Kamino Factory

import java.util.Scanner;

public class Demo {
    public static void main(String[] args) {
        Scanner scanner = new Scanner(System.in);

        int sequenceLength = Integer.parseInt(scanner.nextLine());

        String line = scanner.nextLine();

        int bestLength = 0;
        String bestDna = "";
        int bestIndex = 0;
        int bestSum = 0;
        int bestCounter = 0;
        int counter = 0;
        while (!line.equals("Clone them!")){
            counter++;
            //010101111
            String sequence = line.replaceAll("!",
                    "");

            String[] dnas = sequence.split("0");

            int maxLength = 0;
            int sum = 0;
            String bestLocalDna = "";
            for (int i = 0; i < dnas.length; i++) {
                if(dnas[i].length() > maxLength) {
                    maxLength = dnas[i].length();
                    bestLocalDna = dnas[i];
                }
                sum += dnas[i].length();
            }
            int beginIndex = sequence.indexOf(bestLocalDna);

            if(maxLength > bestLength){
                bestLength = maxLength;
                bestDna = sequence;
                bestIndex = beginIndex;
                bestSum = sum;
                bestCounter = counter;
            }else if(maxLength == bestLength &&
                    (beginIndex < bestIndex || sum > bestSum)){
                bestLength = maxLength;
                bestDna = sequence;
                bestIndex = beginIndex;
                bestSum = sum;
                bestCounter = counter;
            }else if(counter == 1){
                bestLength = maxLength;
                bestDna = sequence;
                bestIndex = beginIndex;
                bestSum = sum;
                bestCounter = counter;
            }

            line = scanner.nextLine();
        }

        System.out.println(String.format("Best DNA sample " +
                "%d with sum: %d.", bestCounter, bestSum));

        for (int i = 0; i < bestDna.length(); i++) {
            System.out.print(bestDna.charAt(i) + " ");
        }
        System.out.println();

    }
}