alignment

gistfile1.java

import java.util.Arrays;


public class alignment {
	
	public static int D= 1;
	public static int MATCH = 2;
	public static int MISMATCH = -1;
	
	public static void main(String[] args){
		//int[][] foo = computeMatrix(Sequenzen.NP_000913, Sequenzen.NP_246273);
		int[][] bar = computeMatrix("IVVGSAAHCYGEDN", "IVLTAAHCVSASGEHN");
		//System.out.println(foo[1][1]);
		System.out.println(bar[1][1]);
		
	}
	
	
	public static int[][] computeMatrix(String seq1, String seq2){
		int[][] matrix = new int[seq1.length()+1][seq2.length()+1];
		for(int i = seq1.length()-1; i>0; i--){
			for(int j=seq2.length()-1; j>0; j--){
				matrix[i][j] = max(matrix, i, j, seq1, seq2);
			}
		}
		return matrix;
	}
	
	public static int max(int[][] matrix, int i, int j, String seq1, String seq2){
		char[] a = StringToArray(seq1);
		char[] b = StringToArray(seq2);
		int [] foo = {matrix[i+1][j+1]+s(matrix, a, b, i, j), matrix[i+1][j] -D , matrix[i][j+1] -D};
		
		Arrays.sort(foo);
		return foo[foo.length-1];
	}
	
	public static char[] StringToArray(String s){
		char[] foo = new char[s.length()+1];
		for(int i=0; i<s.length();i++){
			foo[i+1] = s.charAt(i);
		}
		return foo;
	}
	
	 private static int s(int[][] matrix, char[] t1Array, char[] t2Array, int i, int j) {
		    int hier;
		    if(t1Array[i] == t2Array[j])
		      hier = matrix[i+1][j+1] + MATCH;
		  
		    else
		      hier = matrix[i+1][j+1] + MISMATCH;

		    return hier;
		  }

}