How to edit audio contents? (sample editing)

Hi, I have a problem in editing a recorded audio. Can anyone please help me with this one? The scenario is this...
I get my audio data by reading right from the line using targetdataline read method. Then I store the data in byte arrays. I tried to edit the values of each byte (in the byte array) by converting it to its short value, then alter its value before storing the new value to the source byte address.. Am I doing the right thing in the conversion and editing process?
My audio configuration is this:
audio format = PCM_SIGNED
sample rate = 8000
sample size in bits = 8
channels = mono
big endian = false
Well, I use this for my cryptographic process in a simple VOIP program. I was having a hard time getting the valid values of the recorded audio stored in the byte array. Can anyone enlighten me with this matter?

I have a "Recorder Class" that simply gets the audio data from the line. Here's some part of my code on how I get my audio data.
synchronized public void run() {
        while( !m_bQuitting ) { //m_bquitting is a bolean variable which tells if the recording thread must be stopped
             byte bs[] = new byte[bytesize];
                m_line.read( bs , 0 , bytesize );
             if( m_bRecording ) {
                    byte[] audio = new byte[bs.length];
                    //loop that initializes the temporary byte array to be encrypted
                                //this simple copies the contents of bs to audio byte array
                    for( int i = 0; i < audio.length && i < bs.length; i++ ){
                         audio[i] = bs;
                    if(rsa != null) {
                         /*encryption*/
                         for(int offset=0; offset < audio.length && offset < bs.length; offset++) {
                              short sample = (short)(audio[offset] & 0xff); //convert byte to short
                              short tmp = rsa.code(sample);
                              audio[offset] = (byte)tmp;
                         /*end of encryption*/
          cs.writebyte( audio );
     }else if( onlyonce ){
          cs.writebyte( ("NT|").getBytes() );
          onlyonce = false;     
m_line.stop();
m_line.close();     
My simple VOIP works well without the encryption process. My real problem here is how can I open/edit the data that is stored in the byte array. Simple conversion of each byte to its short value doesn't seem to solve my problem. My RSA works well on data structures integer, string, double, float, hex, biginteger and etc. I have read some articles that says that audio samples are stored depending on the size of the sample bits used, and in my case its 8 bits (-128 to 127). My perception here is that if each sample is stored in a byte, then there would be a corresponding hexadecimal value for that byte. Am I right?(Can anyone enlighten me with this one???) My plan here is to encrypt and decrypt the audio data byte per byte so I need to get the audio sample data of a recorded audio.
PS:
Sorry for my first post. :)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               

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