X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3ffcdd03345cedddd8d039bc624a38f7037b46cb;hb=3d64f036a9efc527f8f45ef43ead4c3bb64ae448;hp=83efe7d162086c484df238589891a99a815208eb;hpb=bd2ad93a3ea4075bc45528e3505e9510ffde835d;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 83efe7d..3ffcdd0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -449,7 +449,7 @@ public class Jalview implements JalviewObjectI
       }
       else if (bootstrapArgs.contains(Arg.DEBUG))
       {
-        logLevel = "DEBUG";
+        logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO";
       }
       if (logLevel == null && !(bootstrapProperties == null))
       {
@@ -837,36 +837,40 @@ public class Jalview implements JalviewObjectI
     }
 
     // Run Commands from cli
-    cmds = new Commands(argparser, headlessArg);
-    cmds.processArgs();
-    boolean commandsSuccess = cmds.argsWereParsed();
-
-    if (commandsSuccess)
+    boolean commandsSuccess = false;
+    if (!(argparser.isMixedStyle() || argparser.isOldStyle()))
     {
-      if (headlessArg)
+      cmds = new Commands(argparser, headlessArg);
+      cmds.processArgs();
+      commandsSuccess = cmds.argsWereParsed();
+
+      if (commandsSuccess)
       {
-        if (argparser.getBoolean(Arg.NOQUIT))
+        if (headlessArg)
         {
-          Console.warn(
-                  "Completed " + Arg.HEADLESS.getName() + " commands, but "
-                          + Arg.NOQUIT + " is set so not quitting!");
-        }
-        else
-        {
-          Jalview.exit("Successfully completed commands in headless mode",
-                  ExitCode.OK);
+          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",
+                    ExitCode.OK);
+          }
         }
+        Console.info("Successfully completed commands");
       }
-      Console.info("Successfully completed commands");
-    }
-    else
-    {
-      if (headlessArg)
+      else
       {
-        Jalview.exit("Error when running Commands in headless mode",
-                ExitCode.ERROR_RUNNING_COMMANDS);
+        if (headlessArg)
+        {
+          Jalview.exit("Error when running Commands in headless mode",
+                  ExitCode.ERROR_RUNNING_COMMANDS);
+        }
+        Console.warn("Error when running commands");
       }
-      Console.warn("Error when running commands");
     }
 
     // Check if JVM and compile version might cause problems and log if it