I would like to remove certain public and protected member funcions from being included in the javadoc output. I have been searching for some time now as to how to do this and I'm getting the sinking feeling it can't be done. Can someone clearify this for me.
Yes, the standard Javadoc (i.e. the Standard Doclet, which powers it) does not support this.
I suggest you to look at this tool:
It is a template-driven doclet. (More exactly, it is a system for rapid development of high quality custom doclets). This is a commercial product. However, the reduced edition of it called DocFlex/Doclet is freeware.
DocFlex/Doclet includes the standard template set, which generates Java API documentation very similar to the standard JavaDoc. In addition, it is able to generate the same documentation in RTF format or even as a single HTML file.
DocFlex/Doclet supports filtering all classes and their member by tags or annotations. That will allow you to solve you problem.
Have a look at https://developer.berlios.de/projects/padoclet/ . PublishedApiDoclet acts as a filter between the javadoc program and any normal doclet. It also contains a doclet to check the (filtered) javadoc for dangling references.
PublishedApiDoclet works for Java 5 and 6 (publishedApiDoclet1.5-0.4.jar) and Java 2 (publishedApiDoclet1.4-0.3.jar). It is available on http://developer.berlios.de/projects/padoclet/. The downloadable jar-files contain the doclet, the documentation and the sources.