The short answer is the Supreme Court will likely issue a narrow opinion specifically ruling on the claims in this case.
The problem is that software is a grey area in US patent law… it is not been directly addressed by either the courts or legislature. Generally, the Court will try to rule narrowly on a particular issue, especially if there is uncertainty in the law. They do not want to be seen as "ruling from the bench"… otherwise they would be usurping the role of the legislature as the rule making body.
A basic principle in patent law is that abstract ideas cannot be the subject of patents. For this reason, a basic software algorithm, like a mathematic algorithm or law of physics, is not patentable. However, if the software is used in a process "carried out with a particular apparatus or else effectuated a transformation of an article from one state to another state or thing", then it may be patentable. Given the arbitrariness of this standard, the USPTO has interpreted the standard broadly and have allowed software patents in a variety of circumstances. I don't think the question at this point is whether software is patentable; the question is what standard the USPTO should use to separate software that is an un-patentable abstract concept from software that should be concretely patentable.
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