X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1f869263b2a54d37cd772aa701fc780ee8f4bcec;hb=5e462885d21193706d23e42cd5e21e88763788cb;hp=895268d3f060a9be394f35fddbcc8050b5955e4c;hpb=adff51745d97ff4fd30a188a68efa29cc83202e3;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 895268d..1f86926 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -49,9 +49,11 @@ import java.util.Vector;
 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;
@@ -68,6 +70,7 @@ import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.bin.argparser.Arg;
 import jalview.bin.argparser.Arg.Opt;
+import jalview.bin.argparser.Arg.Type;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
@@ -76,6 +79,7 @@ import jalview.gui.Desktop;
 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;
@@ -87,6 +91,7 @@ import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -134,6 +139,17 @@ public class Jalview
 
   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())
@@ -289,36 +305,21 @@ public class Jalview
       System.setSecurityManager(null);
     }
 
-    if (args == null)
-      args = new String[] {};
-
-    // 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)
+    if (args == null || args.length == 0 || (args.length == 1
+            && (args[0] == null || args[0].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();
+      args = new String[] {};
     }
 
     // get args needed before proper ArgParser
-    BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+    bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
 
     if (!Platform.isJS())
     {
       // are we being --quiet ?
       if (bootstrapArgs.contains(Arg.QUIET))
       {
+        QUIET = true;
         OutputStream devNull = new OutputStream()
         {
 
@@ -335,29 +336,77 @@ public class Jalview
           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"));
+      if (bootstrapArgs.contains(Arg.HELP)
+              || bootstrapArgs.contains(Arg.VERSION))
+      {
+        QUIET = true;
+      }
+    }
 
-    String val = System.getProperty("sys.install4jVersion");
-    if (val != null)
+    // set individual session preferences
+    if (bootstrapArgs.contains(Arg.P))
     {
-      System.out.println("Install4j version: " + val);
+      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);
+        }
+      }
     }
-    val = System.getProperty("installer_template_version");
-    if (val != 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)
     {
-      System.out.println("Install4j template version: " + val);
+      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("launcher_version");
-    if (val != null)
+
+    if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
     {
-      System.out.println("Launcher 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);
+      }
     }
 
     if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
@@ -367,10 +416,17 @@ public class Jalview
 
     // 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(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);
@@ -410,11 +466,29 @@ public class Jalview
       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);
         }
@@ -428,7 +502,7 @@ public class Jalview
     });
 
     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
@@ -441,13 +515,11 @@ public class Jalview
               "test/jalview/bin/testProps.jvprops", usrPropsFile);
     }
 
-    // new ArgParser
-    ArgParser argparser;
     // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
       argparser = ArgParser.parseArgFiles(
-              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getValueList(Arg.ARGFILE),
               bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
               bootstrapArgs);
     }
@@ -467,26 +539,33 @@ public class Jalview
     {
       if (bootstrapArgs.contains(Arg.HELP))
       {
-        System.out.println(Arg.usage());
+        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"))
       {
+        /*
+         * Now using new usage statement.
         showUsage();
+        */
+        System.out.println(Arg.usage());
         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!
@@ -494,7 +573,7 @@ public class Jalview
       // 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)
@@ -517,7 +596,7 @@ public class Jalview
     List<String> setprops = new ArrayList<>();
     if (bootstrapArgs.contains(Arg.SETPROP))
     {
-      setprops = bootstrapArgs.getList(Arg.SETPROP);
+      setprops = bootstrapArgs.getValueList(Arg.SETPROP);
     }
     else
     {
@@ -586,7 +665,7 @@ public class Jalview
 
     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();
@@ -661,18 +740,18 @@ public class Jalview
           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);
@@ -715,8 +794,8 @@ public class Jalview
 
         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();
         }
@@ -731,11 +810,27 @@ public class Jalview
     // Run Commands from cli
     cmds = new Commands(argparser, headlessArg);
     boolean commandsSuccess = cmds.argsWereParsed();
+
     if (commandsSuccess)
     {
       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
+        {
+          // record usage stats if in headless mode
+          if (Cache.getDefault("USAGESTATS", false))
+          {
+            Cache.initGoogleTracker(headlessArg);
+          }
+          Jalview.exit("Successfully completed commands in headless mode",
+                  0);
+        }
       }
       Console.info("Successfully completed commands");
     }
@@ -917,9 +1012,7 @@ public class Jalview
             ex.printStackTrace(System.err);
           }
         }
-        // TODO - load PDB structure(s) to alignment JAL-629
-        // (associate with identical sequence in alignment, or a specified
-        // sequence)
+
         if (groovyscript != null)
         {
           // Execute the groovy script after we've done all the rendering stuff
@@ -933,100 +1026,109 @@ public class Jalview
         String imageName = "unnamed.png";
         while (aparser.getSize() > 1)
         {
-          String outputFormat = aparser.nextValue();
-          file = aparser.nextValue();
-
-          if (outputFormat.equalsIgnoreCase("png"))
-          {
-            af.createPNG(new File(file));
-            imageName = (new File(file)).getName();
-            System.out.println("Creating PNG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("svg"))
-          {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            af.createSVG(imageFile);
-            System.out.println("Creating SVG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("html"))
+          try
           {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-            htmlSVG.exportHTML(file);
+            String outputFormat = aparser.nextValue();
+            file = aparser.nextValue();
 
