If you have downloaded this distribution of JaxoDraw, you may unpack the tar.gz archive with
tar -xzf jaxodraw-xxx-jre.tar.gz
This will create a directory named JaxoDraw-xxx in the current directory. To run the program type (from inside this folder)
./j2re1.4.2_08/bin/java -jar JaxoDraw.jar
(you might have to make the java binary executable first:
chmod u+x ./j2re1.4.2_08/bin/java).
Note: we recommend installing a Java VM independently of JaxoDraw; like that you will be able to use Java for running other programs, too (unlike Windows, the Java VM under Linux does not get installed globally).