X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=cf73c81030be4e11c7bd22bd25413f5d9a188360;hb=ec24991b1786e17158a43f713c8ae9c4f8647393;hp=0b5fafa4a8d6a85b829541642badb81ea8d3fa8b;hpb=a9f2db2f1688164dd54da7521509c135d7fdf042;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0b5fafa..cf73c81 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,12 +20,15 @@
  */
 package jalview.bin;
 
+import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.OutputStream;
 import java.io.OutputStreamWriter;
+import java.io.PrintStream;
 import java.io.PrintWriter;
 import java.net.MalformedURLException;
 import java.net.URI;
@@ -36,24 +39,43 @@ import java.security.CodeSource;
 import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
+import java.util.Locale;
 import java.util.Map;
+import java.util.Properties;
 import java.util.Vector;
 import java.util.logging.ConsoleHandler;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 import javax.swing.UIManager.LookAndFeelInfo;
+import javax.swing.UnsupportedLookAndFeelException;
 
+import com.formdev.flatlaf.FlatLightLaf;
+import com.formdev.flatlaf.themes.FlatMacLightLaf;
+import com.formdev.flatlaf.util.SystemInfo;
 import com.threerings.getdown.util.LaunchUtil;
 
+//import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.Arg.Opt;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
+import jalview.gui.QuitHandler;
+import jalview.gui.QuitHandler.QResponse;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
@@ -70,6 +92,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.ChannelProperties;
 import jalview.util.HttpUtils;
+import jalview.util.LaunchUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -94,6 +117,10 @@ public class Jalview
   static
   {
     Platform.getURLCommandArguments();
+    Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
+    Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
   }
 
   /*
@@ -103,8 +130,21 @@ public class Jalview
 
   private Desktop desktop;
 
+  protected Commands cmds;
+
   public static AlignFrame currentAlignFrame;
 
+  public ArgParser argparser = null;
+
+  public BootstrapArgs bootstrapArgs = null;
+
+  private boolean QUIET = false;
+
+  public static boolean quiet()
+  {
+    return Jalview.getInstance() != null && Jalview.getInstance().QUIET;
+  }
+
   static
   {
     if (!Platform.isJS())
@@ -255,46 +295,193 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-
     if (!Platform.isJS())
     {
       System.setSecurityManager(null);
     }
 
-    System.out
-            .println("Java version: " + System.getProperty("java.version"));
-    System.out.println("Java Home: " + System.getProperty("java.home"));
-    System.out.println(System.getProperty("os.arch") + " "
-            + System.getProperty("os.name") + " "
-            + System.getProperty("os.version"));
-    String val = System.getProperty("sys.install4jVersion");
-    if (val != null)
+    if (args == null)
+      args = new String[] {};
+
+    // get args needed before proper ArgParser
+    bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+
+    if (!Platform.isJS())
     {
-      System.out.println("Install4j version: " + val);
+      // are we being --quiet ?
+      if (bootstrapArgs.contains(Arg.QUIET))
+      {
+        QUIET = true;
+        OutputStream devNull = new OutputStream()
+        {
+
+          @Override
+          public void write(int b)
+          {
+            // DO NOTHING
+          }
+        };
+        System.setOut(new PrintStream(devNull));
+        // redirecting stderr not working
+        if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
+        {
+          System.setErr(new PrintStream(devNull));
+        }
+      }
+
+      if (bootstrapArgs.contains(Arg.HELP)
+              || bootstrapArgs.contains(Arg.VERSION))
+      {
+        QUIET = true;
+      }
+    }
+
+    // Move any new getdown-launcher-new.jar into place over old
+    // getdown-launcher.jar
+    String appdirString = System.getProperty("getdownappdir");
+    if (appdirString != null && appdirString.length() > 0)
+    {
+      final File appdir = new File(appdirString);
+      new Thread()
+      {
+        @Override
+        public void run()
+        {
+          LaunchUtil.upgradeGetdown(
+                  new File(appdir, "getdown-launcher-old.jar"),
+                  new File(appdir, "getdown-launcher.jar"),
+                  new File(appdir, "getdown-launcher-new.jar"));
+        }
+      }.start();
     }
-    val = System.getProperty("installer_template_version");
-    if (val != null)
+
+    if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
     {
-      System.out.println("Install4j template version: " + val);
+      System.out.println(
+              "Java version: " + System.getProperty("java.version"));
+      System.out.println("Java home: " + System.getProperty("java.home"));
+      System.out.println("Java arch: " + System.getProperty("os.arch") + " "
+              + System.getProperty("os.name") + " "
+              + System.getProperty("os.version"));
+
+      String val = System.getProperty("sys.install4jVersion");
+      if (val != null)
+      {
+        System.out.println("Install4j version: " + val);
+      }
+      val = System.getProperty("installer_template_version");
+      if (val != null)
+      {
+        System.out.println("Install4j template version: " + val);
+      }
+      val = System.getProperty("launcher_version");
+      if (val != null)
+      {
+        System.out.println("Launcher version: " + val);
+      }
     }
-    val = System.getProperty("launcher_version");
-    if (val != null)
+
+    if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
     {
-      System.out.println("Launcher version: " + val);
+      System.setProperty("flatlaf.uiScale", "1");
     }
 
