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In my experience, absolutely. However, It also depends on the size of your arrays and the frequency with which you pass them back and forth through the JNI. JNI calls are expensive, so if you're making many calls, especially on small arrays, it may not be worth it.
Would it still maintain performance advantage over other java based implementations, like https://sites.google.com/site/piotrwendykier/software/jtransforms (single threaded)?
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