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He was opposed to the lawsuit, largely because of Apple's supplier relationship with Samsung, according to Reuters.
Prior to being CEO, Cook was COO and oversaw the supply chain. He worked closely with Samsung, so he was likely to be in a more awkward position once Apple filed its lawsuit.
Suing Samsung, which was copying Apple in many ways, certainly made some sense from Jobs' perspective. He wanted to stop them from ripping off his work.
But in the long run, it's unclear if it was the right decision.
Despite the fact that Apple won its trial against Samsung in California, its litigation results around the world haven't been great. More importantly, the patent suits haven't slowed down the rise of Samsung one bit.
Cook has publicly discussed his distaste for the patent suits. On Apple's Q2 2012 earnings call, he said, "I have always hated litigation, and I continue to hate it. We just want people to invent their own stuff. If we could get to a fair settlement, I would highly prefer to settle versus battle."
And since then, he's done just that. Apple settled with HTC. And Cook has talked to Google and Samsung about settling other lawsuits.