int main(int argc, char **args) {
Forwarder f;
size_t alphabet_size = 3;
f.read_seq_directory("sequences", alphabet_size);
f.write_to_directory("example_out");
Matrix pi, A, B;
read_HMM(pi, A, B, "example.hmm");
std::cout << "log-likelihood: " << f.forward(pi, A, B) << std::endl;
// std::cout << "log-likelihood: " << f.pthread_forward(pi, A, B) << std::endl; // parallelized on the lengths of the sequences
// std::cout << "log-likelihood: " << f.mr_pthread_forward(pi, A, B) << std::endl; // parallelized version on the number of sequences
return 0;
}
int main(int argc, char **args) {
Forwarder f;
size_t alphabet_size = 3;
f.read_seq("example.seq", alphabet_size);
f.write_to_directory("example_out");
Matrix pi, A, B;
read_HMM(pi, A, B, "example.hmm");
std::cout << "log-likelihood: " << f.forward(pi, A, B) << std::endl;
// std::cout << "log-likelihood: " << f.pthread_forward(pi, A, B) << std::endl; # parallelized version
std::vector<unsigned> pd_path;
Matrix pd_table;
posterior_decoding("example.seq", pi, A, B, pd_path, pd_table);
std::cout << "posterior path[0:10]: ";
for(size_t i = 0; i < 10; ++i)
std::cout << pd_path[i] << " ";
std::cout << std::endl;
std::cout << "posterior table column 0 - 9: " << std::endl;
for(size_t r = 0; r < 2; ++r) {
for(size_t c = 0; c < 10; ++c) {
std::cout << pd_table(r, c) << "\t";
}
std::cout << std::endl;
}
std::vector<unsigned> viterbi_path;
double viterbi_ll = viterbi("example.seq", pi, A, B, viterbi_path);
std::cout << "viterbi loglikelihood: " << viterbi_ll << std::endl;
std::cout << "viterbi path[0:10]: ";
for(size_t i = 0; i < 10; ++i)
std::cout << viterbi_path[i] << " ";
std::cout << std::endl;
return 0;
}
