Any suggestions to work with Gumstix Overo Air GPIO pins by Java Library as PI4J I'm using Pinto-TH shield to interface with the board pins.
Control Gumstix Overo GPIO
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Well that library looks pretty self explanatory, and the example is really good. You just DL the library, copy paste code from the example, and look on the breakout board to see what pin numbers are your LEDs and input pins. I suggest putting male headers on the breakout board so it can either plug into a breadboard or you can wirewrap wires to it.
If you would rather do things yourself, you can refer to: http://wiki.gumstix.org/index.php?title=GPIO. This is what I used in a C++ application. I just wrote and read to the system files to access GPIO.