+    // get bootstrap properties (mainly for the logger level)
+    Properties bootstrapProperties = Cache
+            .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
+
     // report Jalview version
-    Cache.loadBuildProperties(true);
+    Cache.loadBuildProperties(
+            !quiet() || bootstrapArgs.contains(Arg.VERSION));
 
+    // stop now if only after --version
+    if (bootstrapArgs.contains(Arg.VERSION))
+    {
+      Jalview.exit(null, 0);
+    }
+
+    // old ArgsParser
     ArgsParser aparser = new ArgsParser(args);
+
+    // old
     boolean headless = false;
+    // new
+    boolean headlessArg = false;
+
+    try
+    {
+      String logLevel = null;
+      if (bootstrapArgs.contains(Arg.TRACE))
+      {
+        logLevel = "TRACE";
+      }
+      else if (bootstrapArgs.contains(Arg.DEBUG))
+      {
+        logLevel = "DEBUG";
+      }
+      if (logLevel == null && !(bootstrapProperties == null))
+      {
+        logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
+      }
+      Console.initLogger(logLevel);
+    } catch (NoClassDefFoundError error)
+    {
+      error.printStackTrace();
+      String message = "\nEssential logging libraries not found."
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+      Jalview.exit(message, 0);
+    }
 
-    String usrPropsFile = aparser.getValue("props");
-    Cache.loadProperties(usrPropsFile); // must do this before
+    // register SIGTERM listener
+    Runtime.getRuntime().addShutdownHook(new Thread()
+    {
+      public void run()
+      {
+        Console.debug("Running shutdown hook");
+        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.
+          Console.debug("Checking for saving files");
+          QuitHandler.getQuitResponse(false);
+        }
+        else
+        {
+          Console.debug("Nothing more to do");
+        }
+        Console.debug("Exiting, bye!");
+        // shutdownHook cannot be cancelled, JVM will now halt
+      }
+    });
+
+    String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
+            ? bootstrapArgs.get(Arg.PROPS)
+            : aparser.getValue("props");
+    // if usrPropsFile == null, loadProperties will use the Channel
+    // preferences.file
+    Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
       System.out.println(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
+      testoutput(bootstrapArgs, Arg.PROPS,
+              "test/jalview/bin/testProps.jvprops", usrPropsFile);
+    }
+
+    // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
+    if (bootstrapArgs.contains(Arg.ARGFILE))
+    {
+      argparser = ArgParser.parseArgFiles(
+              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+              bootstrapArgs);
+    }
+    else
+    {
+      argparser = new ArgParser(args,
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+              bootstrapArgs);
     }
 
