Sequence-matching-1

#include <bits/stdc++.h>

using namespace std;


int main(int argc, char **argv) {

   string s1, s2;

   if (argc > 1) {
       s1 = argv[1];
       s2 = argv[2];
   }
   else {
       cout << "s1: ";
       cin >> s1;
       cout << "s2: ";
       cin >> s2;
   }

   int n = s1.length(), m = s2.length();
   int dp[n+1][m+1] = {0};

   // penalties
   int gap = 2; // penalty for matching a character to a gap
   int mis = 3; // penalty for matching a character to a different character


   for (int i = 1; i < n+1; i++)
       dp[i][0] = i*gap;

   for (int i = 1; i < m+1; i++)
       dp[0][i] = i*gap;

   for (int i = 1; i < n+1; i++)
       for (int j = 1; j < m+1; j++)
       {
           if ( s1[i-1] == s2[j-1]) dp[i][j] = dp[i-1][j-1];
           else dp[i][j] = min({dp[i][j-1] + gap, dp[i-1][j] + gap, dp[i-1][j-1] + mis});
       }

   string s1_out="", s2_out="";

   int i=n, j=m;

   cout << "Gap Score: " << dp[n][m] << endl;

   while (i>0 && j > 0) {
       if (dp[i-1][j] + gap == dp[i][j]) {
           s1_out += s1[i-1];
           s2_out += '-';
           i--;
       }
       else if (dp[i][j-1] + gap == dp[i][j]) {
           s1_out += '-';
           s2_out += s2[j-1];
           j--;
       }
       else if (s1[i-1] == s2[j-1] || dp[i-1][j-1] + mis == dp[i][j]) {
           s1_out += s1[i-1];
           s2_out += s2[j-1];
           i--; j--;
       }
   }

   while (i--)
       s1_out += s1[i];

   while (j--)
       s2_out += s2[j];

   while (s1_out.length() > s2_out.length())
       s2_out += '-';

   while (s2_out.length() > s1_out.length())
       s1_out += '-';

   reverse(s1_out.begin(), s1_out.end());
   reverse(s2_out.begin(), s2_out.end());

   cout << s1_out << '\n' << s2_out << endl;
}