Merge branch 'develop' into feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_na...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cf73c81..615e318 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -49,6 +49,7 @@ 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;
@@ -68,6 +69,7 @@ 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;
@@ -300,8 +302,11 @@ public class Jalview
       System.setSecurityManager(null);
     }
 
-    if (args == null)
+    if (args == null || args.length == 0 || (args.length == 1
+            && (args[0] == null || args[0].length() == 0)))
+    {
       args = new String[] {};
+    }
 
     // get args needed before proper ArgParser
     bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
@@ -344,6 +349,7 @@ public class Jalview
       final File appdir = new File(appdirString);
       new Thread()
       {
+
         @Override
         public void run()
         {
@@ -473,7 +479,7 @@ public class Jalview
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
       argparser = ArgParser.parseArgFiles(
-              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getValueList(Arg.ARGFILE),
               bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
               bootstrapArgs);
     }
@@ -493,7 +499,10 @@ 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"))
@@ -547,7 +556,7 @@ public class Jalview
     List<String> setprops = new ArrayList<>();
     if (bootstrapArgs.contains(Arg.SETPROP))
     {
-      setprops = bootstrapArgs.getList(Arg.SETPROP);
+      setprops = bootstrapArgs.getValueList(Arg.SETPROP);
     }
     else
     {
@@ -765,7 +774,17 @@ public class Jalview
     {
       if (headlessArg)
       {
-        Jalview.exit("Successfully completed commands in headless mode", 0);
+        if (argparser.getBoolean(Arg.NOQUIT))
+        {
+          Console.warn(
+                  "Completed " + Arg.HEADLESS.getName() + " commands, but "
+                          + Arg.NOQUIT + " is set so not quitting!");
+        }
+        else
+        {
+          Jalview.exit("Successfully completed commands in headless mode",
+                  0);
+        }
       }
       Console.info("Successfully completed commands");
     }
@@ -1227,7 +1246,12 @@ public class Jalview
     }
     if (!lafSet)
     {
-      setSystemLookAndFeel();
+      // Flatlaf default for everyone!
+      lafSet = setFlatLookAndFeel();
+      if (!lafSet)
+      {
+        setSystemLookAndFeel();
+      }
       if (Platform.isLinux())
       {
         setLinuxLookAndFeel();
@@ -1424,6 +1448,8 @@ 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));
@@ -1461,6 +1487,7 @@ public class Jalview
     return set;
   }
 
+  /*
   private static void showUsage()
   {
     System.out.println(
@@ -1503,6 +1530,7 @@ 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)
   {
@@ -1696,14 +1724,40 @@ 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);
+    }
   }
 
   /*