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; }