Been a long time since I used an iSeries (heck it wasn't even called iSeries then), but anyway, 2 approaches you can try:
1)
2) checkout this site (there maybe a newer version as this seems to relate to V4R4)
http://publib.boulder.ibm.com/pubs/html/as400/v4r4/ic2924/info/java//rzahh/cmdc.htm There is a group of classes called the "AS/400 toolbox", which incapsulate as/400 objects.
eg. AS400, CommandCall