To avoid zero padding and compute correctly a subset of the DFT, there are specific FFT algorithms like the Fast fractional Fourier transform: David H. Bailey and P. N. Swarztrauber, "The fractional Fourier transform and applications," SIAM Review, vol. 33 no. 3 (Sep 1991), pg. 389-404

http://crd.lbl.gov/~dhbailey/dhbpapers/fracfft.pdf

I read this article and I think it could be worth to implement such algorithms into JTransforms as it already provides FFT related sub routines (bluestein ...). Of course, it requires to implement Fractional FFT 1D that generalizes FFT 1D ...

What is your opinion ?

Could you estimate the implementation cost / difficulty to implement the Fractional FFT algorithm ?