boost::shared_ptr<DParrayConstrained> sample_node_base(data_partition& P,const vector<int>& nodes)
{
default_timer_stack.push_timer("alignment::DP1/3-way");
const Tree& T = *P.T;
assert(P.variable_alignment());
alignment old = *P.A;
// std::cerr<<"old = "<<old<<endl;
/*------------- Compute sequence properties --------------*/
int n0 = nodes[0];
int n1 = nodes[1];
int n2 = nodes[2];
int n3 = nodes[3];
vector<int> columns = getorder(old,n0,n1,n2,n3);
// std::cerr<<"n0 = "<<n0<<" n1 = "<<n1<<" n2 = "<<n2<<" n3 = "<<n3<<std::endl;
// std::cerr<<"old (reordered) = "<<project(old,n0,n1,n2,n3)<<endl;
// Find sub-alignments and sequences
vector<int> seq1;
vector<int> seq2;
vector<int> seq3;
vector<int> seq123;
for(int i=0; i<columns.size(); i++) {
int column = columns[i];
if (not old.gap(column,n1))
seq1.push_back(column);
if (not old.gap(column,n2))
seq2.push_back(column);
if (not old.gap(column,n3))
seq3.push_back(column);
if (not old.gap(column,n1) or not old.gap(column,n2) or not old.gap(column,n3))
seq123.push_back(column);
}
// Map columns with n2 or n3 to single index 'c'
vector<int> icol(seq123.size()+1);
vector<int> jcol(seq123.size()+1);
vector<int> kcol(seq123.size()+1);
icol[0] = 0;
jcol[0] = 0;
kcol[0] = 0;
for(int c=1,i=0,j=0,k=0; c<seq123.size()+1; c++) {
if (not old.gap(seq123[c-1],n1))
i++;
if (not old.gap(seq123[c-1],n2))
j++;
if (not old.gap(seq123[c-1],n3))
k++;
icol[c] = i;
jcol[c] = j;
kcol[c] = k;
}
/*-------------- Create alignment matrices ---------------*/
// Cache which states emit which sequences
vector<int> state_emit(nstates+1);
for(int S2=0; S2<state_emit.size(); S2++) {
state_emit[S2] = 0;
if (di(S2) or dj(S2) or dk(S2))
state_emit[S2] |= (1<<0);
}
vector<int> branches;
for(int i=1; i<nodes.size(); i++)
branches.push_back(T.branch(nodes[0],nodes[i]) );
const Matrix Q = createQ(P.branch_HMMs,branches);
vector<double> start_P = get_start_P(P.branch_HMMs,branches);
// Actually create the Matrices & Chain
boost::shared_ptr<DParrayConstrained>
Matrices( new DParrayConstrained(seq123.size(),state_emit,start_P,Q, P.get_beta())
);
// Determine which states are allowed to match (c2)
for(int c2=0; c2<Matrices->size(); c2++) {
int i2 = icol[c2];
int j2 = jcol[c2];
int k2 = kcol[c2];
Matrices->states(c2).reserve(Matrices->nstates());
for(int i=0; i<Matrices->nstates(); i++) {
int S2 = Matrices->order(i);
//---------- Get (i1,j1,k1) ----------
int i1 = i2;
if (di(S2)) i1--;
int j1 = j2;
if (dj(S2)) j1--;
int k1 = k2;
if (dk(S2)) k1--;
//------ Get c1, check if valid ------
if (c2==0
or (i1 == i2 and j1 == j2 and k1 == k2)
or (i1 == icol[c2-1] and j1 == jcol[c2-1] and k1 == kcol[c2-1]) )
Matrices->states(c2).push_back(S2);
else
{ } // this state not allowed here
}
}
/*------------------ Compute the DP matrix ---------------------*/
// Matrices.prune(); prune is broken!
Matrices->forward();
//------------- Sample a path from the matrix -------------------//
vector<int> path_g = Matrices->sample_path();
vector<int> path = Matrices->ungeneralize(path_g);
*P.A = construct(old,path,n0,n1,n2,n3,T,seq1,seq2,seq3);
for(int i=1; i<4; i++) {
int b = T.branch(nodes[0],nodes[i]);
P.note_alignment_changed_on_branch(b);
}
#ifndef NDEBUG
vector<int> path_new = get_path_3way(project(*P.A,n0,n1,n2,n3),0,1,2,3);
vector<int> path_new2 = get_path_3way(*P.A,n0,n1,n2,n3);
assert(path_new == path_new2); // <- current implementation probably guarantees this
// but its not a NECESSARY effect of the routine.
// get the generalized paths - no sequential silent states that can loop
vector<int> path_new_g = Matrices->generalize(path_new);
assert(path_new_g == path_g);
assert(valid(*P.A));
#endif
default_timer_stack.pop_timer();
return Matrices;
}
boost::shared_ptr<DPmatrixSimple> sample_alignment_base(data_partition& P,int b)
{
default_timer_stack.push_timer("alignment::DP2/2-way");
assert(P.variable_alignment());
dynamic_bitset<> s1 = constraint_satisfied(P.alignment_constraint, *P.A);
const Tree& T = *P.T;
alignment& A = *P.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<A.length();column++)
{
if (not A.gap(column,node1))
seq1.push_back(column);
if (not A.gap(column,node2))
seq2.push_back(column);
if (not A.gap(column,node1) or A.gap(column,node2))
seq12.push_back(column);
}
//FIXME - this makes the debug routines crash
if (not seq1.size() or not seq2.size())
{
default_timer_stack.pop_timer();
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(P,seq1,b,true);
vector< Matrix > dists2 = distributions(P,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.get_beta(),
P.SModel().distribution(), dists1, dists2, frequency)
);
//------------------ Compute the DP matrix ---------------------//
vector<int> path_old = get_path(A,node1,node2);
vector<vector<int> > pins = get_pins(P.alignment_constraint,A,group1,~group1,seq1,seq2,seq12);
vector<int> path = Matrices->forward(pins);
path.erase(path.begin()+path.size()-1);
*P.A = construct(A,path,node1,node2,T,seq1,seq2);
P.LC.invalidate_branch_alignment(T,b);
P.note_alignment_changed_on_branch(b);
#ifndef NDEBUG_DP
assert(valid(*P.A));
vector<int> path_new = get_path(*P.A, node1, node2);
path.push_back(3);
assert(path_new == path);
#endif
default_timer_stack.pop_timer();
return Matrices;
}