BurrowsWheeler.java

import edu.princeton.cs.algs4.BinaryStdIn;
import edu.princeton.cs.algs4.BinaryStdOut;
import java.util.Arrays;

public class BurrowsWheeler {

    // apply Burrows-Wheeler transform,
    // reading from standard input and writing to standard output
    public static void transform() {
        String txt = BinaryStdIn.readString();
        CircularSuffixArray csa = new CircularSuffixArray(txt);
        for (int i = 0; i < txt.length(); i++) { // search i
            if (csa.index(i) == 0)
                BinaryStdOut.write(i);
        }
        for (int j = 0; j < txt.length(); j++) {
            int idx = csa.index(j);
            char ch = txt.charAt((idx - 1 + txt.length()) % txt.length());
            BinaryStdOut.write(ch);
        }
        BinaryStdOut.close();
    }

    // apply Burrows-Wheeler inverse transform,
    // reading from standard input and writing to standard output
    public static void inverseTransform() {
        int first = BinaryStdIn.readInt();
        String txt = BinaryStdIn.readString();
        char[] a = txt.toCharArray();
        int n = a.length;
        int r = 256;
        int[] count = new int[r + 1];
        char[] aux = new char[n]; // the sorted array
        int[] next = new int[n];

        // ==== Key Index Counting Algo ===//
        // first pass: count the frequencies of each letter in txt using the key as an index.
        for (int i = 0; i < n; i++) { // ie. the number of As, Bs, Ds, Es, Fs etc.
            count[a[i] + 1]++; // increment the count of each index[] keys
        }
        // second pass: count the cumulates
        for (int i = 0; i < r; i++) {
            count[i + 1] += count[i];
        }
        // third pass: distribute the items in sorted order. The value of next[i] is
        // exactly the same as the location in the new array where the value is being copied to.
        for (int i = 0; i < n; i++) {
            int p = count[a[i]]++;
            aux[p] = a[i];
            next[p] = i;
        }
        BinaryStdOut.write(reconstructString(first, aux, next));
        BinaryStdOut.close();
    }

    private static String reconstructString(int first, char[] aux, int[] next) {
        int n = next.length;
        char[] res = new char[n];
        int[] copy = Arrays.copyOf(next, n);
        for (int i = 0; i < n; i++) {
            res[i] = aux[first];
            first = copy[first];
        }
        return String.valueOf(res);
    }

    // if args[0] is "-", apply Burrows-Wheeler transform
    // if args[0] is "+", apply Burrows-Wheeler inverse transform
    public static void main(String[] args) {
        if (args[0].equals("-")) transform();
        else if (args[0].equals("+")) inverseTransform();
        else throw new IllegalArgumentException("Illegal command line argument");
    }
}