The usage of fully qualified Java annotations causes Doxygen not to recognize class and method definitions.

In this example, a class is annotated with a fully qualified FindBugs @SuppressWarnings annotation:

    /**
     * This is the Foo class.
     */
    @edu.umd.cs.findbugs.annotations.SuppressWarnings ("HE_EQUALS_USE_HASHCODE")
    public class Foo
    {
        // ...
    }

This is not recognized by Doxygen as a class.  If the annotation is removed or commented out, then it is correctly recognized as a class.

In this example, a method is annotated with a fully qualified FindBugs @SuppressWarnings annotation:

        /**
         * This is the bar method.
         */
        @edu.umd.cs.findbugs.annotations.SuppressWarnings ("DLS_DEAD_LOCAL_STORE")
        public void bar()
        {
            // ...
        }

This is misinterpreted by Doxygen as a method named 'SuppressWarnings' with an argument list consisting of '"DLS_DEAD_LOCAL_STORE"' and a return type of '.umd.cs.findbugs.annotations.'.  If the annotation is removed or commented out, then it is correctly recognized as a method named 'bar' with an empty argument list and a return type of 'void'.

Using just the annotation name without fully qualifying it is not an option for a workaround, since this would cause the FindBugs @SuppressWarnings annotation [edu.umd.cs.findbugs.annotations.SuppressWarnings] to conflict with the JDK @SuppressWarnings annotation [java.lang.SuppressWarnings].