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I am wondering if we can also manually change values in SRAM switches.
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The configuration RAM bits cannot be modified after the FPGA is configured. Some particular things can be changed after configuration though. For certain device families, you can change PLL settings, GX transceiver settings, or data stored in RAM blocks like M9K. To change M9K data after configuring (after the FPGA is running in user mode), use "Tools --> In-System Memory Content Editor". To change M9K initialization data before configuring but without recompiling, use "Processing --> Update Memory Initialization File".
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Also, my another curiosity is: since SRAM stores both switch as well as logic element configuration, is it possible to which is which in .sof file?
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You can write configuration data to a text file format like .ttf or .hex, but you can't really tell what anything is in the configuration data. Also, what you are calling "SRAM switches" are the configuration RAM bits that control the logic element configuration--there isn't something separate in the .sof for logic element configuration.