vector<vector<double>> Alignment::get_q_matrix() {
if(!model) throw Exception("No model has been set.");
RowMatrix<double> gen = model->getGenerator();
size_t nrow = gen.getNumberOfRows();
size_t ncol = gen.getNumberOfColumns();
auto q = vector<vector<double>>(nrow, vector<double>(ncol, 0));
for (size_t i = 0; i < nrow; ++i) {
for (size_t j = 0; j < ncol; ++j) {
q[i][j] = gen(i, j);
}
}
return q;
}
vector<vector<double>> Alignment::get_p_matrix(double time) {
if(!model) throw Exception("No model has been set.");
RowMatrix<double> pijt = model->getPij_t(time);
size_t nrow = pijt.getNumberOfRows();
size_t ncol = pijt.getNumberOfColumns();
auto p = vector<vector<double>>(nrow, vector<double>(ncol, 0));
for (size_t i = 0; i < nrow; ++i) {
for (size_t j = 0; j < ncol; ++j) {
p[i][j] = pijt(i, j);
}
}
return p;
}
vector<vector<double>> Alignment::get_exchangeabilities() {
if(!model) throw Exception("No model has been set.");
RowMatrix<double> exch = model->getExchangeabilityMatrix();
size_t nrow = exch.getNumberOfRows();
size_t ncol = exch.getNumberOfColumns();
auto s = vector<vector<double>>(nrow, vector<double>(ncol, 0));
for (size_t i = 0; i < nrow; ++i) {
vector<double> row;
for (size_t j = 0; j < ncol; ++j) {
s[i][j] = exch(i, j);
}
}
return s;
}