Exemplos de BP::resize em C++ (Cpp)

Exemplo n.º 1

Arquivo: alifold.cpp Projeto: satoken/dafs

void
Alifold::
fold(const ALN& aln, const std::vector<Fasta>& fa, const std::string& str, BP& bp) const
{
  const uint L=aln.front().second.size();
  std::string p(str);
  std::replace(p.begin(), p.end(), '.', 'x');
  std::replace(p.begin(), p.end(), '?', '.');

  int bk = Vienna::fold_constrained;
  Vienna::fold_constrained = 1;

  char** seqs = alloc_aln(aln, fa);

  // scaling parameters to avoid overflow
  std::string res(p);
#ifdef HAVE_VIENNA20
  double min_en = Vienna::alifold((const char**)seqs, &res[0]);
#else
  double min_en = Vienna::alifold(seqs, &res[0]);
#endif
  double kT = (Vienna::temperature+273.15)*1.98717/1000.; /* in Kcal */
  Vienna::pf_scale = exp(-(1.07*min_en)/kT/L);
  Vienna::free_alifold_arrays();

  pair_info* pi;
#ifdef HAVE_VIENNA20
  Vienna::alipf_fold((const char**)seqs, &p[0], &pi);
#else
  Vienna::alipf_fold(seqs, &p[0], &pi);
#endif

  bp.resize(L);
  for (uint k=0; pi[k].i!=0; ++k)
    if (pi[k].p>th_)
      bp[pi[k].i-1].push_back(std::make_pair(pi[k].j-1, pi[k].p));

  free(pi);
  Vienna::free_alipf_arrays();
  free_aln(seqs);
  Vienna::fold_constrained = bk;
}