<java:encoding:dilema/> por Angelos di Avocado

Pasos:

1. convertir los archivos en Inputstream.
2. Buscar el valor hexadecimal del texto --> "encoding="UTF-8"" y "encoding="UTF-16"", siendo estos los siguientes:
   UTF_8 = "656E636F64696E673D225554462D3822"
   UTF_16 = "65006E0063006F00640069006E0067003D0022005500540046002D003100360022"
   
3. Convertir el inputstream en un arreglo de bytes.
4. Extraer los primeros 200 bytes del archivo
5. Buscar/comparar si en esos primeros 200 bytes(del paso 3), existe el valor hexadecimal para UTF8 o UTF16 del paso 2.
6. Heureka

Código:

public class EncodingTest {
private static String       UTF_8    = "656E636F64696E673D225554462D3822";
private static String       UTF_16   =
        "65006E0063006F00640069006E0067003D0022005500540046002D003100360022";
private final static char[] hexArray = "0123456789ABCDEF".toCharArray();

public static InputStream readInputStream(String location) {
    InputStream in = null;
    try {
        in = new FileInputStream(new File(location));
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    }
    return in;
}

public static String testByteEncodingFinder(InputStream inputStream) {
    String ecncodingFormat = null;
    try {
        byte[] bytes = IOUtils.toByteArray(inputStream);
        char[] hexChars = new char[200];
        if (bytes.length > 100)
            for (int i = 0; i < 100; i++) {
                int v = bytes[i] & 0xFF;
                hexChars[i * 2] = hexArray[v >>> 4];
                hexChars[i * 2 + 1] = hexArray[v & 0x0F];
            }
        String text = new String(hexChars);
        if (text.contains(UTF_16)) {
            ecncodingFormat = StandardCharsets.UTF_16.name();
        } else if (text.contains(UTF_8)) {
            ecncodingFormat = StandardCharsets.UTF_8.name();
        }
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    return ecncodingFormat;
}

public static void main(String[] args) {
    testByteEncodingFinder(readInputStream("test_279108466.xml"));
    testByteEncodingFinder(readInputStream("Japanese UTF-16.xml"));
}

}

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Un saludo virtual.