If there is a different way of implementing it than described in the patent, did the patent owner really invent the other method?
Most (all?) patentable subject matters work this way; the abstract process is patentable and the reduction to a specific implementation is protected by copyright because they are unrelated bodies of work. It is not uncommon, for example, to license a chemical process (read: algorithm) patent from one company and license a copyrighted implementation design from another company. Computer algorithm patents work the same way.