sw_base.cpp

#include <iostream>  // std::cout
#include <string>
#include <vector>
#include <utility>
#include <algorithm> // for copy
#include <iterator> // for ostream_iterator
#include "traceback.cpp"


template < typename T >
    void sw_base(std::pair< T, T > data){
        // instantiate a matrix 
        std::vector<std::vector<int>> matrix(data.first.size() + 1,std::vector<int>(data.second.size() + 1,0));

        // populate the matrix
        int gaps(-2), mismatch(-2), match(3);
        int diagonal_value, top_value, left_value;
        int max_element(0), max_element_i(0), max_element_j(0);
        for (long unsigned int i=1; i<data.first.size() + 1; ++i){
            for(long unsigned int j=1; j<data.second.size() + 1; ++j) {
                diagonal_value = matrix[i-1][j-1] + (data.first[i - 1] == data.second[j - 1] ? match : mismatch);
                top_value = matrix[i-1][j] + gaps;
                left_value = matrix[i][j-1] + gaps;
                int target_value = std::max(diagonal_value, std::max(top_value, left_value));
                matrix[i][j] = (target_value > 0) ? target_value : 0;
                if (target_value > max_element) {
                    max_element = target_value;
                    max_element_i = i;
                    max_element_j = j;
                }
            }
        }
        std::cout << max_element << " " << max_element_i << " " << max_element_j << std::endl;

        // // Traceback
        // traceback(matrix, max_element_i, max_element_j);
}