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; }