When researching for a small article that lists WTL resources for Pocket PC native code develores, I found a very interesting piece of information that compares the performance of MFC and ATL (WTL builds on the ATL windowing classes): Oleg Pudeyev's MFC vs ATL. Now, the message processing performance issue is clearly explained. MFC degrades with the number of managed window handles due to its linear search method when mapping an HWND to a function pointer. With ATL's thunking mechanism this is instantaneous.
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4 weeks ago