efloat_t prior_HMM_rootless_scale(const data_partition& P)
{
const Tree& T = *P.T;
#ifndef NDEBUG
assert(P.has_IModel());
check_internal_nodes_connected(*P.A,T);
#endif
efloat_t Pr = 1;
for(int i=T.n_leaves();i<T.n_nodes();i++) {
int l = P.seqlength(i);
efloat_t temp = P.IModel().lengthp(l);
Pr /= (temp*temp);
}
return Pr;
}
/// Probability of a multiple alignment if branch alignments independant
efloat_t prior_HMM_nogiven(const data_partition& P)
{
const alignment& A = *P.A;
const Tree& T = *P.T;
#ifndef NDEBUG
assert(P.has_IModel());
check_internal_nodes_connected(A,T);
#endif
efloat_t Pr = 1;
for(int b=0;b<T.n_branches();b++) {
int target = T.branch(b).target();
int source = T.branch(b).source();
Pr *= prior_branch(A, P.branch_HMMs[b], target, source);
}
return Pr;
}
boost::shared_ptr<DPmatrixSimple> sample_alignment_base(data_partition& P,int b)
{
assert(P.has_IModel());
dynamic_bitset<> s1 = constraint_satisfied(P.alignment_constraint, *P.A);
const Tree& T = *P.T;
//FIXME - partitions
data_partition P0 = P; // We COULD make this conditional... perhaps we should
//FIXME - partitions
alignment& old = *P0.A;
const Matrix frequency = substitution::frequency_matrix(P.SModel());
int node1 = T.branch(b).target();
int node2 = T.branch(b).source();
dynamic_bitset<> group1 = T.partition(node2,node1);
// Find sub-alignments and sequences
vector<int> seq1;
vector<int> seq2;
vector<int> seq12;
for(int column=0;column<old.length();column++)
{
if (not old.gap(column,node1))
seq1.push_back(column);
if (not old.gap(column,node2))
seq2.push_back(column);
if (not old.gap(column,node1) or old.gap(column,node2))
seq12.push_back(column);
}
//FIXME - this makes the debug routines crash
if (not seq1.size() or not seq2.size())
return boost::shared_ptr<DPmatrixSimple>(); //NULL;
/******** Precompute distributions at node2 from the 2 subtrees **********/
distributions_t_local distributions = distributions_tree;
if (not P.smodel_full_tree)
distributions = distributions_star;
vector< Matrix > dists1 = distributions(P0,seq1,b,true);
vector< Matrix > dists2 = distributions(P0,seq2,b,false);
vector<int> state_emit(4,0);
state_emit[0] |= (1<<1)|(1<<0);
state_emit[1] |= (1<<1);
state_emit[2] |= (1<<0);
state_emit[3] |= 0;
boost::shared_ptr<DPmatrixSimple>
Matrices( new DPmatrixSimple(state_emit, P.branch_HMMs[b].start_pi(),
P.branch_HMMs[b], P.beta[0],
P.SModel().distribution(), dists1, dists2, frequency)
);
//------------------ Compute the DP matrix ---------------------//
vector<int> path_old = get_path(old,node1,node2);
vector<vector<int> > pins = get_pins(P.alignment_constraint,old,group1,~group1,seq1,seq2,seq12);
vector<int> path = Matrices->forward(pins);
path.erase(path.begin()+path.size()-1);
*P.A = construct(old,path,node1,node2,T,seq1,seq2);
P.LC.set_length(P.A->length());
P.LC.invalidate_branch_alignment(T,b);
P.note_alignment_changed_on_branch(b);
#ifndef NDEBUG_DP
assert(valid(*P.A));
dynamic_bitset<> s2 = constraint_satisfied(P.alignment_constraint, *P.A);
report_constraints(s1,s2);
vector<int> path_new = get_path(*P.A, node1, node2);
path.push_back(3);
assert(path_new == path);
#endif
return Matrices;
}