// The "DNA" class.
import java.awt.*;
import hsa.Console;
/*
Name: Mujtaba Meher
Teacher: S. Drajner
Description: This program finds the
*/

public class DNA
{
    static Console c;           // The output console

    public static void main (String[] args)
    {
        c = new Console ();

        String[] codons =
            {
            "TTT", "TTC", "TTA", "TTG", "TCT", "TCC", "TCA", "TCG", "TAT", "TAC",
            "TAA", "TAG", "TGT", "TGC", "TGA", "TGG", "CTT", "CTC", "CTA", "CTG",
            "CCT", "CCC", "CCA", "CCG", "CAT", "CAC", "CAA", "CAG", "CGT", "CGC",
            "CGA", "CGG", "ATT", "ATC", "ATA", "ATG", "ACT", "ACC", "ACA", "ACG",
            "AAT", "AAC", "AAA", "AAG", "AGT", "AGC", "AGA", "AGG", "GTT", "GTC",
            "GTA", "GTG", "GCT", "GCC", "GCA", "GCG", "GAT", "GAC", "GAA", "GAG",
            "GGT", "GGC", "GGA", "GGG"
            };

        String[] aminoAcids =
            {
            "F", "F", "L", "L", "S", "S", "S", "S", "S", "Y", "Y", "STOP", "STOP", "C", "C", "STOP",
            "W", "L", "L", "L", "L", "P", "P", "P", "P", "H", "H", "Q", "Q", "R", "R", "R", "R", "I",
            "I", "I", "M", "T", "T", "T", "T", "N", "N", "K", "K", "S", "S", "R", "R", "V", "V", "V",
            "V", "A", "A", "A", "A", "D", "D", "E", "G", "G", "G", "G", "G"
            };

        String dna, converted, index;
        int check, counter = 0, offset = 0;

        //^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^VARIABLE_DECLARATION^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^//

        c.print ("Enter the DNA sequence: ");
        dna = c.readString ();


        do
        {
            for (int x = offset ; x <= dna.length () ; x += 3)
            {



                if (dna.substring (x, x + 3).compareTo (codons [35]) == 0)
                {

                    for (int y = x ; y < dna.length () ; y += 3)
                    {

                        counter++;

                        if (dna.substring (y, y + 3).compareTo (codons [11]) == 0 || dna.substring (y, y + 3).compareTo (codons [12]) == 0 || dna.substring (y, y + 3).compareTo (codons [15]) == 0)
                        {
                            c.print ("The dna starts at " + x / 3 + " and ends at " + y / 3);
                            y = dna.length ();

                        }
                    }
                }

                if ((x + 3) > dna.length ())

                    x = dna.length ();

            }

            offset++;
        }
        while (offset != 2);

    } // main method
} // DNA class