This is a very specific question in specific discipline. There might be someone here who knows exactly what you are talking about, but then maybe not. I am not entirely certain this is a Perl question.

Would help if you could show a bit more of your code. At least list the module(s) you are using. You describe the specifics of what you want to solve nicely, but not how you expect Perl to do it.

Could you describe that a little more clearly? Seems to be an interesting problem...