-            System.out.println("Creating HTML image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("biojsmsa"))
-          {
-            if (file == null)
+            if (outputFormat.equalsIgnoreCase("png"))
             {
-              System.err.println("The output html file must not be null");
-              return;
+              System.out.println("Creating PNG image: " + file);
+              af.createPNG(new File(file));
+              imageName = (new File(file)).getName();
+              continue;
             }
-            try
+            else if (outputFormat.equalsIgnoreCase("svg"))
             {
-              BioJsHTMLOutput.refreshVersionInfo(
-                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-            } catch (URISyntaxException e)
+              System.out.println("Creating SVG image: " + file);
+              File imageFile = new File(file);
+              imageName = imageFile.getName();
+              af.createSVG(imageFile);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("html"))
             {
-              e.printStackTrace();
+              File imageFile = new File(file);
+              imageName = imageFile.getName();
+              HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+
+              System.out.println("Creating HTML image: " + file);
+              htmlSVG.exportHTML(file);
+              continue;
             }
-            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-            bjs.exportHTML(file);
-            System.out
-                    .println("Creating BioJS MSA Viwer HTML file: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("imgMap"))
-          {
-            af.createImageMap(new File(file), imageName);
-            System.out.println("Creating image map: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("eps"))
-          {
-            File outputFile = new File(file);
-            System.out.println(
-                    "Creating EPS file: " + outputFile.getAbsolutePath());
-            af.createEPS(outputFile);
-            continue;
-          }
-          FileFormatI outFormat = null;
-          try
-          {
-            outFormat = FileFormats.getInstance().forName(outputFormat);
-          } catch (Exception formatP)
-          {
-            System.out.println("Couldn't parse " + outFormat
-                    + " as a valid Jalview format string.");
-          }
-          if (outFormat != null)
-          {
-            if (!outFormat.isWritable())
+            else if (outputFormat.equalsIgnoreCase("biojsmsa"))
             {
+              if (file == null)
+              {
+                System.err.println("The output html file must not be null");
+                return;
+              }
+              try
+              {
+                BioJsHTMLOutput.refreshVersionInfo(
+                        BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+              } catch (URISyntaxException e)
+              {
+                e.printStackTrace();
+              }
+              BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
               System.out.println(
-                      "This version of Jalview does not support alignment export as "
-                              + outputFormat);
+                      "Creating BioJS MSA Viwer HTML file: " + file);
+              bjs.exportHTML(file);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("imgMap"))
+            {
+              System.out.println("Creating image map: " + file);
+              af.createImageMap(new File(file), imageName);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("eps"))
+            {
+              File outputFile = new File(file);
+              System.out.println(
+                      "Creating EPS file: " + outputFile.getAbsolutePath());
+              af.createEPS(outputFile);
+              continue;
+            }
+
+            FileFormatI outFormat = null;
+            try
+            {
+              outFormat = FileFormats.getInstance().forName(outputFormat);
+            } catch (Exception formatP)
+            {
+              System.out.println("Couldn't parse " + outFormat
+                      + " as a valid Jalview format string.");
             }
-            else
+            if (outFormat != null)
             {
-              af.saveAlignment(file, outFormat);
-              if (af.isSaveAlignmentSuccessful())
+              if (!outFormat.isWritable())
               {
-                System.out.println("Written alignment in "
-                        + outFormat.getName() + " format to " + file);
+                System.out.println(
+                        "This version of Jalview does not support alignment export as "
+                                + outputFormat);
               }
               else
               {
-                System.out.println("Error writing file " + file + " in "
-                        + outFormat.getName() + " format!!");
+                af.saveAlignment(file, outFormat);
+                if (af.isSaveAlignmentSuccessful())
+                {
+                  System.out.println("Written alignment in "
+                          + outFormat.getName() + " format to " + file);
+                }
+                else
+                {
+                  System.out.println("Error writing file " + file + " in "
+                          + outFormat.getName() + " format!!");
+                }
               }
             }
+          } catch (ImageOutputException ioexc)
+          {
+            System.out.println(
+                    "Unexpected error whilst exporting image to " + file);
+            ioexc.printStackTrace();
           }
 
