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I don't really get it.
Could you please tell me what he think?
All this time I think I could send my data from fpga to pc using virtual jtag via hyperterminal just like usb to ttl(serial) do.
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What your professor is wisely telling you is that you should take the 'easiest' approach. If you use a standard serial port device on the PC-end to communicate with your FPGA, then the 'work' is at the FPGA end. However, you now have to have two pieces of hardware hanging off your PC USB ports (the FPGA board and the serial adapter) and then you have to wire the serial cable into the DE0-nano board.
The JTAG interface provides a mixture of work at both ends. At the FPGA side, you have to write some logic to interface to the component. At the PC end, you have to use the Altera Tcl scripting interface.
Using the Tcl scripting language, its fairly simple to create a server, i.e., a program that provides clients access to the FPGA hardware.
The tutorial shows how to create an FPGA design, provides Tcl scripts that implement a server, and a client Tcl/Tk GUI for turning LEDs on or off. You can show your professor this interface, and he can then decide whether or not he likes it.
Cheers,
Dave