JAL-629 Remove argfiles from the hashset of used argfiles once it has been used....

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 1b8e6ad..155f69e 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -318,9 +318,13 @@ public class ArgParser
     }
 
     if (bsa != null)
+    {
       this.bootstrapArgs = bsa;
+    }
     else
+    {
       this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+    }
     parse(args, initsubstitutions, allowPrivate);
   }
 

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index d32a5b2..5c21d03 100644 (file)
--- 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)