Technical details
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Communication with devices
Here is a commented log when formatting a SSSD floppy disk with the TI disk controller. Actually, this dump was achieved using MESS and putting in some printf lines.
Setting up RXTX for Java
RXTX is a serial and parallel port API implementation which is available for Windows and Unix systems, as binary and source code files. The complete documentation and the download location is at http://rxtx.qbang.org/wiki/index.php/Main_Page. You should build the binaries for 64 bit systems from the sources.