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Afaik the controller itself is not encrypted, but the control logic is encrypted.
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I re-checked and I could open every file shown in the Navigator panel, hence my surprise ...
Previously the controller was encrypted, and the AltMemPHY (or the Legacy PHY) was not.
--- 22-11-2011 ---
I did put in an SR.
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With hindsight I decided to take a look at the doc for 11.1 and this is what I found for DDR2 in Cyclone III :
Memory width Logic Registers Logic cells M9K blocks Memory Bits
16 2,915 5,351 9 9,392
So I will get no pie ...