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executing a jar  RSS feed

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I'm not sure if this is something very specific to my class or not. When I run a dot class file from the dos prompt using the java command, it runs fine. When I compile the same class file into a jar file (setting up the manifest file to point to this class as its main class), and run the jar file using the java command, I get an exception when I exit.
The exception is an IllegalThreadStateException.
It appears that a class file triggered from within the jar and triggered from the dos prompt are not in the same state. Is there anything else I need to set into the manifest or something? I don't have access to the source code of this class file - I'm only running it.
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