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local_affinegap.cpp
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local_affinegap.cpp
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#include<bits/stdc++.h>
using namespace std;
int D(char x,char y,int match,int mismatch){
if(x==y) return match;
else return -1*mismatch;
}
int max_4(int a,int b,int c,int d){
return max(max(a,b),max(c,d));
}
void print_in80s(vector <char> v1,vector <char> v2){
//int itr = 1;
int len = v1.size();
cout << "Length of local alignment = " << len << endl;
int i = 0;
while(i<len){
//cout << "ee";
for(int j=i;j<min(len,i+80);j++){
cout << v1[j];
//cout << "ee";
}
cout << "\n";
for(int j=i;j<min(len,i+80);j++){
cout << v2[j];
}
cout << "\n\n";
i = i+80;
}
}
int main(){
string s1 ;
string s2 ; //sequences to be aligned
int match;
int mismatch;
int d; //d in -d - sigma
int x; //sigma
cin >> match >> mismatch >> d >> x;
cin >> s1;
cin >> s2;
int m1[s1.length()+1][s2.length()+1];
int m2[s1.length()+1][s2.length()+1];
int m[s1.length()+1][s2.length()+1];
for(int i=0;i<1;i++){
for(int j=0;j<s2.length()+1;j++){
m1[i][j]=0;
m2[i][j]=0;
m[i][j] =0;
}
}
for(int i=0;i<s1.length()+1;i++){
for(int j=0;j<1;j++){
m1[i][j]=0;
m2[i][j]=0;
m[i][j] =0;
}
}
int max_score = 0;
vector <pair <int,int> > pos;
vector <char> from[s1.length()+1][s2.length()+1]; //= N null 0,T top 1,L left 2,D diagonal 3
for(int i=0;i<1;i++){
for(int j=0;j<s2.length()+1;j++){
from[i][j].push_back('N');
}
}
for(int i=0;i<s1.length()+1;i++){
for(int j=0;j<1;j++){
if(i!=0 || j!=0)from[i][j].push_back('N');
}
}
for(int i=1;i<s1.length()+1;i++){
for(int j=1;j<s2.length()+1;j++){
m1[i][j] = max(m1[i-1][j] - x,m[i-1][j] - d - x);
m2[i][j] = max(m2[i][j-1] - x,m[i][j-1] - d - x);
m[i][j] = max_4(m[i-1][j-1] + D(s1[i-1],s2[j-1],match,mismatch),m1[i][j],m2[i][j],0);
if(max_score<m[i][j]){
max_score = m[i][j];
}
//trace path
if(m[i][j]==0){
from[i][j].push_back('N');
}
if(m[i][j]==m[i-1][j-1] + D(s1[i-1],s2[j-1],match,mismatch)){
from[i][j].push_back('D');
}
if(m[i][j]==m1[i][j]){
from[i][j].push_back('T');
}
if(m[i][j]==m2[i][j]){
from[i][j].push_back('L');
}
}
}
//getting score and positions
if(max_score!=0){
cout << "--- MAXIMUM SCORE = "<< max_score << " ---"<< endl;
for(int i=1;i<s1.length()+1;i++){
for(int j=1;j<s2.length()+1;j++){
if(m[i][j]==max_score) pos.push_back(make_pair(i,j));
}
}
}
else {
cout << "--- MAXIMUM SCORE is NULL ---" << endl;
exit(0);
}
pair <int,int> pos_start[pos.size()];
vector <char> path[pos.size()];
//preparing data
for(int i=0;i<pos.size();i++){
int x_end = pos[i].first;
int y_end = pos[i].second;
int x = pos[i].first;
int y = pos[i].second;
while(from[x][y][0]!='N'){
path[i].push_back(from[x][y][0]);
if(from[x][y][0]=='D'){
x--;
y--;
}
else if(from[x][y][0]=='T'){
x--;
}
else if(from[x][y][0]=='L'){
y--;
}
}
int x_st = x;
int y_st = y;
pos_start[i] = make_pair(x_st,y_st);
}
//putting paths in order
for(int i=0;i<pos.size();i++){
reverse(path[i].begin(),path[i].end());
}
//printing matrices
/*for(int i=0;i<pos.size();i++){
for(int j=0;j<path[i].size();j++){
cout << path[i][j] << ' ';
}
cout << endl;
}
for(int i=0;i<s1.length()+1;i++){
for(int j=0;j<s2.length()+1;j++){
cout << m1[i][j] << ' ';
}
cout << endl;
}
for(int i=0;i<s1.length()+1;i++){
for(int j=0;j<s2.length()+1;j++){
cout << m2[i][j] << ' ';
}
cout << endl;
}
for(int i=0;i<s1.length()+1;i++){
for(int j=0;j<s2.length()+1;j++){
cout << m[i][j] << ' ';
}
cout << endl;
}
for(int i=0;i<s1.length()+1;i++){
for(int j=0;j<s2.length()+1;j++){
for(int k=0;k<from[i][j].size();k++){
cout << from[i][j][k];
}
cout << ' ';
}
cout << endl;
}*/
//printing alignments
int n_al = pos.size(); //number of alignments to be printed
for(int i=0;i<n_al;i++){
cout << "--- ALIGNMENT " << i+1 << " ---" << endl;
cout << "Indexes of alignments in sequences : ";
cout<<'('<<pos_start[i].first+1<<","<<pos[i].first<<')'<<" AND "<<'('<<pos_start[i].second+1<<","<<pos[i].second<<')'<<endl;
pair <int,int> start = pos_start[i];
pair <int,int> end = pos[i];
vector <char> align1;
vector <char> align2;
int itr = 0;
while((start!=end) && itr < path[i].size()){
if(path[i][itr]=='D'){
start.first = start.first + 1;
start.second = start.second + 1;
align1.push_back(s1[start.first-1]);
align2.push_back(s2[start.second-1]);
}
else if(path[i][itr]=='T'){
start.first = start.first + 1;
align1.push_back(s1[start.first-1]);
align2.push_back('-');
}
else if(path[i][itr]=='L'){
start.second = start.second + 1;
align1.push_back('-');
align2.push_back(s2[start.second-1]);
}
itr++;
}
/*for(int len=0;len<align1.size();len++){
cout << align1[len];
}
cout << endl;
for(int len=0;len<align2.size();len++){
cout << align2[len];
}
cout << endl;
cout << "new output\n";*/
print_in80s(align1,align2);
}
return 0;
}