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Is the protocol to program Altera ICs (via JTAG) protected?
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No. And it is well documented.
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I would imagine that the IP in Altera's Cyclone II Kit (MAX 3000 CPLD - EPM3128AT) or the standalone USB Blaster (EPM7064), could be re-written based on the (published?) protocol, no?
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Yes, you could do that. But then it won't work anymore with Altera tools.
The Altera tools (Programmer, Signal Tap II, etc) all depend on a specific USB Blaster protocol. Is this protocol that it is undisclosed. Otherwise you could make your own Max II IP compatible with the USB Blaster protocol.
And also the jtagserver protocol is undisclosed. If the latter was published, you could replace Altera's jtagserver with your own.
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