Write a program Huntingtons.java to read in a human DNA sequence from a file and identify whether the patient is at risk for HD by determining the maximum number of CAG repeats. Output the maximum number of repeats, and an appropriate medical diagnosis based on the table above. The data file format will consist of a sequence of the letters A, C, G, and T, along with arbitrary amounts of whitespace separating the letters. For full credit, your program should use regular expressions and should identify CAG repeats, even if there is intervening whitespace.

For example, the following sequence has a CAG repeat of size 4.

TTTTTTTTTT TTTTTTTTTT TTTTTTTTCA
GCAGCAGCAG TTTCAGCAGT TTTTTTTTTT 
TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT
TTTCAGTTTT TTTTTTTTTT T

% java Huntingtons test1.txt
max number of CAG repeats = 4
not human

Use this Turing machine simulator to develop your machine. Your job is to create and submit a text file comparator.tur containing the description of your Turing machine like the one below, but instead of adding the two binary numbers, it should compare them.

title Binary Adder description Add two binary numbers, and leave the result on the tape. vertices 2 R 0.25 0.75 0 L 0.25 0.25 1 L 0.75 0.25 3 L 0.75 0.75 4 R 0.40 0.50 5 H 0.60 0.50 edges 0 0 0 1 135 0 1 1 0 0 4 + # 1 3 + + 2 0 # # 3 2 # 1 0.2 3 2 0 1 -0.2 3 3 1 0 -30 4 4 1 # -135 4 5 # # tapes [1] 0 1 0 + 1 1 1 1 [1] 0 0 + 1 1 1 [1] 1 0 0 + 1 1 [1] 0 1 0 + 1 0 0 1 0 1

The data file is divided into 5 sections (title, description, vertices, edges, tapes), and each section begins with the corresponding name. Each vertex (state) is specified with 4 required values: its name (a string), its type (L, R, Y, N, H), and its x- and y-coordinates (between 0 and 1). The first state listed is the start state. Each edge (transition) is specified with 4 required values: the starting state, the ending state, the symbol to read, and the symbol to write. An optional 5th parameter specifies the curvature with which to draw the edge (straight line by default). Each sample input tape is specified by listing its symbols, separated by spaces. The tape head starts at the symbol delimited by square braces - for this assignment, it should always be the leftmost non-blank character.

Extra credit. Design an efficient Turing machine for adding binary numbers. The Turing machine above takes more than 2ⁿ steps to add two n-bit numbers; your challenge is to design a machine that adds two n-bit numbers in time proportional to n².

Deliverables. Submit Huntingtons.java, comparator.tur, and readme.txt.