I have an array of audio data I am passing to a reader:
recorder.read(audioData,0,bufferSize);
The instantiation is as follows:
Some of the details will depend on the purpose of your FFT.
The length of the FFT required depends on the frequency resolution and time accuracy (which are inversely related), that you wish in your analysis, which may or may not be anywhere near the length of an audio input buffer. Given those differences in length, you may have to combine multiple buffers, segment a single buffer, or some combination of the two, to get the FFT window length that meets your analysis requirements.