     if (!Platform.isJS())
@@ -304,20 +491,42 @@ public class Jalview
      * @j2sIgnore
      */
     {
+      if (bootstrapArgs.contains(Arg.HELP))
+      {
+        System.out.println(Arg.usage());
+        Jalview.exit(null, 0);
+      }
       if (aparser.contains("help") || aparser.contains("h"))
       {
+        /*
+         * Now using new usage statement.
         showUsage();
-        System.exit(0);
+        */
+        System.out.println(Arg.usage());
+        Jalview.exit(null, 0);
+      }
+
+      if (bootstrapArgs.contains(Arg.HEADLESS))
+      {
+        System.setProperty("java.awt.headless", "true");
+        // new
+        headlessArg = bootstrapArgs.getBoolean(Arg.HEADLESS);
       }
       if (aparser.contains("nodisplay") || aparser.contains("nogui")
               || aparser.contains("headless"))
       {
         System.setProperty("java.awt.headless", "true");
+        // old
         headless = true;
       }
       // anything else!
 
-      final String jabawsUrl = aparser.getValue("jabaws");
+      // allow https handshakes to download intermediate certs if necessary
+      System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
+
+      String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+      if (jabawsUrl == null)
+        jabawsUrl = aparser.getValue("jabaws");
       if (jabawsUrl != null)
       {
         try
@@ -325,6 +534,8 @@ public class Jalview
           Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
           System.out.println(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+          testoutput(bootstrapArgs, Arg.JABAWS,
+                  "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
         } catch (MalformedURLException e)
         {
           System.err.println(
@@ -333,26 +544,40 @@ public class Jalview
       }
     }
 
-    String defs = aparser.getValue("setprop");
-    while (defs != null)
+    List<String> setprops = new ArrayList<>();
+    if (bootstrapArgs.contains(Arg.SETPROP))
+    {
+      setprops = bootstrapArgs.getList(Arg.SETPROP);
+    }
+    else
+    {
+      String sp = aparser.getValue("setprop");
+      while (sp != null)
+      {
+        setprops.add(sp);
+        sp = aparser.getValue("setprop");
+      }
+    }
+    for (String setprop : setprops)
     {
-      int p = defs.indexOf('=');
+      int p = setprop.indexOf('=');
       if (p == -1)
       {
-        System.err.println("Ignoring invalid setprop argument : " + defs);
+        System.err
+                .println("Ignoring invalid setprop argument : " + setprop);
       }
       else
       {
-        System.out.println("Executing setprop argument: " + defs);
+        System.out.println("Executing setprop argument: " + setprop);
         if (Platform.isJS())
         {
-          Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+          Cache.setProperty(setprop.substring(0, p),
+                  setprop.substring(p + 1));
         }
         // DISABLED FOR SECURITY REASONS
         // TODO: add a property to allow properties to be overriden by cli args
-        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+        // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
       }
-      defs = aparser.getValue("setprop");
     }
     if (System.getProperty("java.awt.headless") != null
             && System.getProperty("java.awt.headless").equals("true"))
@@ -361,20 +586,23 @@ public class Jalview
     }
     System.setProperty("http.agent",
             "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
     try
     {
-      Cache.initLogger();
-    } catch (NoClassDefFoundError error)
+      Console.initLogger();
+    } catch (
+
+    NoClassDefFoundError error)
     {
       error.printStackTrace();
-      System.out.println("\nEssential logging libraries not found."
-              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
-      System.exit(0);
+      String message = "\nEssential logging libraries not found."
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+      Jalview.exit(message, 0);
     }
-
     desktop = null;
 
-    setLookAndFeel();
+    if (!(headless || headlessArg))
+      setLookAndFeel();
 
     /*
      * configure 'full' SO model if preferences say to, else use the default (full SO)
@@ -386,9 +614,11 @@ public class Jalview
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
 
