Java is Write-Once/Run-Anywhere, so direct invocation of any OS-specific service or non-Java code isn't possible. If your iSeries system allows you to present these commands as web services or remote method calls, you might be able to get away with pure Java. Otherwise, your best bet is to just supply JNI glue API modules. Or, if possible run them as command-line processes, via the java Runtime exec functionality.
An IDE is no substitute for an Intelligent Developer.