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15.GAP.cpp

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+/*
+ * This program finds the best global alingment for two strings
+ * using Dynamic Programming
+ *
+ *      Coded by: Abdurrezak EFE
+ * */
+
+#include <iostream>
+#include <algorithm>
+#include <string>
+#include <stdio.h>
+using namespace std;
+
+
+
+int d[10000][10000]; // dynamic programming table
+char t[10000][10000]; //traceback table
+int mismatch_pen = 3;
+int match_rew = 5;
+int indel_pen = 1;
+
+string str1;
+string str2;
+
+string reverser(string str)
+{
+    string s="";
+    for(int i = str.size()-1;i>-1;i--)
+        s+=str[i];
+    return s;
+}
+
+void GA(string s1, string s2)
+{
+
+    for(int i=0;i<=s1.size();i++) // initiating first row as zeros
+        d[0][i] = (-1)*i*indel_pen, t[0][i] = 'l';
+
+    for(int i=0;i<=s2.size();i++) // initiating first column as zero
+        d[i][0] = (-1)*i*indel_pen, t[i][0] = 'u';
+
+
+    d[0][0] = 0;
+
+    for(int i=1; i<=s1.size(); i++)
+    {
+        for(int j=1; j<=s2.size(); j++)
+        {
+            if(s1[i-1] == s2[j-1])
+                d[i][j] = max(max(d[i-1][j-1] + match_rew, d[i-1][j]-indel_pen), d[i][j-1]-indel_pen);
+            else
+                d[i][j] = max(max(d[i-1][j]-indel_pen, d[i][j-1]-indel_pen), d[i-1][j-1]-mismatch_pen);
+
+            if(d[i][j] == d[i-1][j-1]-mismatch_pen ) //mismatch
+                t[i][j] = 'n';
+            else if(d[i][j] == d[i-1][j-1] + match_rew && s1[i-1] == s2[j-1]) //match
+                t[i][j] = 'p';
+            else if(d[i][j] == d[i-1][j] - indel_pen) //indel
+                t[i][j] = 'u';
+            else
+                t[i][j] = 'l';
+
+            //cout << d[i][j] << " ";
+        }
+        //cout << endl;
+    }
+
+    str1=""; //getting alignment of s1
+    str2=""; //getting alignment of s2
+
+    int i= s1.size();
+    int j= s2.size();
+
+    while(i>0 || j>0)
+    {
+        if(t[i][j] == 'u')
+        {
+            str1 += s1[i-1];
+            str2 += '-';
+            i--;
+        }
+        else if(t[i][j] == 'l')
+        {
+            str1 += '-';
+            str2 += s2[j-1];
+            j--;
+        }else
+        {
+            str1 += s1[i-1];
+            str2 += s2[j-1];
+            i--,j--;
+        }
+
+
+    }
+    str1 = reverser(str1);
+    str2 = reverser(str2);
+}
+
+int main()
+{
+    string s1,s2;
+
+    cin >> s1 >> s2;
+
+    GA(s1,s2);
+
+    cout << str1 << endl << str2 << endl;
+}