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I'm trying to convert the Python program located at
https://github.com/rraval/pied-piper/blob/master/decode.py
to an Android Java file.

The first step is to identify the dominant frequency. I have written the following Java program to do that

private class RecordAudio
 extends AsyncTask<Void, Void, Void> {

 @Override
 protected Void doInBackground(Void... paramVarArgs) 
 int audioSource = AudioSource.MIC;
 int sampleRateInHz = 44100;
 int channelConfig = AudioFormat.CHANNEL_IN_MONO;
 int audioFormat = AudioFormat.ENCODING_PCM_16BIT;
 int bufferSizeInBytes = AudioRecord.getMinBufferSize(sampleRateInHz, channelConfig, audioFormat);
 byte Data = new byte[bufferSizeInBytes];

 AudioRecord audioRecorder = new AudioRecord(audioSource,
 sampleRateInHz,
 channelConfig,
 audioFormat,
 bufferSizeInBytes);
 audioRecorder.startRecording();

 boolean isRecording = true;
 while (isRecording) 
 audioRecorder.read(Data, 0, Data.length);
 fftPrint(Data, bufferSizeInBytes);
 
 return null;
 

 boolean fftPrint(byte waveArray, int bufferSizeInBytes) 
 double HANDSHAKE_START_HZ = 8192;
 double HANDSHAKE_END_HZ = 8192 + 512;
 int len = waveArray.length;
 double waveTransformReal = new double[len];
 double waveTransformImg = new double[len];

 for (int i = 0; i < len; i++) 
 waveTransformReal[i] = waveArray[i]; //copy of original
 waveTransformImg[i] = waveArray[i]; //FFT transformed below
 

 RealDoubleFFT p = new RealDoubleFFT(bufferSizeInBytes);
 p.ft(waveTransformImg);

 //Calculating abs
 double abs = new double[len];
 for (int i = 0; i < len; i++) 
 abs[i] = (Math.sqrt(waveTransformReal[i] * waveTransformReal[i] + waveTransformImg[i] * waveTransformImg[i]));
 

 //calculating maxIndex
 int maxIndex = 0;
 for (int i = 0; i < len; i++) 
 if (abs[i] > abs[maxIndex])
 maxIndex = i;
 

 double dominantFrequency = (maxIndex * 44100) / len;
 if (dominantFrequency > 0) Log.d("Freq: ", String.format("%f", dominantFrequency));

 if (match(dominantFrequency, HANDSHAKE_START_HZ)) 
 Log.i("Handshake start:", "FOUND START");
 
 if (match(dominantFrequency, HANDSHAKE_END_HZ)) 
 Log.i("Handshake end:", "FOUND END");
 return true;
 
 return false;
 

 boolean match(double freq1, double freq2) 
 return (Math.abs(freq1 - freq2) < 20);
 

Note: RealDoubleFFT is from ca.uol.aig.fftpack

Am not sure if I have done it right. I'm getting the frequencies printed in the Logcat, but they are not finding the HANDSHAKE_START_HZ, which is present in the audio being played. What am I doing wrong?

Note that the frequency resolution of a FFT magnitude peak depends on the length of the FFT (and the window, etc.). This length is not specified or constrained in your code, so you won't know whether it is even possible for any FFT result bin to be within 20 Hz of your target frequencies.