Bracket expressions (1 loop less)

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

public class Main {

    public static void main(String[] args) throws IOException {
        BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
        String input = in.readLine();

        boolean[] markedAsUsed = new boolean[input.length()];
        int indexOpen = -1;
        int indexClose = -1;
//        int count = 0;
        int count = 1;
//        for (int i = 0; i < input.length(); i++) {
//            if (input.charAt(i) == ')') {
//                count ++;
//            }
//        }
        for (int k = 0; k < count; k++) {
            boolean programDone = false;
            if (k == 0) {
                count = 0;
            }
            for (int i = 0; i < input.length(); i++) {
                if (input.charAt(i) == ')' && markedAsUsed[i] == false && programDone == false) {
                    indexClose = i;
                    markedAsUsed[i] = true;
                    programDone = true;
                }
                if (input.charAt(i) == ')' && k == 0) {
                    count++;
                }
            }
            for (int j = 0; j < indexClose; j++) {
                if (input.charAt(j) == '(' && markedAsUsed[j] == false) {
                indexOpen = j;
                }
            }
            markedAsUsed[indexOpen] = true;
            System.out.println(input.substring(indexOpen, indexClose + 1));
        }
    }
}