With IntelliJ IDEA JAVA IDE (my best IDE because it is close to Visual Studio Experience) there is build in feature to generate HTML Java Doc from JAVA source code.
Be sure to have all the references to all the JARS and make sure that your project build using ANT XML script. Go to Tool and then select Generate Java Doc. Much more easy than using Java Doc in command line. Sweeeet
http://java.sun.com/j2se/javadoc/
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