//// This file contains some example code, which may be used to call // the sequence algorithms class.//// This code is not necessarily meant to be useful in itself, but is provided as // an example of how the class may be used.//// Copyright (C) 1999 Software Engineering Group, Crystallography Department,// Birkbeck College, Malet Street, London WC1E 7HX, U.K.// (d.moss@mail.cryst.bbk.ac.uk or m.williams@biochemistry.ucl.ac.uk)// // This library is free software; you can redistribute it and/or modify it // under the terms of the GNU Library General Public License as published by // the Free Software Foundation; either version 2 of the License, or (at your// Handle) any later version.  This library is distributed in the hope// that it will be useful, but WITHOUT ANY WARRANTY; without even the// implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR// PURPOSE.  See the GNU Library General Public License for more details.// You should have received a copy of the GNU Library General Public// License along with this library; if not, write to the Free Software// Foundation, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.///////////////////////////////////////////////////////////////////////////////////////// Author: Mark Williams // /////////////////////////////////////////////////////////////////////////////////////// // Brief Description of Code:// // Find the number of elements that that are identical between two aligned sequences.//// For further details of the btl_sequence_algorithms, see the documentation for// the class./////////////////////////////////////////////////////////////////////////////////////#include <vector>#include <iostream>using namespace std;#include "btl_sequence_algorithms.h"using namespace btl;int main() {   // The sequences need to be held in containers that provide appropriate iterators    // for the BTL alignment algorithms. In this case, the sequences are entered from the keyboard and   // the standard STL member function push_back() is used to place the data in STL vectors.   vector<char> sequence, target; char temp[80];   cout << "Please enter the first sequence (maximum 80 characters); \n";   cin >> temp;   int i = 0;   while (temp[i] != '\0'){       sequence.push_back(temp[i]);        i++;    }    cout << "Please enter the second sequence (maximum 80 characters); \n";    cin >> temp;    i = 0;    while (temp[i] != '\0'){         target.push_back(temp[i]);         i++;    }    // Calculate the similarity score for the two sequences using the default identity matrix scoring scheme in     // the BTL pairwise alignment algorithm. The iterators pointing to the beginning and end of each sequence     // are found using the standard begin() and end() STL container member functions.    float score = 0.0;    score = needleman_wunsch_similarity(sequence.begin(),sequence.end(),target.begin(),target.end(),1,0,0,0,score);    cout << "\nThe number of identities between the aligned sequences is " << score << "\n";	    return 0;}