>  Hey, 
>    
>  Quick question.  In the part of the assignment where we're supposed to 
>  time the program, should we use the EditDistanceTimer.java program 
>  included in the sequence folder?   

Yup, looks like it.

>  In other words, is the time supposed 
>  to be only for the distance() function or is it also for the 
>  showAlignment() function?   
>    
>  Thanks, 
>  Rachel 

Just distance().

(1) distance() is the one that really takes time.  It's O(N^2).  It
    takes bulk of the time, so it's the real one that counts.

(2) showAlignment() is O(N) so its time is not interesting.
    showAlignment spends most of the time in printing things.
    Printing things is not interesting from timing analysis point of
    view.

Randy