JNI only adds a few clock cycles to every call. On my machine it was like 5-10 nanoseconds.
So if your function call takes 1millisecond without JNI, it will take 1,000005 milliseconds with JNI.
IMO this is negligible overhead. Unless of course you are calling very short running JNI functions (a few nanoseconds) in a tight loop.
But if that is being done, your are most certainly doing it VERY WRONG



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