         }
@@ -1045,7 +1147,8 @@ public class Jalview
 
     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())
     /**
@@ -1123,88 +1226,102 @@ public class Jalview
 
   private static void setLookAndFeel()
   {
-    // 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");
-    String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
-    String laf = "none";
-    if (lafProp != null)
-    {
-      laf = lafProp;
-    }
-    else if (lafSetting != null)
-    {
-      laf = lafSetting;
-    }
-    boolean lafSet = false;
-    switch (laf)
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-    case "crossplatform":
-      lafSet = setCrossPlatformLookAndFeel();
-      if (!lafSet)
+      // 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");
+      String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
+      String laf = "none";
+      if (lafProp != null)
       {
-        Console.error("Could not set requested laf=" + laf);
+        laf = lafProp;
       }
-      break;
-    case "system":
-      lafSet = setSystemLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "gtk":
-      lafSet = setGtkLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "metal":
-      lafSet = setMetalLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "nimbus":
-      lafSet = setNimbusLookAndFeel();
-      if (!lafSet)
+      else if (lafSetting != null)
       {
-        Console.error("Could not set requested laf=" + laf);
+        laf = lafSetting;
       }
-      break;
-    case "flat":
-      lafSet = setFlatLookAndFeel();
-      if (!lafSet)
+      boolean lafSet = false;
+      switch (laf)
       {
-        Console.error("Could not set requested laf=" + laf);
+      case "crossplatform":
+        lafSet = setCrossPlatformLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "system":
+        lafSet = setSystemLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "gtk":
+        lafSet = setGtkLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "metal":
+        lafSet = setMetalLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "nimbus":
+        lafSet = setNimbusLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "flat":
+        lafSet = setFlatLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "mac":
+        lafSet = setMacLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "none":
+        break;
+      default:
+        Console.error("Requested laf=" + laf + " not implemented");
       }
-      break;
-    case "mac":
-      lafSet = setMacLookAndFeel();
       if (!lafSet)
       {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "none":
-      break;
-    default:
-      Console.error("Requested laf=" + laf + " not implemented");
-    }
-    if (!lafSet)
-    {
-      setSystemLookAndFeel();
-      if (Platform.isLinux())
-      {
-        setLinuxLookAndFeel();
-      }
-      if (Platform.isMac())
-      {
-        setMacLookAndFeel();
+        // Flatlaf default for everyone!
+        lafSet = setFlatLookAndFeel();
+        if (!lafSet)
+        {
+          setSystemLookAndFeel();
+        }
+        if (Platform.isLinux())
+        {
+          setLinuxLookAndFeel();
+        }
+        if (Platform.isMac())
+        {
+          setMacLookAndFeel();
+        }
       }
     }
   }
@@ -1394,6 +1511,8 @@ public class Jalview
       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));
@@ -1431,6 +1550,7 @@ public class Jalview
     return set;
   }
 
+  /*
   private static void showUsage()
   {
     System.out.println(
@@ -1473,6 +1593,7 @@ public class Jalview
                     + "-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)
   {
@@ -1480,10 +1601,9 @@ public class Jalview
      * start a User Config prompt asking if we can log usage statistics.
      */
     PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
-            "USAGESTATS", "Jalview Usage Statistics",
-            "Do you want to help make Jalview better by enabling "
-                    + "the collection of usage statistics with Google Analytics ?"
-                    + "\n\n(you can enable or disable usage tracking in the preferences)",
+            "USAGESTATS",
+            MessageManager.getString("prompt.google_analytics_title"),
+            MessageManager.getString("prompt.google_analytics"),
             new Runnable()
             {
               @Override
@@ -1666,18 +1786,50 @@ public class Jalview
 
   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 string values
+  /******************************
+   * 
+   * TEST OUTPUT METHODS
+   * 
+   ******************************/
+  /**
+   * method for reporting string values parsed/processed during tests
+   * 
    */
   protected static void testoutput(ArgParser ap, Arg a, String s1,
           String s2)
@@ -1701,6 +1853,10 @@ public class Jalview
     testoutput(true, a, s1, s2);
   }
 
+  /**
+   * method for reporting string values parsed/processed during tests
+   */
+
   protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
           String s2)
   {
@@ -1725,6 +1881,9 @@ public class Jalview
     testoutput(true, a, s1, s2);
   }
 
+  /**
+   * report value set for string values parsed/processed during tests
+   */
   private static void testoutput(boolean yes, Arg a, String s1, String s2)
   {
     if (yes && ((s1 == null && s2 == null)
@@ -1736,7 +1895,7 @@ public class Jalview
   }
 
   /*
-   * testoutput for boolean values
+   * testoutput for boolean and unary values
    */
   protected static void testoutput(ArgParser ap, Arg a)
   {
@@ -1779,7 +1938,15 @@ public class Jalview
 
   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);
   }
 }