/// Find the probabilities of each letter at the root, given the data at the nodes in 'group'
vector<Matrix>
get_column_likelihoods(const data_partition& P, const vector<int>& b,
const vector<int>& req,const vector<int>& seq,int delta)
{
const alphabet& a = P.get_alphabet();
const alignment& A = *P.A;
const Tree& T = *P.T;
Likelihood_Cache& LC = P.LC;
#ifndef NDEBUG
subA_index_check_footprint(A,T);
subA_index_check_regenerate(A,T);
#endif
//------ Check that all branches point to a 'root' node -----------//
assert(b.size());
int root = T.directed_branch(b[0]).target();
for(int i=1;i<b.size();i++)
assert(T.directed_branch(b[i]).target() == root);
LC.root = root;
ublas::matrix<int> index = subA_index_any(b,A,T,req,seq);
IF_DEBUG(int n_br =) calculate_caches(P);
#ifndef NDEBUG
std::clog<<"get_column_likelihoods: Peeled on "<<n_br<<" branches.\n";
#endif
vector<Matrix> L;
L.reserve(A.length()+2);
Matrix& S = LC.scratch(0);
const int n_models = S.size1();
const int n_states = S.size2();
//Add the padding matrices
{
for(int i=0;i<S.size1();i++)
for(int j=0;j<S.size2();j++)
S(i,j) = 0;
for(int i=0;i<delta;i++)
L.push_back(S);
}
const vector<unsigned>& smap = P.SModel().state_letters();
for(int i=0;i<index.size1();i++) {
for(int m=0;m<n_models;m++) {
for(int s=0;s<n_states;s++)
S(m,s) = 1;
//-------------- Propagate and collect information at 'root' -----------//
for(int j=0;j<b.size();j++) {
int i0 = index(i,j);
if (i0 != alphabet::gap)
for(int s=0;s<n_states;s++)
S(m,s) *= LC(i0,b[j])(m,s);
}
if (root < T.n_leaves()) {
int rl = A.seq(root)[i];
if (a.is_letter_class(rl))
for(int s=0;s<n_states;s++)
if (not a.matches(smap[s],rl))
S(m,s) = 0;
}
}
L.push_back(S);
}
return L;
}
