Moriarty, the name given to the mouse, refers to Sherlock Holmes' criminal adversary.
When Alden talks about Tom building a raft and floating down a river, he is referring to Mark Twain's Tom Sawyer.
Tom's position within the police force is somewhat unclear. At the crime scene, he seems to be doing much of the work of a uniformed police constable. However, questioning of the suspects and witnesses is usually the work of a detective.