You should write your method and file headers in such a way as to make them readable by javadoc. You can find excellent directions for this in Appendix H of Main.
Here is a sample file, TemperatureConversion.java, created by Michael Main (see pg. 15). He has commented the program beautifully. You will note that some of his comments include HTML tags (such as <CODE>, etc.) You don't have to use those in your own comments, but certainly can if you would like.
Here is the .html web page (TemperatureConversion.html) that results from running javadoc on the java file.
javadoc is typically run simultaneously on all the classes of a program. This is because running javadoc on just one file typically creates a number of .html files, most of which have to do with the program itself, rather than with just the one file. For example, the javadoc command:
javadoc -author -source 1.4 -public -tag param -tag precondition:a:"Precondition:"
-tag postcondition:a:"Postcondition:" -tag return -tag throws -tag
example:a:"Example:" TemperatureConversion.java
creates several .html files, among them help-doc.html. Many of these pages are linked to from the TemperatureConversion.html file.