/**
 * @(#)ValidDNA.java
 *
 *
 * @author Evan Schwartz
 * @version 1.00 2011/10/12
 */

import java.io.File;
import java.io.FileNotFoundException;
import java.util.Scanner;

public class ValidDNA
{

    public static void main (String[] args)throws FileNotFoundException
    {
        Scanner file=new Scanner(new File("sampleTranscript.txt"));
        String id=file.nextLine();
        System.out.println("Transcript ID is "+id.substring(1));
        String dna= "";

        while(file.hasNext()==true)
            {
                dna += file.nextLine();
            }
        System.out.println(dna);
//length
        if(dna.length()%3 == 0)
        {
            System.out.println("Right Length");
        }
        else
        {
            System.out.println("Incorrect Length");
        }
//Start Codon
        if(dna.substring(0,3).equals("ATG"))
        {
            System.out.println("Starts with right triple");
        }
        else
        {
            System.out.println("Does not start with right triple");
        }
//End Codon
        if(dna.substring(324,327).equals("TAG") || dna.substring(324,327).equals("TAA") || dna.substring(324,327).equals("TGA"))
        {
            System.out.println("Correct Stop Codon");
        }
        else
        {
            System.out.println("Missing Stop Codon");
        }

    }


}