-    if (!headless)
+    if (!(headless || headlessArg))
     {
-      Desktop.nosplash = aparser.contains("nosplash");
+      Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+              || aparser.contains("nosplash")
+              || Cache.getDefault("SPLASH", "true").equals("false");
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -397,13 +627,13 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        Cache.log.info("Cannot set Taskbar");
-        Cache.log.error(e.getMessage());
+        Console.info("Cannot set Taskbar");
+        Console.error(e.getMessage());
         // e.printStackTrace();
       } catch (Throwable t)
       {
-        Cache.log.info("Cannot set Taskbar");
-        Cache.log.error(t.getMessage());
+        Console.info("Cannot set Taskbar");
+        Console.error(t.getMessage());
         // t.printStackTrace();
       }
 
@@ -419,27 +649,73 @@ public class Jalview
        * @j2sIgnore
        */
       {
-        if (!aparser.contains("nowebservicediscovery"))
+
+        /**
+         * Check to see that the JVM version being run is suitable for the Java
+         * version this Jalview was compiled for. Popup a warning if not.
+         */
+        if (!LaunchUtils.checkJavaVersion())
+        {
+          Console.warn("The Java version being used (Java "
+                  + LaunchUtils.getJavaVersion()
+                  + ") may lead to problems. This installation of Jalview should be used with Java "
+                  + LaunchUtils.getJavaCompileVersion() + ".");
+
+          if (!LaunchUtils
+                  .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
+          {
+            Object[] options = {
+                MessageManager.getString("label.continue") };
+            JOptionPane.showOptionDialog(null,
+                    MessageManager.formatMessage(
+                            "warning.wrong_jvm_version_message",
+                            LaunchUtils.getJavaVersion(),
+                            LaunchUtils.getJavaCompileVersion()),
+                    MessageManager
+                            .getString("warning.wrong_jvm_version_title"),
+                    JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+                    null, options, options[0]);
+          }
+        }
+
+        boolean webservicediscovery = bootstrapArgs
+                .getBoolean(Arg.WEBSERVICEDISCOVERY);
+        if (aparser.contains("nowebservicediscovery"))
+          webservicediscovery = false;
+        if (webservicediscovery)
         {
           desktop.startServiceDiscovery();
         }
-        if (!aparser.contains("nousagestats"))
+        else
+        {
+          testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
+        }
+
+        boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+        if (aparser.contains("nousagestats"))
+          usagestats = false;
+        if (usagestats)
         {
           startUsageStats(desktop);
+          testoutput(argparser, Arg.USAGESTATS);
         }
         else
         {
-          System.err.println("CMD [-nousagestats] executed successfully!");
+          System.out.println("CMD [-nousagestats] executed successfully!");
+          testoutput(argparser, Arg.USAGESTATS);
         }
 
-        if (!aparser.contains("noquestionnaire"))
+        boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
+        if (aparser.contains("noquestionnaire"))
+          questionnaire = false;
+        if (questionnaire)
         {
           String url = aparser.getValue("questionnaire");
           if (url != null)
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            Cache.log.debug("Starting questionnaire url at " + url);
+            Console.debug("Starting questionnaire url at " + url);
             desktop.checkForQuestionnaire(url);
             System.out.println("CMD questionnaire[-" + url
                     + "] executed successfully!");
@@ -454,7 +730,7 @@ public class Jalview
               // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
               // //
               String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
-              Cache.log.debug(
+              Console.debug(
                       "Starting questionnaire with default url: " + defurl);
               desktop.checkForQuestionnaire(defurl);
             }
@@ -462,41 +738,62 @@ public class Jalview
         }
         else
         {
-          System.err
+          System.out
                   .println("CMD [-noquestionnaire] executed successfully!");
+          testoutput(argparser, Arg.QUESTIONNAIRE);
         }
 
-        if (!aparser.contains("nonews"))
+        if ((!aparser.contains("nonews")
+                && Cache.getProperty("NONEWS") == null
+                && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
+                || "true".equals(bootstrapArgs.get(Arg.NEWS)))
         {
           desktop.checkForNews();
         }
 
