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After installing, you need to update the '/usr/java' sym link to point to your new root installation. For example, I installed jdk1_5_16 at /usr/jdk/jdk1.5.0_16/ and then added this symlink:
ln -s /usr/jdk/jdk1.5.0_16/ /usr/java
You may need to remove the symlink that is already there before it will allow you to successfully create the new one.
There are several other dependent symlinks in /usr/bin that use /usr/java, but you only have to update /usr/java.
From one noob to another.