De2-115 windows application to control Cyclone chip

Everything is possible, but using JTAG directly isn't documented so you are on your own and must reverse engineer a lot. I really think learning to use SOPC Builder / QSys and system console would me a more productive use of your time ;)

You can find a tutorial here: http://www.alterawiki.com/wiki/using_the_usb-blaster_as_an_sopc/qsys_avalon-mm_master_tutorial (thanks Dave for reminding me about this tutorial in another thread!)

For very simple tests (LEDs, buttons) you just need to use PIO components. For more complex interfaces or modules, you can write your own VHDL code and integrate it as a custom component in your SOPC design.