GeneFind.java in progrme

GeneFind.java

public class GeneFind

{

    public static void main(String[] args) 

   {

        String start = args[0];

        String stop  = args[1];

        String genome = StdIn.readAll();

        System.out.println("genome = '" + genome + "'");

        System.out.println("start  = '" + start  + "'");

        System.out.println("stop   = '" + stop   + "'");

        int beg = -1;

        for (int i = 0; i < genome.length() - 2; i++)

        {

            String codon = genome.substring(i, i+3);

            if (codon.equals(start)) beg = i;

            if ((codon.equals(stop)) && (beg != -1) && (beg + 3 < i))

               {

                String gene = genome.substring(beg+3, i);

                if (gene.length() % 3 == 0)

               {

                    System.out.println(gene);

                    beg = -1;

                }

            }

        }

    }

}