recursion

Genes.java

import java.util.Scanner;
public class Genes {
	public static void main(String[] args) {
		Scanner stdin = new Scanner(System.in);
		String gene = stdin.next();
		String result = findGene(gene, "");
		if (!result.isEmpty()) {
			System.out.println(result);
		} else {
			System.out.println("No valid genes were detected.");
		}
	}

	public static String findGene(String s1, String allGenes) {
		String start = "ATG";
		String[] ends = {"TAG", "TAA", "TGA"};
		int starter = s1.indexOf(start);
		int ender = s1.indexOf(ends[0]);
		for (int i = 1; i < 3; i++) {
			if (s1.indexOf(ends[i]) == -1) continue;
			if ((s1.indexOf(ends[i]) < ender && s1.indexOf(ends[i]) > starter) || ender == -1) {
				ender = s1.indexOf(ends[i]);
			}
		}
		if (s1.isEmpty() || starter == -1 || ender == -1) return allGenes;
		if (s1.substring(starter + 3, ender).length() % 3 == 0) {
			allGenes = s1.substring(starter + 3, ender) + "\n";
		}
		s1 = s1.substring(ender + 3, s1.length());
		return allGenes + findGene(s1, "");
	}
}