No they aren't the exact same thing.
It all depends on the school you are going to and what the focus and emphasis is. At my college Computer Science was more math intensive, it focused more on mathematically equations used in things like circuit boards and electronics.
Computer information systems was more program intensive - but even then it wasn't the sole thing you did. You'd learn about server administration and what not.
Again, with the java question it all depends on the school - it isn't the same across the board. You need to consult your schools brochure or advisor.