X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=d0e76f2014cdcaa845b343202f8d183909e9a8b3;hb=404d5b51a7a7781ad6924df6a7ce63c754370f16;hp=0870ecb0b42cf62afa6b10a7baef29416dcf8b55;hpb=ad47e73ed0aaa1a24a976802084c3912422f2be7;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0870ecb..d0e76f2 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -432,12 +432,14 @@ public class Jalview
     // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
-      argparser = ArgParser
-              .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
+      argparser = ArgParser.parseArgFiles(
+              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
     else
     {
-      argparser = new ArgParser(args);
+      argparser = new ArgParser(args,
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
 
     if (!Platform.isJS())