{
if (argFiles.contains(inArgFile))
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Looped argfiles detected: '" + inArgFile.getPath() + "'");
return;
}
// 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))
{
- System.err.println("###### Found an output");
- System.err.println("###### val='" + val + "'");
- System.err
- .println("###### next arg='" + args.get(i + 1) + "'");
- 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;
- System.err.println("###### Expecting output to stdout");
}
}
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));
}
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)
{
}
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))