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Question:
I would like to know if it is possible to use the qualification function (function of the GPIO) when the input is dedicated to a peripheral (in my case trip zone)?
Answer:
The qualification circuitry is active regardless of the setting of the GPIO mux. So, yes, you can use the qualification for the peripheral function (trip zone).
Also refer to: http://processors.wiki.ti.com/index.php/Category:General_Purpose_IO_for_C2000