First off, I am not a lawyer. I do, however have quite a few patents. My experience is that a patent needs to contain a single invention. Claims may cover several permutations, but of the same core invention. If the examiner feels there are two separate inventions, they may require a second patent application. This has happened to me. I had a patent application on an algorithm to evaluate real time PCR data. The algorithm generated two different measures that could be used separately or in combination. The US patent examiner made us separate the invention into three applications one each for the different measures and one for the combination. I felt this was not justified, but my patent attorney decided to just do what the examiner requested. This, of course increased the costs, but as I was working for a large corporation that was not a significant issue. The same invention is covered by a single patent in other countries.