X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=5f1f228ba4c7af0b116a059c7b30dbafb9eb4b6e;hb=9f4be220ec9450a669805117a30df98b7848b82c;hp=19de95e0d316598dc6232274d0f6e48183ade492;hpb=76cfeb5e50dd69a3ba963096556f9677c9eea55a;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 19de95e..5f1f228 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;
@@ -37,20 +40,38 @@ import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
 import java.util.HashMap;
+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.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;
@@ -65,7 +86,9 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 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;
@@ -87,6 +110,15 @@ import jalview.ws.jws2.Jws2Discoverer;
  */
 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");
+  }
+
   /*
    * singleton instance of this class
    */
@@ -94,26 +126,36 @@ public class Jalview
 
   private Desktop desktop;
 
+  protected Commands cmds;
+
   public static AlignFrame currentAlignFrame;
 
   static
   {
-    // grab all the rights we can the JVM
-    Policy.setPolicy(new Policy()
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      @Override
-      public PermissionCollection getPermissions(CodeSource codesource)
+      // grab all the rights we can for the JVM
+      Policy.setPolicy(new Policy()
       {
-        Permissions perms = new Permissions();
-        perms.add(new AllPermission());
-        return (perms);
-      }
+        @Override
+        public PermissionCollection getPermissions(CodeSource codesource)
+        {
+          Permissions perms = new Permissions();
+          perms.add(new AllPermission());
+          return (perms);
+        }
 
-      @Override
-      public void refresh()
-      {
-      }
-    });
+        @Override
+        public void refresh()
+        {
+        }
+      });
+    }
   }
 
   /**
@@ -188,22 +230,113 @@ public class Jalview
    */
   public static void main(String[] args)
   {
+    // setLogging(); // BH - for event debugging in JavaScript
     instance = new Jalview();
     instance.doMain(args);
   }
 
+  private static void logClass(String name)
+  {
+    // BH - for event debugging in JavaScript
+    ConsoleHandler consoleHandler = new ConsoleHandler();
+    consoleHandler.setLevel(Level.ALL);
+    Logger logger = Logger.getLogger(name);
+    logger.setLevel(Level.ALL);
+    logger.addHandler(consoleHandler);
+  }
+
+  @SuppressWarnings("unused")
+  private static void setLogging()
+  {
+
+    /**
+     * @j2sIgnore
+     * 
+     */
+    {
+      System.out.println("not in js");
+    }
+
+    // BH - for event debugging in JavaScript (Java mode only)
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      Logger.getLogger("").setLevel(Level.ALL);
+      logClass("java.awt.EventDispatchThread");
+      logClass("java.awt.EventQueue");
+      logClass("java.awt.Component");
+      logClass("java.awt.focus.Component");
+      logClass("java.awt.focus.DefaultKeyboardFocusManager");
+    }
+
+  }
+
   /**
    * @param args
    */
   void doMain(String[] args)
   {
-    System.setSecurityManager(null);
+
+    if (!Platform.isJS())
+    {
+      System.setSecurityManager(null);
+    }
+
+    // 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();
+    }
+
+    // get args needed before proper ArgParser
+    BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+
+    if (!Platform.isJS())
+    {
+      // are we being --quiet ?
+      if (bootstrapArgs.contains(Arg.QUIET))
+      {
+        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));
+        }
+      }
+    }
+
     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)
     {
@@ -220,45 +353,133 @@ public class Jalview
       System.out.println("Launcher version: " + val);
     }
 
+    if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
+    {
+      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);
 
+    // old ArgsParser
     ArgsParser aparser = new ArgsParser(args);
+
+    // old
     boolean headless = false;
+    // new
+    boolean headlessArg = false;
 
-    if (aparser.contains("help") || aparser.contains("h"))
+    try
     {
-      showUsage();
-      System.exit(0);
-    }
-    if (aparser.contains("nodisplay") || aparser.contains("nogui")
-            || aparser.contains("headless"))
+      String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
+      if (logLevel == null && !(bootstrapProperties == null))
+      {
+        logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
+      }
+      Console.initLogger(logLevel);
+    } catch (NoClassDefFoundError error)
     {
-      System.setProperty("java.awt.headless", "true");
-      headless = true;
+      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");
+    Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
       System.out.println(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
     }
 
-    // anything else!
+    // new ArgParser
+    ArgParser argparser;
+    // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
+    if (bootstrapArgs.contains(Arg.ARGFILE))
+    {
+      argparser = ArgParser
+              .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
+    }
+    else
+    {
+      argparser = new ArgParser(args);
+    }
 
