// NW.java
// Rhys Price Jones -- 6.i.2004, updated 24ix09
//
// Simple Needleman-Wunsch global alignment of 
//   two strings entered on command line
// Example usage:
// java NW IamAGoodString IamAnotherString

public class NW {
    // Using simple linear gap score (-2 per indel)
    // and 4 for a match, -1 for a mismatch
    // Feel free to change this
    public static final int gapscore = -2;
    public static final int matchscore = 4;
    public static final int mismatchscore = -1;
    
    private String x;  // First string
    private String y;  // Second string
    private int xlen, ylen; // their lengths
    private int[][] scoreArray;
    
    public NW(String a, String b) {
        x = a;
        y = b;
        xlen = x.length();
        ylen = y.length();
        scoreArray = new int[ylen+1][xlen+1];
    } 
    
    public void fillScoreArray() {
        int row, col;    // for indexing through array
        int northwest, north, west;  // (row, col) entry will be max of these
        int best;   // will be the max
        // Fill the top row and left column:
        for (col=0; col <= xlen; col++) scoreArray[0][col] = gapscore*col;
        for (row=0; row <= ylen; row++) scoreArray[row][0] = gapscore*row;
        // Now fill in the rest of the array:
        for (row=1; row <= ylen; row++) {
            for (col=1; col <= xlen; col++) {
                if (x.charAt(col-1)==y.charAt(row-1)) 
                    northwest = scoreArray[row-1][col-1] + matchscore;
                else northwest = scoreArray[row-1][col-1] + mismatchscore;
                west = scoreArray[row][col-1] + gapscore;
                north = scoreArray[row-1][col] + gapscore;
                best = northwest;
                if (north>best) best = north;
                if (west>best) best = west;
                scoreArray[row][col] = best;
            }
        }
    }
    
    public void print3(int x) {
        // Print x in 3 spaces
        String s = ""+x;
        if (s.length() == 1) System.out.print("  "+s);
        else if (s.length() == 2) System.out.print(" "+s);
        else if (s.length() == 3) System.out.print(s);
        else System.out.print("***");
    }
    
    public void printArray() {
        for (int row=0; row < scoreArray.length; row++) {
            for (int col=0; col < scoreArray[row].length; col++) 
                print3(scoreArray[row][col]);
            System.out.println();
        }
    }
    
    public static void main(String[] args) {
        NW nw = new NW(args[0], args[1]);
        nw.fillScoreArray();
        nw.printArray();
    }
}