Example #1
0
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;
}
Example #2
0
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;
}
Example #3
0
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;
}