-    final String jabawsUrl = aparser.getValue("jabaws");
-    if (jabawsUrl != null)
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      try
+      if (aparser.contains("help") || aparser.contains("h")
+              || argparser.getBool(Arg.HELP))
       {
-        Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-        System.out.println(
-                "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
-      } catch (MalformedURLException e)
+        showUsage();
+        Jalview.exit(null, 0);
+      }
+
+      if (bootstrapArgs.contains(Arg.HEADLESS))
       {
-        System.err.println(
-                "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        System.setProperty("java.awt.headless", "true");
+        // new
+        headlessArg = argparser.getBool(Arg.HEADLESS);
+      }
+      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");
+
+      final String jabawsUrl = aparser.getValue("jabaws");
+      if (jabawsUrl != null)
+      {
+        try
+        {
+          Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+          System.out.println(
+                  "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+        } catch (MalformedURLException e)
+        {
+          System.err.println(
+                  "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        }
       }
     }
 
@@ -273,6 +494,10 @@ public class Jalview
       else
       {
         System.out.println("Executing setprop argument: " + defs);
+        if (Platform.isJS())
+        {
+          Cache.setProperty(defs.substring(0, p), defs.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));
@@ -286,33 +511,37 @@ 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 (SO
-     * Lite)
+     * configure 'full' SO model if preferences say to, else use the default (full SO)
+     * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
      */
-    if (Cache.getDefault("USE_FULL_SO", true))
+    boolean soDefault = !Platform.isJS();
+    if (Cache.getDefault("USE_FULL_SO", soDefault))
     {
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
 
-    if (!headless)
+    if (!(headless || headlessArg))
     {
-
+      Desktop.nosplash = aparser.contains("nosplash");
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -321,95 +550,153 @@ 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();
       }
 
+      // set Proxy settings before all the internet calls
+      Cache.setProxyPropertiesFromPreferences();
+
       desktop.setVisible(true);
-      desktop.startServiceDiscovery();
-      if (!aparser.contains("nousagestats"))
-      {
-        startUsageStats(desktop);
-      }
-      else
-      {
-        System.err.println("CMD [-nousagestats] executed successfully!");
-      }
 
-      if (!aparser.contains("noquestionnaire"))
+      if (!Platform.isJS())
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
       {
-        String url = aparser.getValue("questionnaire");
-        if (url != null)
+
+        /**
+         * 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())
         {
-          // Start the desktop questionnaire prompter with the specified
-          // questionnaire
-          Cache.log.debug("Starting questionnaire url at " + url);
-          desktop.checkForQuestionnaire(url);
-          System.out.println(
-                  "CMD questionnaire[-" + url + "] executed successfully!");
+          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]);
+          }
+        }
+
+        if (!aparser.contains("nowebservicediscovery"))
+        {
+          desktop.startServiceDiscovery();
+        }
+        if (!aparser.contains("nousagestats"))
+        {
+          startUsageStats(desktop);
         }
         else
         {
-          if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+          System.err.println("CMD [-nousagestats] executed successfully!");
+        }
+
+        if (!aparser.contains("noquestionnaire"))
+        {
+          String url = aparser.getValue("questionnaire");
+          if (url != null)
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            // String defurl =
-            // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
-            // //
-            String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
-            Cache.log.debug(
-                    "Starting questionnaire with default url: " + defurl);
-            desktop.checkForQuestionnaire(defurl);
+            Console.debug("Starting questionnaire url at " + url);
+            desktop.checkForQuestionnaire(url);
+            System.out.println("CMD questionnaire[-" + url
+                    + "] executed successfully!");
+          }
+          else
+          {
+            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            {
+              // Start the desktop questionnaire prompter with the specified
+              // questionnaire
+              // String defurl =
+              // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+              // //
+              String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
+              Console.debug(
+                      "Starting questionnaire with default url: " + defurl);
+              desktop.checkForQuestionnaire(defurl);
+            }
           }
         }
-      }
-      else
-      {
-        System.err.println("CMD [-noquestionnaire] executed successfully!");
-      }
+        else
+        {
+          System.err
+                  .println("CMD [-noquestionnaire] executed successfully!");
+        }
 
-      if (!aparser.contains("nonews")
-              || Cache.getProperty("NONEWS") == null)
+        if (!aparser.contains("nonews")
+                || Cache.getProperty("NONEWS") == null)
+        {
+          desktop.checkForNews();
+        }
+
+        if (!aparser.contains("nohtmltemplates")
+                || Cache.getProperty("NOHTMLTEMPLATES") == null)
+        {
+          BioJsHTMLOutput.updateBioJS();
+        }
+      }
+    }
+    // Run Commands from cli
+    cmds = new Commands(argparser, headlessArg);
+    boolean commandsSuccess = cmds.argsWereParsed();
+    if (commandsSuccess)
+    {
+      if (headlessArg)
       {
-        desktop.checkForNews();
+        Jalview.exit("Successfully completed commands in headless mode", 0);
       }
-
-      if (!aparser.contains("nohtmltemplates")
-              || Cache.getProperty("NOHTMLTEMPLATES") == null)
+      Console.info("Successfully completed commands");
+    }
+    else
+    {
+      if (headlessArg)
       {
-        BioJsHTMLOutput.updateBioJS();
+        Jalview.exit("Error when running Commands in headless mode", 1);
       }
+      Console.warn("Error when running commands");
     }
 
