To get the contents from a file into Processing, see the examples that come with Processing or search the forum. This is pretty basic and has been covered countless times. You can use loadStrings() and other available methods.

If you want FFT, you could use Minim.

If you want DFT, you could use some other java library, for example JTransforms.

First step: loadStrings(), if you don't already have it...
Then, to create an ArrayList from it, try something like this:

1. ArrayList  list = new ArrayList(Arrays.asList(inputArray));