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;
}
void test_forwarder_multiple_seqs() {
Forwarder forwarder;
Matrix pi, A, B;
size_t no_states, alphabet_size;
std::cout << "Testing forwarder with multiple sequences: ";
std::cout.flush();
read_HMM(pi, A, B, "../test_data/multiple_seqs.hmm");
no_states = pi.get_height();
alphabet_size = B.get_width();
forwarder.read_seq_directory("../test_data/seqs_directory", alphabet_size, no_states, 50);
assertClose(forwarder.forward(pi, A, B), -52287.6, "Forwarder: Difference in loglikelihood:", 0.0001);
assertClose(forwarder.pthread_forward(pi, A, B), -52287.6, "pthread_forward: Difference in loglikelihood:", 0.0001);
assertClose(forwarder.mr_pthread_forward(pi, A, B), -52287.6, "mr_pthread_forward: Difference in loglikelihood:", 0.0001);
std::cout << "ok." << std::endl;
}
void test_forwarder_long_sequence(const std::string &hmmFilename, const std::string &seqFilename, double expected_ll) {
Matrix pi, A, B;
size_t no_states, alphabet_size;
std::cout << "Testing " << hmmFilename << " " << seqFilename << ": ";
std::cout.flush();
read_HMM(pi, A, B, hmmFilename);
no_states = pi.get_height();
alphabet_size = B.get_width();
Forwarder forwarder;
forwarder.read_seq(seqFilename, alphabet_size, 500);
SimpleForwarder s_forwarder(seqFilename);
assertClose(forwarder.forward(pi, A, B), expected_ll, "Forwarder: Difference in likelihood log likelihood:", 0.0001);
assertClose(forwarder.pthread_forward(pi, A, B), expected_ll, "pthread_forward: Difference in likelihood log likelihood:", 0.0001);
assertClose(s_forwarder.forward(pi, A, B), expected_ll, "s_forward: Difference in log likelihood:", 0.0001);
std::cout << "ok." << std::endl;
}
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;
}
