/*
 * A simple program to illustrate arrays: declaration, creation, and use.
 * Reads two DNA sequences and finds SNPs (Single Nucleotide Polymorphism and pronounced as "snips").
 * SNPs are saved in anotyher aray.
 * 
 * To learn more about genome, DNA and related material visit:
 * 
 * http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp1_1_1.shtml
 * 
 * For a tutorial on SNPs visit:
 * 
 * http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml
 * 
 * Author: Aditya Mathur
 * Original: September 13, 14, 2008
 * For use in: CS 190M.
 */

import java.util.Scanner;

class BioInformaticsApp{   
  // Obtain DNA sequence from inut source.
  
  static String getDNASeq(char[] DNA, Scanner s){
    
    int bases=0;   
    
    System.out.print("Next DNA sequence please:");    
    String DNAString=s.next(); // Get a DNA sequence.
    
    while (bases<DNAString.length()){
      char ntide=DNAString.charAt(bases);
      DNA[bases]=ntide;
      bases++;
    }
    return(DNAString);
  }
  
  // Compare two DNA sequences to determine any SNP.
  
  static int findSNP(char [] dOne, char [] dTwo, int [] snpPos, int seqSize){
    int snpsFound=0;
    int nextBase=0;
    while (nextBase<seqSize){
      System.out.println("Bases to compare: "+dOne[nextBase]+" and "+ dTwo[nextBase]);
      if(dOne[nextBase]!=dTwo[nextBase]){
        snpPos[snpsFound]=nextBase;
        snpsFound++;
      }
      nextBase++;
    }
    return(snpsFound);
  }
  
  public static void main(String[] args){
    char [] dnaOne;
    char[] dnaTwo;
    int [] snpPos;    
    int seqSize;
   
    int snpsFound=0;
    final int seqLen=10;
    
    Scanner k=new Scanner(System.in); // Create scanner from keyboard.
    
    dnaOne=new char [seqLen]; // Create all three arrays.
    dnaTwo=new char[seqLen];
    snpPos=new int[seqLen];
    
    // Read and display the two DNA seqeunces.
    String DNA=getDNASeq(dnaOne, k);
    System.out.println("First DNAsequence: "+ DNA);
    DNA=getDNASeq(dnaTwo,k);
    System.out.println("Second DNAsequence: "+ DNA);
    seqSize=DNA.length(); // Assuming seqeunces of same size.
    
    // Find and display SNPs.
    
    snpsFound=findSNP(dnaOne, dnaTwo, snpPos, seqSize);
    System.out.println("SNPs found: "+snpsFound);
    
    for (int i=0; i<snpsFound; i++){
      System.out.println("SNP at position: "+snpPos[i]+ " : "+ dnaOne[snpPos[i]]+" ," +dnaTwo[snpPos[i]]);
    }
  }
}