X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2Fargparser%2FBootstrapArgs.java;h=d32a5b29f1ef394754ff71b8d5a928aee929e897;hb=61c5b7072f14e1328bde5b5bf896affd3eb5a626;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..d32a5b2 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;
             }
@@ -284,7 +292,7 @@ public class BootstrapArgs
   private void add(Arg a, Type t, String s)
   {
     List<Map.Entry<Type, String>> l = getOrCreateList(a);
-    if (a.hasOption(Opt.MULTI) || l.size() == 0)
+    if (a.hasOption(Opt.MULTIVALUE) || l.size() == 0)
     {
       l.add(entry(t, s));
     }
@@ -293,7 +301,7 @@ public class BootstrapArgs
   private void addAll(Arg a, Type t, List<String> al)
   {
     List<Map.Entry<Type, String>> l = getOrCreateList(a);
-    if (a.hasOption(Opt.MULTI))
+    if (a.hasOption(Opt.MULTIVALUE))
     {
       for (String s : al)
       {
@@ -376,7 +384,7 @@ public class BootstrapArgs
     }
     else if (this.contains(Arg.HEADLESS))
     {
-      // --headless, --noheadless specified => use value
+      // --headless has been specified on the command line => headless
       isHeadless = this.getBoolean(Arg.HEADLESS);
     }
     else if (this.argsHaveOption(Opt.OUTPUTFILE))