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byte array to short array and back again in java

I'm having some issues taking audio data stored in a byte array, converting it to a big-endian short array, encoding it, then changing it back into a byte array. Here is what I have. The original audio data is stored in audioBytes2. I am using the same format for decode with a minus on the cos function instead. Unfortunately, changing the byte and short data types is non-negotiable.

    short[] audioData = null;
    int nlengthInSamples = audioBytes2.length / 2;
    audioData = new short[nlengthInSamples];

    for (int i = 0; i < nlengthInSamples; i++) {
       short MSB = (short) audioBytes2[2*i+1];
       short LSB = (short) audioBytes2[2*i];
       audioData[i] = (short) (MSB << 8 | (255 & LSB));
    }

    int i = 0;
    while (i < audioData.length) {
        audioData[i] = (short)(audioData[i] + (short)5*Math.cos(2*Math.PI*i/(((Number)EncodeBox.getValue()).intValue())));
        i++;
    }

    short x = 0;
    i = 0;
    while (i < audioData.length) {
        x = audioData[i];
        audioBytes2[2*i+1] = (byte)(x >>> 0);
        audioBytes2[2*i] = (byte)(x >>> 8);
        i++;
    }

I have done everything that I can think of to make this work, but the closest I've come is getting it to work every other encode/decode and I have no idea why. Thanks for any help.

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I also suggest you try ByteBuffer.

byte[] bytes = {};
short[] shorts = new short[bytes.length/2];
// to turn bytes to shorts as either big endian or little endian. 
ByteBuffer.wrap(bytes).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().get(shorts);

// to turn shorts back to bytes.
byte[] bytes2 = new byte[shortsA.length * 2];
ByteBuffer.wrap(bytes2).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().put(shortsA);

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