[inlinecode]
 
 
 
import java.io.*;
 
import java.util.Scanner;
 
 
 
public class GenetiCode
 
{
 
	//main method
 
	public static void main(String[]code) throws IOException 
 
    {
 
 
 
	FileReader file = new FileReader("D:\\dna.txt");
 
	BufferedReader fileInput = new BufferedReader(file);
 
 
 
		try
 
			{
 
				PrintStream outStream = new PrintStream(new FileOutputStream("D:\\dna.txt"));
 
				outStream.close();
 
			}
 
		catch (IOException e)
 
			{
 
				System.out.println("Error: File could not be opened.");
 
			}
 
 
 
	Scanner scan = new Scanner(System.in);
 
 
 
	String dna=null;
 
	String dnas[]=new String[5];
 
 
 
	//asks for the input
 
	System.out.println("What combination would you like to look for? ");
 
    String combi = scan.nextLine();
 
 
 
    String[] array=new String[combi.length()];
 
	scan.close();
 
 
 
	array=toArray(combi);
 
 
 
	//loop starts here	
 
	for(int i=0; i<dnas.length; i++)
 
			{
 
				if (dnas[i]==array[0])
 
				{
 
					for (int j=0; j<array.length &&(i+j)< dnas.length && dnas[i+j]==array[j]; j++)
 
					{
 
						if(j==array.length-1)
 
						{
 
							int occur=0;
 
							occur+=1;
 
							System.out.println(occur + " position is at " + i);
 
						}
 
					}
 
				}
 
				System.out.println("The number of occurence is: " + occur);
 
 
 
				printArray(dnas);
 
				printArray(array);
 
			}
 
 
 
	//converts it to array
 
	private static String[] toArray(String dna)
 
		{
 
			String seq[]=new String[dna.length()];
 
			int x=0;
 
 
 
			for(int i=0; i<dna.length(); i++)
 
			{
 
				char z=dna.charAt(i);
 
				if(true)
 
				{
 
					System.out.println("Char z=" + z);
 
					seq[x++]=String.valueOf(z);
 
				}
 
			}
 
			return seq;
 
		}
 
 
 
	//prints the array
 
	public static void printArray(String dnas[])
 
		{
 
			for(int i=0; i<dnas.length; i++)
 
			{
 
				System.out.println("DNA[" + i + "]=" + dnas[i]);
 
			}
 
		}
 
}[/inlinecode]