Walker.gat

/*

****          Do you run the walker or walk it?!?!?        *********

Emma Bernstein
Mary McGreal
Instructions to walk a DNA walker in paraGAT
*/

/*
Definitions---------------------------------------------------------
SCAFFOLD - long strand that holds pegs.
PEG - short strands that allow the walker to move along the base
	in the image these include a, b, and c strands.
BASE - scaffold and pegs
FOOT - stands on the walker that may bind or unbind ("walk") 
	along the base, using tape and untape strands.  
	x or y in the image.
WALKER - the mobile structure composed of two feet that 
	traverses the base. See x and y structure in the image.
*/

/*
Constructor for Stack-----------------------------------------------
This file assumes that the scaffold and pegs have been
constructed and then released into the test tube. [This could occur
within the same test tube, prior to "running" walker 
operations  with a specific set of "constructor" gates to 
unlock only "peg" stacks (a tick/tock stack with a, b, and c 
strands as in the image).]  These processes are defined in 
WalkerSetup.gat.
*/

import WalkerSetup.gat
paraGAT WalkerSetup.gat

/*
It is assumed that for any strand in this file, x complement implies 
t complement tail, and y complement implies an s complement 
tail.

Tape----------------------------------------------------------------
Tape releases a strand (the "tape")
to latch onto a "peg" of the scaffold, with a 
segment which binds to the mobile "walker" and a tail for the untape 
operation (s and t in the image).
Tape takes two parameters, which define the tape strand to 
be released.  This strand will consist of a peg complement, 
a foot complement, and a tail to move the walker forward.
It will bind to the next free peg.
Same peg, but a different foot from three lines before!

Untape--------------------------------------------------------------
Untape releases a strand (the "untape") to unlock one 
"foot" of the mobile walker so that it is free to 
continue traversing the base.  
Untape takes two parameters, which define the tape strand to 
be released.  This strand will be a tape complement of the 
tape prior to the previous tape.
Same peg, same foot as three lines before!

Walker-------------------------------------------------------------
*/
//We assume peg one is a c peg

begin sync
	tape[c,y] //attach the initial leg to a peg
end sync

barrier sync //may or may not be needed b/c in loop

for (int peg = 0; peg < numpegs; peg+=6) {    
	begin sync      // each time you cycle through 6 pegs
		tape[a,x]   //Not sure how tape naming works; pref tapeAX?               
		untape[c,y] //1
		tape[b,y]
		untape[a,x] //2
		tape[c,x]
		untape[b,y] //3
		tape[a,y]
		untape[c,x] //4
		tape[b,x]
		untape[a,y] //5
		tape[c,y]
		untape[b,x] //6
	end sync
}