X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FBootstrapArgs.java;h=5c21d03e5768be034f119e2add7669b9e1b0c39e;hb=df111c6157ad56b53c87eb2b20a6856eeea2d0fc;hp=d32a5b29f1ef394754ff71b8d5a928aee929e897;hpb=58735c979dbb573eb12d57e33ef7d6e3f3a82c8e;p=jalview.git

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index d32a5b2..5c21d03 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -214,6 +214,13 @@ public class BootstrapArgs
         }
       }
     }
+
+    // if in an argfile, remove it from the hashset so it can be re-used in
+    // another argfile
+    if (inArgFile != null)
+    {
+      argFiles.remove(inArgFile);
+    }
   }
 
   public boolean contains(Arg a)