unsigned n_nuc_differences(const Triplets& T,int i,int j)
{
unsigned n=0;
for(int pos=0;pos<3;pos++)
if (T.sub_nuc(i,pos) != T.sub_nuc(j,pos))
n++;
return n;
}
valarray<double> get_codon_frequencies_from_independent_nucleotide_frequencies(const Triplets& C,const valarray<double>& fN ) {
valarray<double> fC(C.size());
for(int i=0;i<fC.size();i++) {
fC[i] = 1.0;
for(int pos=0;pos<3;pos++)
fC[i] *= fN[ C.sub_nuc(i,pos) ];
}
fC /= fC.sum();
return fC;
}
valarray<double> get_nucleotide_counts_from_codon_counts(const Triplets& C,const valarray<double>& C_counts) {
const Nucleotides& N = C.getNucleotides();
valarray<double> N_counts(0.0,N.size());
// For each codon type
for(int i=0;i<C.size();i++) {
// For each position in the codon
for(int pos=0;pos<3;pos++)
// Cound the nucleotides that occur there
N_counts[ C.sub_nuc(i,pos) ] += C_counts[i];
}
return N_counts;
}