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:
making sure that your 'JAVA_HOME' is set to the proper folder in your .bashrc:
Or make an alias in your .bashrc for '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)