-        BioJsHTMLOutput.updateBioJS();
+        if (!aparser.contains("nohtmltemplates")
+                && Cache.getProperty("NOHTMLTEMPLATES") == null)
+        {
+          BioJsHTMLOutput.updateBioJS();
+        }
       }
     }
-
-    // Move any new getdown-launcher-new.jar into place over old
-    // getdown-launcher.jar
-    String appdirString = System.getProperty("getdownappdir");
-    if (appdirString != null && appdirString.length() > 0)
+    // Run Commands from cli
+    cmds = new Commands(argparser, headlessArg);
+    boolean commandsSuccess = cmds.argsWereParsed();
+    if (commandsSuccess)
     {
-      final File appdir = new File(appdirString);
-      new Thread()
+      if (headlessArg)
       {
-        @Override
-        public void run()
-        {
-          LaunchUtil.upgradeGetdown(
-                  new File(appdir, "getdown-launcher-old.jar"),
-                  new File(appdir, "getdown-launcher.jar"),
-                  new File(appdir, "getdown-launcher-new.jar"));
-        }
-      }.start();
+        Jalview.exit("Successfully completed commands in headless mode", 0);
+      }
+      Console.info("Successfully completed commands");
+    }
+    else
+    {
+      if (headlessArg)
+      {
+        Jalview.exit("Error when running Commands in headless mode", 1);
+      }
+      Console.warn("Error when running commands");
+    }
+
+    // Check if JVM and compile version might cause problems and log if it
+    // might.
+    if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
+    {
+      Console.warn("The Java version being used (Java "
+              + LaunchUtils.getJavaVersion()
+              + ") may lead to problems. This installation of Jalview should be used with Java "
+              + LaunchUtils.getJavaCompileVersion() + ".");
     }
 
     String file = null, data = null;
+
     FileFormatI format = null;
+
     DataSourceType protocol = null;
+
     FileLoader fileLoader = new FileLoader(!headless);
 
     String groovyscript = null; // script to execute after all loading is
@@ -505,11 +802,11 @@ public class Jalview
     groovyscript = aparser.getValue("groovy", true);
     file = aparser.getValue("open", true);
 
-    if (file == null && desktop == null)
+    if (file == null && desktop == null && !commandsSuccess)
     {
-      System.out.println("No files to open!");
-      System.exit(1);
+      Jalview.exit("No files to open!", 1);
     }
+
     long progress = -1;
     // Finally, deal with the remaining input data.
     if (file != null)
@@ -534,11 +831,12 @@ public class Jalview
         {
           if (!(new File(file)).exists())
           {
-            System.out.println("Can't find " + file);
             if (headless)
             {
-              System.exit(1);
+              Jalview.exit(
+                      "Can't find file '" + file + "' in headless mode", 1);
             }
+            Console.warn("Can't find file'" + file + "'");
           }
         }
       }
@@ -573,7 +871,7 @@ public class Jalview
           if (cs != null)
           {
             System.out.println(
-                    "CMD [-color " + data + "] executed successfully!");
+                    "CMD [-colour " + data + "] executed successfully!");
           }
           af.changeColour(cs);
         }
@@ -769,25 +1067,28 @@ public class Jalview
         }
       }
     }
+
     AlignFrame startUpAlframe = null;
     // We'll only open the default file if the desktop is visible.
     // And the user
     // ////////////////////
 
     if (!Platform.isJS() && !headless && file == null
-            && Cache.getDefault("SHOW_STARTUP_FILE", true))
+            && Cache.getDefault("SHOW_STARTUP_FILE", true)
+            && !cmds.commandArgsProvided())
+    // don't open the startup file if command line args have been processed
+    // (&& !Commands.commandArgsProvided())
     /**
      * Java only
      * 
      * @j2sIgnore
      */
     {
-      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
-              jalview.bin.Cache.getDefault("www.jalview.org",
-                      "https://www.jalview.org")
+      file = Cache.getDefault("STARTUP_FILE",
+              Cache.getDefault("www.jalview.org", "https://www.jalview.org")
                       + "/examples/exampleFile_2_7.jvp");
-      if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+              || file.equals(
                       "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
         file.replace("http:", "https:");
@@ -817,6 +1118,10 @@ public class Jalview
 
