int GBKernelComputation::calc()
{
// First find the skeleton
for (int i = 0; i < gb.length(); i++) new_pairs(i);
// Debug code
GBMatrix *mm = new GBMatrix(G);
for (int p = 0; p < syzygies.length(); p++)
mm->append(GR->gbvector_copy(syzygies[p]));
buffer o;
Matrix *m = mm->to_matrix();
if (M2_gbTrace >= 5)
{
o << "skeleton = " << newline;
m->text_out(o);
emit(o.str());
}
// Sort the skeleton now?
// Now reduce each one of these elements
for (int j = 0; j < syzygies.length(); j++)
{
gbvector *v = s_pair(syzygies[j]);
reduce(v, syzygies[j]);
}
return COMP_DONE;
}
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);
}
}
