I suggest using IBM's Java Toolbox for Java. Put the JT400.jar into your classpath (or JT400Ntv.jar if the Java is running on the iSeries). I've used both the ProgramCall class and the CommandCall classes.
The com.ibm.as400.access.CommandCall class is easy to use. It has a simple constructor that you pass a com.ibm.as400.access.AS400 class to. Then just use the run method like this:
CommandCall command = new CommandCall(as400);
command.run("CPYF FROMFILE(BLAH) TOFILE(BLAHBLAH) CRTFILE(*YES)");
Of course, you wouldn't use that particular CL command, but you get the idea. When using the CommandCall class, it's always a good idea to process any messages that came from the command. In the one program I use this for, I display the messages to the user in a textbox on their screen like this:
AS400Message[] messageList = command.getMessageList();
for (int i=0;i < messageList.length;i++) {
String sMessageText = messageList[i].getText();
sMessage+=sMessageText + "\n";
}
The com.ibm.as400.access.ProgramCall class takes more work, but it allows you to access the returned parameters. I use this one more often because I'm usually calling existing RPG worker programs that return values. For this, define a com.ibm.as400.access.ProgramParameter array. When you pass parameters to a program from Java, remember to convert them to AS/400-friendly values using a class like com.ibm.as400.access.AS400Text. The details of the ProgramCall command are better researched using IBM's documentation: http://publib.boulder.ibm.com/infocenter/iseries/v5r4/index.jsp?topic=/rzahh/page1.htm