Okay, I understand the problem.  I would do something like the solution
you propose, except that in the input file, trees span multiple lines.  So
the input file looks something like:

(:cat S
 :subs ((() (:cat NP
             :subs ((() (:surf "John")))))
        (() (:cat VP
             :subs ((() (:surf "bought"))
                    (() (:cat NP
                         :subs ((() (:surf "two"))
                                (() (:surf "cars"))))))))
        (() (:surf "."))))


and then there will be another one directly following it (i detect the
breaks because each one is completely surrounded in parens).

So a line-by-line parse solution won't really do the job...

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