Calling another program and waiting for output

Hi,
I'm writing a program that passes a file created for an application called Net Sim but has to wait for the output. Net Sim lies in another directory from the java files and I don't know how to call the program with the file created as a parameter, such as:
ns2 network1.tcl
where 'ns2' is the dos command to run net sim and 'network1.tcl' is a file passed as a parameter to the program.
I've tried
try{
Runtime r = Runtime.getRuntime();
r.exec(" <directory> ");
}catch(IOException e){
System.out.println("Error " +e);
This doesn't work though and I could use some help, as well as how to save the file created by the program in another directory.
Finally, I need to know how to make the program wait for the output from net sim which is a file I intend to use. Can I do this with a while loop etc.?
I thank you in advance for any help,
Regards,
Gary.

Here's an article from JavaWorld describing some of the pitfalls when using Runtime.exec() that might help you:
http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html

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