-    // 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)
+    // Check if JVM and compile version might cause problems and log if it
+    // might.
+    if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
     {
-      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();
+      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
@@ -420,9 +707,9 @@ public class Jalview
 
     if (file == null && desktop == null)
     {
-      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)
@@ -436,20 +723,29 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      protocol = AppletFormatAdapter.checkProtocol(file);
-
-      if (protocol == DataSourceType.FILE)
+      if (!Platform.isJS())
+      /**
+       * ignore in JavaScript -- can't just file existence - could load it?
+       * 
+       * @j2sIgnore
+       */
       {
-        if (!(new File(file)).exists())
+        if (!HttpUtils.startsWithHttpOrHttps(file))
         {
-          System.out.println("Can't find " + file);
-          if (headless)
+          if (!(new File(file)).exists())
           {
-            System.exit(1);
+            if (headless)
+            {
+              Jalview.exit(
+                      "Can't find file '" + file + "' in headless mode", 1);
+            }
+            Console.warn("Can't find file'" + file + "'");
           }
         }
       }
 
+      protocol = AppletFormatAdapter.checkProtocol(file);
+
       try
       {
         format = new IdentifyFile().identify(file, protocol);
@@ -478,7 +774,7 @@ public class Jalview
           if (cs != null)
           {
             System.out.println(
-                    "CMD [-color " + data + "] executed successfully!");
+                    "CMD [-colour " + data + "] executed successfully!");
           }
           af.changeColour(cs);
         }
@@ -652,18 +948,20 @@ public class Jalview
             }
             else
             {
-              if (af.saveAlignment(file, outFormat))
+              af.saveAlignment(file, outFormat);
+              if (af.isSaveAlignmentSuccessful())
               {
-                System.out.println("Written alignment in " + format
-                        + " format to " + file);
+                System.out.println("Written alignment in "
+                        + outFormat.getName() + " format to " + file);
               }
               else
               {
                 System.out.println("Error writing file " + file + " in "
-                        + format + " format!!");
+                        + outFormat.getName() + " format!!");
               }
             }
           }
+
         }
 
         while (aparser.getSize() > 0)
@@ -672,17 +970,25 @@ public class Jalview
         }
       }
     }
+
     AlignFrame startUpAlframe = null;
     // We'll only open the default file if the desktop is visible.
     // And the user
     // ////////////////////
 
-    if (!headless && file == null
-            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+    if (!Platform.isJS() && !headless && file == null
+            && 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(
@@ -693,7 +999,7 @@ public class Jalview
         file.replace("_2_3", "_2_7");
         file.replace("2_7.jar", "2_7.jvp");
         // and remove the stale setting
-        jalview.bin.Cache.removeProperty("STARTUP_FILE");
+        Cache.removeProperty("STARTUP_FILE");
       }
 
       protocol = AppletFormatAdapter.checkProtocol(file);
@@ -715,6 +1021,10 @@ 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.
     }
 
@@ -746,8 +1056,8 @@ 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");
@@ -768,71 +1078,64 @@ 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.isAMac())
+      if (Platform.isMac())
       {
         setMacLookAndFeel();
       }
@@ -841,28 +1144,33 @@ public class Jalview
 
   private static boolean setCrossPlatformLookAndFeel()
   {
-    return setGenericLookAndFeel(false);
+    boolean set = false;
+    try
+    {
+      UIManager.setLookAndFeel(
+              UIManager.getCrossPlatformLookAndFeelClassName());
+      set = true;
+    } catch (Exception ex)
+    {
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
+    }
+    return set;
   }
 
   private static boolean setSystemLookAndFeel()
   {
-    return setGenericLookAndFeel(true);
-  }
-
-  private static boolean setGenericLookAndFeel(boolean system)
-  {
     boolean set = false;
     try
     {
-      UIManager.setLookAndFeel(
-              system ? UIManager.getSystemLookAndFeelClassName()
-                      : UIManager.getCrossPlatformLookAndFeelClassName());
+      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
       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;
   }
@@ -876,9 +1184,10 @@ 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;
@@ -888,9 +1197,9 @@ 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;
   }
@@ -913,32 +1222,145 @@ 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()
   {
     boolean set = false;
     System.setProperty("com.apple.mrj.application.apple.menu.about.name",
-            "Jalview");
+            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;
   }
 
@@ -1000,17 +1422,17 @@ 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);
@@ -1152,19 +1574,12 @@ 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()
@@ -1176,4 +1591,22 @@ public class Jalview
   {
     Jalview.currentAlignFrame = currentAlignFrame;
   }
+
+  protected Commands getCommands()
+  {
+    return cmds;
+  }
+
+  public static void exit(String message, int exitcode)
+  {
+    System.err.println("####### EXITING HERE!");
+    Console.debug("Using Jalview.exit");
+    if (message != null)
+      if (exitcode == 0)
+        Console.info(message);
+      else
+        Console.error(message);
+    if (exitcode > -1)
+      System.exit(exitcode);
+  }
 }