I am currently developing a schematic based on the ATmega32U4. I need to be able to program the embedded chip, so with ISP or JTAG (preferably). The problem is, I also need the analogs functions of the port F (where JTAG is), and the port B (ISP) to link with a can interface. So far my understanding of the datasheet of the chip and of the jtagice debugger I am using goes, I should be able to load the program and then disable the JTAG pins in order for the pins to run correctly.
What I don't understand is whether I can "reenable" these pins with the JTAG interface (or ISP, same problem) in case I need to reprogram, or something is wrong and I have to debug. Is it possible? If not, what could be a work around in order to have all the functionalities needed?