JAL-629 Fix --headless for new args. Fix progressbar for non-headless commands. Add...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 04cf2a3..c792a96 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -379,7 +379,16 @@ public class Jalview
     }
 
     // new ArgParser
-    ArgParser argparser = new ArgParser(args);
+    ArgParser argparser;
+    // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
+    if (bootstrapArgs.containsKey(Arg.ARGFILE))
+    {
+      argparser = ArgParser.parseArgFile(bootstrapArgs.get(Arg.ARGFILE));
+    }
+    else
+    {
+      argparser = new ArgParser(args);
+    }
 
     if (!Platform.isJS())
     /**
@@ -608,7 +617,7 @@ public class Jalview
       }
     }
     // Run Commands from cli
-    boolean commandsSuccess = Commands.processArgs(argparser, headless);
+    boolean commandsSuccess = Commands.processArgs(argparser, headlessArg);
     if (commandsSuccess)
     {
       Console.info("Successfully completed commands");
@@ -937,7 +946,10 @@ public class Jalview
     // ////////////////////
 
     if (!Platform.isJS() && !headless && file == null
-            && Cache.getDefault("SHOW_STARTUP_FILE", true))
+            && Cache.getDefault("SHOW_STARTUP_FILE", true)
+            && !Commands.commandArgsProvided())
+    // don't open the startup file if command line args have been processed
+    // (&& !Commands.commandArgsProvided())
     /**
      * Java only
      *