GUI

gui.java     - main class (compile and run it to start the program)
/main/       - contains custom panel classes, one for(almost) 
               every section of the main frame
/service/    - contains service classes (data containers and etc.) 
               to simplify operation
/custom/     - contains custom action listeners, threads and 
               a file chooser class
/lib/        - external libraries (jfreechart, miglayout)

RUN:

In Terminal compile and execute (in the main GUI project directory:) 
1) javac gui.java
2) java gui
3) Pop up window comes up, choose main project directory 
4) Wait a bit, GUI should load now.

USE:
1) Select all the relevant file (4 total, at the upper part of the gui)
  a) Nios2 shell file: /home/user/altera/13.1/nios2eds/nios2_command_shell.sh
  b) Firmware fiie: ../gen2dom-fw/ddc2_sockit_nios2/quartus_project/output_files/ddc2_sockit_nios2_time_limited.sof
  c) Config file: ../gen2dom-fw/ddc2_sockit_nios2/qsys_nios2/software/ddc2_nios2_sw/ddc2_nios2_sw.elf
  d) Congig file: ../gen2dom-fw/ddc2_sockit_nios2/qsys_nios2/software/ddc2_nios2_sw/config.sh
2) Press Enter NIOS2 (two Altera command shell messages should appear in command output)
3) Make sure your laptop is commected to JTAG USB and FPGA is on and press Load Firmware.
  Wait until success message.
4) Press Load NIOS2
5) Now it should be running. If data is comming in it should be displayed in a plot and histogramm windows.
6) To save data select saving directory and press save data. It should start creating txt files in the directory.
7)
Known bugs to correct: