void read_HMM_spec(size_t &no_states, size_t &alphabet_size, std::istream &in) {
read_token_or_exit(in, "no_states");
no_states = read_or_exit<size_t>(in, "number of states");
read_token_or_exit(in, "alphabet_size");
alphabet_size = read_or_exit<size_t>(in, "number of observables");
}
void Forwarder::read_data_structure_from_stream(std::ifstream &in) {
read_token_or_exit(in, "orig_alphabet_size");
orig_alphabet_size = read_or_exit<size_t>(in, "original alphabet size");
read_token_or_exit(in, "orig_seq_length");
orig_seq_length = read_or_exit<size_t>(in, "original alphabet size");
read_token_or_exit(in, "nStates2alphabet_size");
while(!read_token_or_tell(in, "symbol2pair")) {
size_t no_states = read_or_exit<size_t>(in, "no_states");
nStates2alphabet_size[no_states] = read_or_exit<size_t>(in, "alphabet_size");
}
for(size_t i = orig_alphabet_size; i < nStates2alphabet_size.begin()->second; ++i) {
unsigned pair_symbol = read_or_exit<unsigned>(in, "pair symbol");
unsigned left_symbol = read_or_exit<unsigned>(in, "left symbol");
unsigned right_symbol = read_or_exit<unsigned>(in, "right symbol");
symbol2pair[pair_symbol] = s_pair(left_symbol, right_symbol);
}
}
void read_HMM(Matrix &result_pi, Matrix &result_A, Matrix &result_B, std::istream &in) {
size_t no_states;
size_t alphabet_size;
read_HMM_spec(no_states, alphabet_size, in);
read_token_or_exit(in, "pi");
result_pi.reset(no_states, 1);
for(size_t i = 0; i < no_states; ++i)
result_pi(i, 0) = read_or_exit<double>(in, "initial probability");
read_token_or_exit(in, "A");
result_A.reset(no_states, no_states);
for(size_t from = 0; from < no_states; ++from) {
for(size_t to = 0; to < no_states; ++to)
result_A(from, to) = read_or_exit<double>(in, "transition probability");
}
read_token_or_exit(in, "B");
result_B.reset(no_states, alphabet_size);
for(size_t i = 0; i < no_states; ++i) {
for(size_t ob = 0; ob < alphabet_size; ++ob)
result_B(i, ob) = read_or_exit<double>(in, "emission probability");
}
}
