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Calculating frequencies from .mp3 or .wav files?

I'm trying to do some note recognition on mp3 or wav files.

The problem is: How do I use the FFT on the files?

I prefer Java solutions, but I'm up for suggestions.

Spectrum Analysis using Java, Sampling Frequency, Folding Frequency, and the FFT Algorithm http://www.developer.com/java/other/article.php/3380031

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