From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 11 Oct 2023 12:14:30 +0000 (+0100)
Subject: JAL-629 Remove argfiles from the hashset of used argfiles once it has been used.... 
X-Git-Tag: Release_2_11_4_0~131^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=df111c6157ad56b53c87eb2b20a6856eeea2d0fc;p=jalview.git

JAL-629 Remove argfiles from the hashset of used argfiles once it has been used.  More like (though not) a stack of argfiles
---

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 1b8e6ad..155f69e 100644
--- 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
--- 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)