Basically finished with my cs546 project, just need to add some error checking to make it nice, its all of 114 lines of perl and 20 or so of that is comments and debugging stuff. very nice. the input and output are as follows:
[jeff@disco cs546]$ ./turing.pl 0Xq0q1r1Xq0q3r00q1q1r11q1q1rB0q1q2l00q2q2l11q2q2lXXq2q0r0Xq3q1r1Xq3qhr,000010011
X X X X X X X X X 0 0 0 0 0 0
the first part is the program, the stuff followed by the "," is the input to the program, the bottom is the out put, the example shows a programs that adds the 0’s up.

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