Still lots and lots of compiler errors when I try to compile the wrapper function--even though SWIG itself runs without any errors at all. They look like scoping and syntax errors, but I'm not sure what's causing them. I've been working with very a simple C++ file, with a single object, and no namespace issues. Using that, I get the same errors as when I try to compile the Bio++ wrappers.
One thing I have discovered--this is language invariant. It doesn't matter if I try to use Java, Python, etc.--they all get the same errors.
Reread Chapters 5 and 6 of the SWIG docs today, very carefully. Found very little of any relevance. Finally posted a note to the SWIG mailing list. I feel like an idiot doing so, but this needs to get done.