int find_best_pos(const std::string &sa, const std::string &sb) {
char cc[4] = {'A', 'G', 'T', 'C'};
std::vector<int> va, vb, res, ans;
ans.resize(sa.length() - sb.length() + 1, 0);
int sh = sa.length() - 1 + sb.length();
for (int c_it = 0; c_it < 4; ++c_it) {
strings_to_vectors(sa, sb, va, vb, cc[c_it]);
/* std::cerr << "va: ";
for (int i = 0; i < va.size(); ++i)
std::cerr << va[i] << " ";
std::cerr << std::endl;
std::cerr << "vb: ";
for (int i = 0; i < vb.size(); ++i)
std::cerr << vb[i] << " ";
std::cerr << std::endl; */
multiply_vec(va, vb, res);
for (int i = sh; i < sh + sa.length() - sb.length() + 1; ++i) {
ans[ans.size() - 1 - (i - sh)] += res[i];
}
/* std::cerr << "re: ";
for (int i = 0; i < res.size(); ++i)
std::cerr << res[i] << " ";
std::cerr << std::endl; */
// std::cerr << std::endl;
}
int max = -1, _ans = 0;
for (int i = 0; i < ans.size(); ++i) {
// std::cerr << ans[i] << " ";
if (ans[i] > max) {
max = ans[i];
_ans = i;
}
}
// std::cerr << std::endl;
return _ans + 1;
}
//solves the CG algorithm
int CGSolver(std::vector<double> &val,
std::vector<int> &row_ptr,
std::vector<int> &col_idx,
std::vector<double> &b,
std::vector<double> &x,
double tol,
std::string soln_prefix)
{
//initializes variables
std::vector<double> r;
std::vector<double> Ax = multiply_vec(val, col_idx, row_ptr, x); //make multiply vec
double l2norm0;
r=subtract_vec(b,Ax);
l2norm0 = l2normer(r);// finds norm of l
std::vector<double> p=r;
int niter = 1;
// write the initial guess
std::stringstream s;
s << std::setfill('0') << std::setw(3) << 0;
//--compile_0
//--Originally, this was left `std::string filename = soln_` where soln_ undefined
//--and the line missing a closing semi-colon. Also, `ix` not defined below...
std::string filename = soln_prefix;
//ix + s.str() + ".txt"; // This line was left-in (not commented upon submission) but it doesn't perform any assignment or operation!
WriteSoln(x, filename);
//--END
while (niter<row_ptr.size()){
niter = niter +1;
//multiply p from first 3 inpouts
std::vector<double> Ap = multiply_vec(val, col_idx, row_ptr,p);
//get dot product
double r_initial = dot_product(r,r);
double alpha = r_initial/dot_product(p,Ap);
//multiply vector by coeffifient alpha, also single for loop
x= add_vec(x, multiply_coeff(alpha,p));
// add vector adds two vectors . will be similar to dot product but will add instead
r = add_vec(r,multiply_coeff(-alpha,Ap));
double l2normr=l2normer(r);
//returns the number of iterations
if (l2normr/l2norm0 < tol){
std::stringstream s;
s << std::setfill('0') << std::setw(3) << niter;
std::string filename = soln_prefix + s.str() + ".txt";
WriteSoln(x, filename);
return int(niter);
}
double beta = dot_product(r,r)/r_initial;
p=add_vec(r, multiply_coeff(beta,p));
if (niter % 10==0) {
std::stringstream s;
s << std::setfill('0') << std::setw(3) << niter;
std::string filename = soln_prefix + s.str() + ".txt";
WriteSoln(x, filename);
}
}
// otherwise the algorithm diverges
return -1;
}
