void count_pair_distances::operator()(const SequenceTree& T)
{
if (not initialized) {
N = T.n_leaves();
names = T.get_leaf_labels();
m1.resize(N*(N-1)/2);
m2.resize(N*(N-1)/2);
m1 = 0;
m2 = 0;
initialized = true;
}
n_samples++;
// Theoretically, we could do this much faster, I think.
// vector<vector<int> > leaf_sets = partition_sets(T);
int k=0;
for(int i=0;i<N;i++)
for(int j=0;j<i;j++,k++)
{
double D = 0;
if (RF)
D = T.edges_distance(i,j);
else
D = T.distance(i,j);
m1[k] += D;
m2[k] += D*D;
}
}
Matrix getSimilarity(const SequenceTree& T,substitution::MultiModel& SM) {
int n = T.n_leaves();
Matrix S(n,n);
for(int i=0;i<n;i++)
for(int j=0;j<i;j++)
S(i,j) = S(j,i) = getSimilarity(T.distance(i,j),SM);
return S;
}