JAL-629 Doing things with the command line arguments

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1428906..6f000dd 100755 (executable)
--- 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;