X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=6f000ddacda9043b8e6339ba4c4d95b1f1efa7d1;hb=4d4e95690af1676f81cc520ba7618c3e69ba99ba;hp=142890675af84e3f5ee3bb998bd75f73f39f1071;hpb=0f771e8985d361950c537aa52269746fe8ab456b;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1428906..6f000dd 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -298,7 +298,10 @@ public class Jalview
     // report Jalview version
     Cache.loadBuildProperties(true);
 
+    // old ArgsParser
     ArgsParser aparser = new ArgsParser(args);
+    // new ArgParser
+    ArgParser argparser = new ArgParser(args);
     boolean headless = false;
 
     String usrPropsFile = aparser.getValue("props");
@@ -554,6 +557,8 @@ public class Jalview
       }.start();
     }
 
+    Commands.processArgs(argparser, headless);
+
     String file = null, data = null;
     FileFormatI format = null;
     DataSourceType protocol = null;