if (a.hasOption(Opt.UNARY))
+ {
+ message = a.argString() + (yes ? " was set" : " was not set");
+ }
+ System.out.println("[TESTOUTPUT] arg " + message);
}
}
git://source.jalview.org / jalview.git / blobdiff