JAL-629 Fix --structureimage and options

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e229079..6c33812 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -811,6 +811,7 @@ public class Jalview
     }
     // Run Commands from cli
     cmds = new Commands(argparser, headlessArg);
+    cmds.processArgs();
     boolean commandsSuccess = cmds.argsWereParsed();
 
     if (commandsSuccess)
@@ -1781,7 +1782,7 @@ public class Jalview
     Jalview.currentAlignFrame = currentAlignFrame;
   }
 
-  protected Commands getCommands()
+  public Commands getCommands()
   {
     return cmds;
   }