Huntingtons.java

public class Huntingtons {

    // Returns the maximum number of consecutive repeats of CAG in the DNA string.
    public static int maxRepeats(String dna) {
        int count = 0, max = 0, x;
        for (int i = 0; i < dna.length() - 2; i += x) {
            String s = dna.substring(i, i + 3);
            if (s.equals("CAG")) {
                count++;
                x = 3;
            }
            else {
                count = 0;
                x = 1;
            }
            if (count > max) max = count;
        }
        return max;
    }

    // Returns a copy of s, with all whitespace (spaces, tabs, and newlines) removed.
    public static String removeWhitespace(String s) {
        String s1 = s.replace(" ", "");
        String s2 = s1.replace("\t", "");
        String s3 = s2.replace("\n", "");
        return s3;
    }

    // Returns one of these diagnoses corresponding to the maximum number of repeats:
    // "not human", "normal", "high risk", or "Huntington's".
    public static String diagnose(int maxRepeats) {
        String result;
        if (maxRepeats >= 0 && maxRepeats <= 9) result = "not human";
        else if (maxRepeats >= 10 && maxRepeats <= 35) result = "normal";
        else if (maxRepeats >= 36 && maxRepeats <= 39) result = "high risk";
        else if (maxRepeats >= 40 && maxRepeats <= 180) result = "Huntington" + "'" + "s";
        else result = "not human";
        return result;
    }

    // Take the name of a file as a command-line argument.
    // Read the genetic sequence from the file using the In class.
    public static void main(String[] args) {
        In in = new In(args[0]);
        String s = in.readAll();
        String dna = removeWhitespace(s);
        int maxRepeats = maxRepeats(dna);
        System.out.println("max repeats = " + maxRepeats + "\n" + diagnose(maxRepeats));
    }
}