in reply to arrays of arrays

You've gotten several good answers on the problem you think you have. But you have a larger problem.

If this Perl code is really meant for linguistic research, (as opposed to being a toy program for a computational-linguistics 101) don't roll your own parser / tokenizer. Already your approach embodies design-decisions that will bite you.

I encourage you to check out IBM's (free, open-standard) UIMA.

throop