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why do i get an exception?

 
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I am running this on a windows machine. It goes into the windows clause and it assigns cls to my var, but I get an IOException and my cmd window is not cleared. Does anyone know why?
 
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Probably because here's no "cls.exe"; it's a command built into the shell. You'd have to exec something like "cmd /E cls" -- i.e., run the shell, and tell it to execute the cls command.

But -- and this is a big "but" -- that shell wouldn't be connected to a terminal window; it takes input from the Java process. So the cls command would have no effect!

There are two ways to clear a terminal window from a Java program: first, send a (platform dependent) escape sequence to the terminal to clear it (Google for "ANSI escape codes" to learn more) or just print a bunch of blank lines to make the contents of the screen scroll away!
 
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Navigate yourself around pitfalls related to the Runtime.exec() method
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