From 83e8fe02aad5dd5d4db76ff7acc09eafb5aa4bd1 Mon Sep 17 00:00:00 2001
From: Abdurrezzak Efe <abdurrezak.efe@ug.bilkent.edu.tr>
Date: Wed, 8 Nov 2017 22:04:09 +0200
Subject: [PATCH] Add files via upload

---
 16.LAP.cpp | 111 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 111 insertions(+)
 create mode 100644 16.LAP.cpp

diff --git a/16.LAP.cpp b/16.LAP.cpp
new file mode 100644
index 0000000..8f301de
--- /dev/null
+++ b/16.LAP.cpp
@@ -0,0 +1,111 @@
+/*
+ * This program finds the best local alignment for two strings
+ * using Dynamic Programming (Smith- Waterman Algorithm)
+ *
+ *      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 LA(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';
+
+    int max_value = -100000; //biggest value in dynamic table yet
+    int maxi = 0;
+    int maxj = 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(max(d[i-1][j-1] + match_rew, d[i-1][j]-indel_pen), d[i][j-1]-indel_pen), 0);
+            else
+                d[i][j] = max(max(max(d[i-1][j]-indel_pen, d[i][j-1]-indel_pen), d[i-1][j-1]-mismatch_pen), 0);
+
+            if(d[i][j] > max_value) //keeping the biggest value
+                max_value = d[i][j], maxi = i, maxj = j;
+
+            if(d[i][j] == 0)
+                t[i][j] = 's';
+            else if(d[i][j] == d[i-1][j-1]-mismatch_pen ) //mismatch(negative)
+                t[i][j] = 'n';
+            else if(d[i][j] == d[i-1][j-1] + match_rew && s1[i-1] == s2[j-1]) //match(positive)
+                t[i][j] = 'p';
+            else if(d[i][j] == d[i-1][j] - indel_pen) //indel up
+                t[i][j] = 'u';
+            else //indel left
+                t[i][j] = 'l';
+
+        }
+    }
+
+    str1=""; //getting local part of s1
+    str2=""; //getting local part of s2
+
+    int i= maxi;
+    int j= maxj;
+
+
+    while(d[i][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;
+
+    LA(s1,s2);
+
+    cout << str1 << endl << str2 << endl;
+}