Crap! Now I've got it all screwed up. I copied my java directory from home to usr/bin and now when I do which java I get this:

which java
/usr/bin/which: no java in (/home/Thomas/java/j2re/j2re1.4.1_01/bin:/usr/
kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/
bin)

I get the same thing after cd'ing to the /usr/bin/java directory.