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
+      // don't ask to save when quitting if only the startup file has been
+      // opened
+      Console.debug("Resetting up-to-date flag for startup file");
+      startUpAlframe.getViewport().setSavedUpToDate(true);
       // extract groovy arguments before anything else.
     }
 
@@ -848,8 +1153,8 @@ public class Jalview
 
   private static void setLookAndFeel()
   {
-    // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
-    // "mac"
+    // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
+    // "mac" or "flat"
     // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
     // try Quaqua/Vaqua.
     String lafProp = System.getProperty("laf");
@@ -870,69 +1175,62 @@ public class Jalview
       lafSet = setCrossPlatformLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "system":
       lafSet = setSystemLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "gtk":
       lafSet = setGtkLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "metal":
       lafSet = setMetalLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "nimbus":
       lafSet = setNimbusLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "quaqua":
-      lafSet = setQuaquaLookAndFeel();
-      if (!lafSet)
-      {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
-    case "vaqua":
-      lafSet = setVaquaLookAndFeel();
+    case "flat":
+      lafSet = setFlatLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "mac":
       lafSet = setMacLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "none":
       break;
     default:
-      Cache.log.error("Requested laf=" + laf + " not implemented");
+      Console.error("Requested laf=" + laf + " not implemented");
     }
     if (!lafSet)
     {
       setSystemLookAndFeel();
       if (Platform.isLinux())
       {
-        setMetalLookAndFeel();
+        setLinuxLookAndFeel();
       }
       if (Platform.isMac())
       {
@@ -951,9 +1249,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.log.error("Unexpected Look and Feel Exception");
-      Cache.log.error(ex.getMessage());
-      Cache.log.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -967,9 +1265,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.log.error("Unexpected Look and Feel Exception");
-      Cache.log.error(ex.getMessage());
-      Cache.log.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -983,9 +1281,10 @@ public class Jalview
       for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
       {
         if (info.getName() != null && nameStartsWith
-                ? info.getName().toLowerCase()
-                        .startsWith(name.toLowerCase())
-                : info.getName().toLowerCase().equals(name.toLowerCase()))
+                ? info.getName().toLowerCase(Locale.ROOT)
+                        .startsWith(name.toLowerCase(Locale.ROOT))
+                : info.getName().toLowerCase(Locale.ROOT)
+                        .equals(name.toLowerCase(Locale.ROOT)))
         {
           className = info.getClassName();
           break;
@@ -995,9 +1294,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.log.error("Unexpected Look and Feel Exception");
-      Cache.log.error(ex.getMessage());
-      Cache.log.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -1020,18 +1319,115 @@ public class Jalview
             "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
   }
 
