Don't know much about it, and it is not clear to me why this should be
java related, but I'd assume it would be simpler to buy a barcode
reader, connect it to a (serial) port, and programmatically access it.

We once had to deal with barcode recognition of spectroscopic masks to
be mounted on an instrument on the VLT (Very Large Telescope). The
barcodes were cut in invar foils by a laser cutting machine (but I used
to produce paper mockups in Postscript). We bought a few commercial
barcode readers from Datalogic.

These devices had to be attached to the serial port of a PC (at the
time). A maintenance program came with the readers, which had to be used
only once to configure their EEPROMs. In particular the readers
supported a wide range of commercial barcode standards (we selected the
2/5 interleaved).

After that we could just trigger a read from the serial port and obtain
in return a 6-digit numeric code. The basic communication protocol was
clearly explained in the docs, and we just wrapped it into an higher
level protocol to read exactly 6 digits and handle wait. At the time we
did that programmatically within a Visual Basic program, but any
language should do.

see http://mindprod.com/jgloss/barcodes.html

There are a number of libraries mentioned. I think most are for
printing, but it might get you started.