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You have actually picked two good examples to explain an odd corner of Japanese. 〜と思う and 〜ことにする both are "state-change" verbs regarding things that happen in people's heads. These sorts of verbs have rules. 〜と思う Plain: State-change （私は）ジョンが大丈夫だと思う。 Lit. "I just had the thought that Jon is okay." "I think that Jon is okay." 〜ている: Stative ...
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