“I have documented methods in my C++ class but they are not appearing in the HTML output.”

Surprised?

Doxygen ignores the documentation of global entities (like functions) if the file that contains these is, itself, not documented.

“To document a member of a C++ class, you must also document the class itself. The same holds for namespaces. To document a global C function, typedef, enum or preprocessor definition you must first document the file that contains it (usually this will be a header file, because that file contains the information that is exported to other source files).

In other words, there must at least be a

/*! \file */

or a

/** @file */

line in this file.

See:
http://www.stack.nl/~dimitri/doxygen/docblocks.html#structuralcommands: