Yes, you are missing something - download a JDK from the Sun web site: java.sun.com. The libgcj JDK is inadequate for running any serious Java apps.
Using apt, you can search for and get the Sun JRE fro the repository. But I am not sure if the IDE bundle will be happy with just a JRE.
You could also look into downloading the OpenJDK (if you are running Ubuntu 8.04), it might do the job also (not sure of the package name).
ok downloaded ,
then downloaded j2ee europa ,
then used the link from http://docs.jboss.com/jbosside/install/build/en/html/index.html
downloaded the server and go it to connect ok ,
the only issue that remains for me is the mysql schemas don't work , it pings ok and i can see the databases but not the tables , weird must be a solution on some other forum cheers for the advice
Java, as PeterJ mentioned, should be in the repos, but you might have to enable the multiverse and universe repos as well.
Then just apt-get/aptitude install the jdk and you should be fine.
Make sure you get the one with the version you like and not the virtual package. Sometimes the virtual ones are linked to older versions.
MySql also comes with a few tools packaged. The manager and query iirc.
You can use the manager to see your table and allow access to them.