Most of the time to set up an alternative do the following command:
sudo alternatives --install
For example if I have jdk1.6.0_21 & jdk1.6.0_23 installed and I want to use the latter's compiler I would do,
sudo alternatives --verbose --install /usr/bin/javac javac /usr/java/jdk1.6.0_23/bin/javac 16023
That way if jdk1.60.21's files are untouched by the symlink /usr/bin/javac now points to /usr/java/jdk
From what I have read so far alternatives is a good way of managing symlinks on your system.
Wporta shows how to install and configure Java for a 64 bit system. I might write a bash script to automate this configuration if there is a need. Another good resource is here.
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