X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FBootstrapArgs.java;h=a9892062741291b0aed7a7fed8ea3e710303a1c7;hb=585dbfeb3c901e3ca234a74c51a01c9e84132ef9;hp=32eb91a905c62781a337a8b112ef731c5bbe904a;hpb=c932f0e85a8852824cdd8ce790af68682732c85c;p=jalview.git

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index 32eb91a..a989206 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -152,11 +152,19 @@ public class BootstrapArgs
           // not a bootstrap arg
 
           // make a check for an output going to stdout
-          if (a != null && a.hasOption(Opt.OUTPUTFILE))
+          if (a != null && a.hasOption(Opt.OUTPUTFILE)
+                  && a.hasOption(Opt.STDOUT))
           {
-            if ((val == null && i + 1 < args.size()
-                    && ArgParser.STDOUTFILENAME.equals(args.get(i + 1)))
-                    || ArgParser.STDOUTFILENAME.equals(val))
+            if (val == null && i + 1 < args.size())
+            {
+              val = args.get(i + 1);
+            }
+            if (val.startsWith("[") && val.indexOf(']') > 0)
+            {
+              val = val.substring(val.indexOf(']') + 1);
+            }
+
+            if (ArgParser.STDOUTFILENAME.equals(val))
             {
               this.outputToStdout = true;
             }