add Sequence Alignment

Author: younghoh

08/SequenceAlignment.java

@@ -0,0 +1,88 @@
+package hw08;
+
+import java.util.Scanner;
+
+public class SequenceAlignment {
+    private int gapCost = 1;
+    private int mismatchCost = 2;
+    private String str1 = null, str2 = null;
+    private int[][] M = null;
+
+    public SequenceAlignment(){
+        Scanner sc = new Scanner(System.in);
+        System.out.print("String1 : ");
+        str1 = sc.nextLine();
+        System.out.print("String2 : ");
+        str2 = sc.nextLine();
+        M = new int[str1.length()+1][str2.length()+1];
+    }
+
+    public void sequenceAlignment(){
+        for(int i = 0; i<str2.length() + 1; i++){
+            M[0][i] = i * gapCost;
+        }
+
+        for(int i = 0; i<str1.length() + 1; i++){
+            M[i][0] = i * gapCost;
+        }
+
+        for(int i = 1; i<str1.length()+1 ;i ++){
+            for(int j = 1; j<str2.length()+1 ; j++){
+                M[i][j] = Math.min(Math.min(calcMismatchCost(i - 1,j - 1) + M[i-1][j-1], gapCost + M[i-1][j]), gapCost + M[i][j-1]);
+            }
+        }
+    }
+
+    private int calcMismatchCost(int x, int y){
+        if(str1.charAt(x) == str2.charAt(y)){
+            return 0;
+        }
+        return mismatchCost;
+    }
+
+    // 배열로도 구할수 있지 않을까?
+    private void printRoute(int x, int y){
+        System.out.print("M[" + x +"][" + y +"] => ");
+        if(x == 0 && y == 0){
+            return ;
+        }else if(y == 0){
+            printRoute(x - 1, y);
+        }else if(x == 0){
+            printRoute(x, y-1);
+        }else if(calcMismatchCost(x - 1,y - 1) + M[x-1][y-1] < gapCost + M[x-1][y]){
+            if(calcMismatchCost(x - 1,y - 1) + M[x-1][y-1] < gapCost + M[x][y-1]){
+                printRoute(x-1,y-1);
+            }
+            else{
+                printRoute(x,y-1);
+            }
+        }else{
+            if(gapCost + M[x-1][y] < gapCost + M[x][y-1]){
+                printRoute(x-1,y);
+            }else{
+                printRoute(x,y-1);
+            }
+        }
+    }
+
+    public void print(){
+        System.out.println("MIN COST : " + M[str1.length()][str2.length()]);
+
+        System.out.print("      ");
+        for(int i = 0; i<str2.length(); i++){
+            System.out.printf("%3s", str2.charAt(i));
+        }
+        System.out.println();
+
+        for(int i = 0; i<str1.length()+1 ;i ++){
+            for(int j = 0; j<str2.length()+1 ; j++){
+                if( i == 0  && j == 0) System.out.print("   ");
+                else if( i > 0 && j == 0 ) System.out.printf("%3s", str1.charAt(i-1));
+                System.out.printf("%3s", M[i][j]);
+            }
+            System.out.println();
+        }
+
+        printRoute(str1.length(), str2.length());
+    }
+}

README.md

@@ -6,3 +6,4 @@
 5. Minimize Lateness / Huffman Code
 6. Dijkstra / Prim
 7. Knapsack
+8. Sequence Alignment