I suspect it's a matter optimization; the quadratic algorithm possibly works faster at the number of nodes we have in vanilla, but gets inefficient (due to the quadratic factor) with more nodes.
I don't see how that would occur in this case. #0 would be computed before the start of the game, #1-3 are directly displayed so there's no way around computing them, and I can't think of a more straightforward way to compute #4. Matter of fact, I don't see how a quadratic algorithm would fit the current system at all, barring AI as dezuman mentioned---but given the less strict definition of AI behavior you can blame any running time on AI, and it would probably involve a lot more than the number of trade nodes. Again, the trade system seems to be designed to allow a linear algorithm; for example, the cycle-less structure and trade good market shares being computed only from local trade value and trade power share.
Or maybe we're just all misinterpreting what Johan meant by "NxN". I and probably others were operating on the assumption that N referred to the number of trade nodes since that was the subject of discussion.
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