-  private static boolean setQuaquaLookAndFeel()
+  private static boolean setFlatLookAndFeel()
   {
-    return setSpecificLookAndFeel("quaqua",
-            ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
-                    .getName(),
-            false);
-  }
+    boolean set = false;
+    if (SystemInfo.isMacOS)
+    {
+      try
+      {
+        UIManager.setLookAndFeel(
+                "com.formdev.flatlaf.themes.FlatMacLightLaf");
+        set = true;
+        Console.debug("Using FlatMacLightLaf");
+      } catch (ClassNotFoundException | InstantiationException
+              | IllegalAccessException | UnsupportedLookAndFeelException e)
+      {
+        Console.debug("Exception loading FlatLightLaf", e);
+      }
+      System.setProperty("apple.laf.useScreenMenuBar", "true");
+      System.setProperty("apple.awt.application.name",
+              ChannelProperties.getProperty("app_name"));
+      System.setProperty("apple.awt.application.appearance", "system");
+      if (SystemInfo.isMacFullWindowContentSupported
+              && Desktop.desktop != null)
+      {
+        Console.debug("Setting transparent title bar");
+        Desktop.desktop.getRootPane()
+                .putClientProperty("apple.awt.fullWindowContent", true);
+        Desktop.desktop.getRootPane()
+                .putClientProperty("apple.awt.transparentTitleBar", true);
+        Desktop.desktop.getRootPane()
+                .putClientProperty("apple.awt.fullscreenable", true);
+      }
+      SwingUtilities.invokeLater(() -> {
+        FlatMacLightLaf.setup();
+      });
+      Console.debug("Using FlatMacLightLaf");
+      set = true;
+    }
+    if (!set)
+    {
+      try
+      {
+        UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+        set = true;
+        Console.debug("Using FlatLightLaf");
+      } catch (ClassNotFoundException | InstantiationException
+              | IllegalAccessException | UnsupportedLookAndFeelException e)
+      {
+        Console.debug("Exception loading FlatLightLaf", e);
+      }
+      // Windows specific properties here
+      SwingUtilities.invokeLater(() -> {
+        FlatLightLaf.setup();
+      });
+      Console.debug("Using FlatLightLaf");
+      set = true;
+    }
+    else if (SystemInfo.isLinux)
+    {
+      try
+      {
+        UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+        set = true;
+        Console.debug("Using FlatLightLaf");
+      } catch (ClassNotFoundException | InstantiationException
+              | IllegalAccessException | UnsupportedLookAndFeelException e)
+      {
+        Console.debug("Exception loading FlatLightLaf", e);
+      }
+      // enable custom window decorations
+      JFrame.setDefaultLookAndFeelDecorated(true);
+      JDialog.setDefaultLookAndFeelDecorated(true);
+      SwingUtilities.invokeLater(() -> {
+        FlatLightLaf.setup();
+      });
+      Console.debug("Using FlatLightLaf");
+      set = true;
+    }
 
-  private static boolean setVaquaLookAndFeel()
-  {
-    return setSpecificLookAndFeel("vaqua",
-            "org.violetlib.aqua.AquaLookAndFeel", false);
+    if (!set)
+    {
+      try
+      {
+        UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+        set = true;
+        Console.debug("Using FlatLightLaf");
+      } catch (ClassNotFoundException | InstantiationException
+              | IllegalAccessException | UnsupportedLookAndFeelException e)
+      {
+        Console.debug("Exception loading FlatLightLaf", e);
+      }
+    }
+
+    if (set)
+    {
+      UIManager.put("TabbedPane.tabType", "card");
+      UIManager.put("TabbedPane.showTabSeparators", true);
+      UIManager.put("TabbedPane.showContentSeparator", true);
+      UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
+      UIManager.put("TabbedPane.tabsOverlapBorder", true);
+      UIManager.put("TabbedPane.hasFullBorder", true);
+      UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
+      UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
+      UIManager.put("TabbedPane.smoothScrolling", true);
+      UIManager.put("TabbedPane.tabWidthMode", "compact");
+      UIManager.put("TabbedPane.selectedBackground", Color.white);
+    }
+
+    Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
+    return set;
   }
 
   private static boolean setMacLookAndFeel()
@@ -1040,12 +1436,28 @@ public class Jalview
     System.setProperty("com.apple.mrj.application.apple.menu.about.name",
             ChannelProperties.getProperty("app_name"));
     System.setProperty("apple.laf.useScreenMenuBar", "true");
+    /*
+     * broken native LAFs on (ARM?) macbooks
     set = setQuaquaLookAndFeel();
     if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
-            .toLowerCase().contains("quaqua"))
+            .toLowerCase(Locale.ROOT).contains("quaqua"))
     {
       set = setVaquaLookAndFeel();
     }
+     */
+    set = setFlatLookAndFeel();
+    return set;
+  }
+
+  private static boolean setLinuxLookAndFeel()
+  {
+    boolean set = false;
+    set = setFlatLookAndFeel();
+    if (!set)
+      set = setMetalLookAndFeel();
+    // avoid GtkLookAndFeel -- not good results especially on HiDPI
+    if (!set)
+      set = setNimbusLookAndFeel();
     return set;
   }
 
