In running java on Linux you need access to three different programs:

Setting up access

In your Linux account there will be a file called .login (if you cant see it do "ls -a" which shows all the hidden files with a "." in front of them).
In this file there will be a line which looks like:
setenv PATH "$HOME/bin:$PATH"

change this to read:
setenv PATH "$HOME/bin:/usr/local/share/jdk1.3/bin:/usr/local/share/jikes/bin:$PATH"
To test if this worked do:
$ which java javac jikes
/usr/local/share/jdk1.3/bin/java
/usr/local/share/jdk1.3/bin/javac
/usr/local/share/jikes/bin/jikes

There will also be a line which looks something like
setenv MANPATH "$HOME/man:$MANPATH"

change this to read:
setenv MANPATH "$HOME/man:/usr/local/share/jikes/man:$MANPATH"

check this by running:
$ man jikes

To get jikes settup you will need to include something like the following in your .profile:
setenv BOOTCLASSPATH /usr/local/share/jdk1.3.1/jre/lib/rt.jar

jikes is faster, less dependent on getting things compiled in the right order (it will hunt out other source files that are needed) but has less informative error messages than javac.