By default Ubuntu runs GCJ, the GNU Java, instead of Sun's Java.

The 'easiest' way to enable Sun's Java is to run it from your launcher. For example:

/usr/lib/jvm/java-1.5.0-sun/bin/java -Dplugins.dir=/home/<YOURHOME>/ImageJ 
    -Xmx128m -cp /opt/ImageJ/ij.jar:/usr/lib/jvm/java-1.5.0-sun/lib/tools.jar ij.ImageJ

this command line specifies the location of your plugins directory (-Dplugins.dir), sets memory to 128 Mb (-Xmx128m) and allows plugins to be compiled (/usr/lib/jvm/java-1.5.0-sun/lib/tools.jar). Note that this is for Sun's Java 1.5 - it will need to be changed accordingly to the version you are running.

Additionally, you can export the Java classpath in your .bashrc:

export PATH=/usr/lib/jvm/java-1.5.0-sun/bin:$PATH

making sure that your 'JAVA_HOME' is set to the proper folder in your .bashrc:

export JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun

Or make an alias in your .bashrc for 'java':

alias java='/usr/lib/jvm/java-1.5.0-sun/bin/java'

(Based on Albert Cardona's email to the mailing list.)

A Debian-based repository can also be used, contributed and tested by Paolo Ariano. It can be downloaded from: http://www.personalweb.unito.it/paolo.ariano/software.html

First install the Java version you want/need:

sudo apt-get install sun-java6-jre sun-java6-plugin sun-java6-fonts

replace the 6 by 5, if you need a Java 5. You can also replace the jre by jdk if you want a javac.

To change the default java command:

sudo update-alternatives --config java

and select the Version you want.

You can check the result by:

user@ubuntu:~$ java -version
java version "1.5.0_15"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_15-b04)
Java HotSpot(TM) Server VM (build 1.5.0_15-b04, mixed mode)