There's an input stream decorator, java.security.DigestInputStream, so that you can compute the digest while using the input stream as you normally would, instead of having to make an extra pass over the data.
MessageDigest md = MessageDigest.getInstance("MD5");
try (InputStream is = Files.newInputStream(Paths.get("file.txt"));
DigestInputStream dis = new DigestInputStream(is, md))
/* Read decorated stream (dis) to EOF as normal... */
byte digest = md.digest();