@@ -1107,17 +1519,17 @@ public class Jalview
               @Override
               public void run()
               {
-                Cache.log.debug(
+                Console.debug(
                         "Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
-                Cache.log.debug("Tracking enabled.");
+                Console.debug("Tracking enabled.");
               }
             }, new Runnable()
             {
               @Override
               public void run()
               {
-                Cache.log.debug("Not enabling Google Tracking.");
+                Console.debug("Not enabling Google Tracking.");
               }
             }, null, true);
     desktop.addDialogThread(prompter);
@@ -1132,7 +1544,7 @@ public class Jalview
    *          the Jalview Desktop object passed in to the groovy binding as the
    *          'Jalview' object.
    */
-  private void executeGroovyScript(String groovyscript, AlignFrame af)
+  protected void executeGroovyScript(String groovyscript, AlignFrame af)
   {
     /**
      * for scripts contained in files
@@ -1259,19 +1671,12 @@ public class Jalview
   }
 
   /**
-   * Quit method delegates to Desktop.quit - unless running in headless mode
-   * when it just ends the JVM
+   * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
    */
   public void quit()
   {
-    if (desktop != null)
-    {
-      desktop.quit();
-    }
-    else
-    {
-      System.exit(0);
-    }
+    // System.exit will run the shutdownHook first
+    Jalview.exit("Quitting now. Bye!", 0);
   }
 
   public static AlignFrame getCurrentAlignFrame()
@@ -1283,4 +1688,128 @@ public class Jalview
   {
     Jalview.currentAlignFrame = currentAlignFrame;
   }
+
+  protected Commands getCommands()
+  {
+    return cmds;
+  }
+
+  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 (exitcode > -1)
+      System.exit(exitcode);
+  }
+
+  /*
+   * testoutput for string values
+   */
+  protected static void testoutput(ArgParser ap, Arg a, String s1,
+          String s2)
+  {
+    BootstrapArgs bsa = ap.getBootstrapArgs();
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+    {
+      Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+              + s2 + "' for arg " + a.argString());
+      return;
+    }
+    boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+            : ap.isSet(a);
+    if (!isset)
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(true, a, s1, s2);
+  }
+
+  protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
+          String s2)
+  {
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+    {
+      Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+              + s2 + "' for arg " + a.argString());
+      return;
+    }
+    if (!a.hasOption(Opt.BOOTSTRAP))
+    {
+      Console.error("Non-bootstrap Arg '" + a.getName()
+              + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
+    }
+    if (!bsa.contains(a))
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(true, a, s1, s2);
+  }
+
+  private static void testoutput(boolean yes, Arg a, String s1, String s2)
+  {
+    if (yes && ((s1 == null && s2 == null)
+            || (s1 != null && s1.equals(s2))))
+    {
+      System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+              + "' was set");
+    }
+  }
+
+  /*
+   * testoutput for boolean values
+   */
+  protected static void testoutput(ArgParser ap, Arg a)
+  {
+    if (ap == null)
+      return;
+    BootstrapArgs bsa = ap.getBootstrapArgs();
+    if (bsa == null)
+      return;
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
+            : ap.getBoolean(a);
+    boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+            : ap.isSet(a);
+    if (!isset)
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(val, a);
+  }
+
+  protected static void testoutput(BootstrapArgs bsa, Arg a)
+  {
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!a.hasOption(Opt.BOOTSTRAP))
+    {
+      Console.warn("Non-bootstrap Arg '" + a.getName()
+              + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
+
+    }
+    if (!bsa.contains(a))
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(bsa.getBoolean(a), a);
+  }
+
+  private static void testoutput(boolean yes, Arg a)
+  {
+    System.out.println("[TESTOUTPUT] arg "
+            + (yes ? a.argString() : a.negateArgString()) + " was set");
+  }
 }