DNA Mutator

Lab4.java

//************************
// Colton McCurdy
// CMPSC 111 Fall 2013
// Lab 4
// Date: 9-19-2013 
//
//Purpose: to create a program that simulates manipulations to DNA strands

import java.util.*; //imports

public class Lab4
{
  //-----------------------
	//main method starts
	//-----------------------
	public static void main(String[] args) 
	{

	//Variable Dictionary
	Scanner scan = new Scanner(System.in); //used for input
	Random random = new Random(); //inserting randoms
	
	String dna; //original DNA String
	String dnaComplement; //DNA Complement
	String dnaInsert; //Inserting into original DNA
	String dnaDelete; //Deleting portion of orignal DNA
	String dnaChange; //Changing character in original DNA

  char changeChar; //changing character
	char c; //random character
	int len; //length of DNA String
  int place; //random place in DNA String
  int place2; //a different random place in a different DNA String
  int place3; //another random place

  //Label output with name and date:
	System.out.println("Colton McCurdy\nLab 4 " + "\n" + new Date() + "\n");
	System.out.print("Enter a string containing only C, G, T,and A: ");
	
	dna = scan.nextLine(); //user input
	dna = dna.toUpperCase(); //formating input to all CAPS

  len = dna.length(); //length of DNA String
  place = random.nextInt(len); //random place
  place2 = random.nextInt(len); //different random place
  place3 = random.nextInt(len); //another random place 
  c = "CGTA".charAt(random.nextInt(len)); //random character

  //making a complement to the original dna strand
  dnaComplement = dna.replace('A', 'Z')
    .replace('C', 'Y')
    .replace('T', 'X')
    .replace('G', 'W')
    .replace('Z', 'T')
    .replace('Y', 'G')
    .replace('X', 'A')
    .replace('W', 'C');

 //***************
 //  Outputs
 //***************

  //complement
  System.out.println("Complement of " + dna + " is " +
     dnaComplement);

  //insertion
  dnaInsert = dna.substring(0, place) + c + dna.substring(place); //insert
	System.out.println("Inserting " + c + " at position " +
       place + " gives " + dnaInsert );

  //deletion
  dnaDelete = dna.substring(0, place2) + dna.substring(place2 + 1); 
  System.out.println("Deleting from position " + place2+ " gives " +
       dnaDelete);

  //change
  changeChar = dna.charAt(place3);
  dnaChange = dna.replace(changeChar, c); //replacing a character with a random
  System.out.println("Changing position " + place3 +
       " gives " + dnaChange); 

  //formatting in terminal
  System.out.println(); //blank line after output

  }
}