int readseqs(char *filename)
{
int i, l1, no_seqs;
FILE *fin = fopen(filename, "r");
char *seq1, chartab[128];
if (!fin) {
bots_message("Could not open sequence file (%s)\n", filename);
exit (-1);
}
if ( fscanf(fin,"Number of sequences is %d", &no_seqs) == EOF ) {
bots_message("Sequence file is bogus (%s)\n", filename);
exit(-1);
};
fill_chartab(chartab);
bots_message("Sequence format is Pearson\n");
alloc_aln(no_seqs);
for (i = 1; i <= no_seqs; i++) {
seq1 = get_seq(names[i], &l1, chartab, fin);
seqlen_array[i] = l1;
seq_array[i] = (char *) malloc((l1 + 2) * sizeof (char));
encode(seq1, seq_array[i], l1);
free(seq1);
}
return no_seqs;
}
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;
}
float
Alifold::
energy_of_struct(const ALN& aln, const std::vector<Fasta>& fa,
const std::string& str, float& cv) const
{
const uint L=aln.front().second.size();
const uint N=aln.size();
std::string res(L+1, ' ');
char** seqs = alloc_aln(aln, fa);
#ifdef HAVE_VIENNA20
float min_en = Vienna::energy_of_alistruct((const char **)seqs, str.c_str(), N, &cv);
#else
std::vector<float> cv_temp(2);
float min_en = Vienna::energy_of_alistruct(seqs, str.c_str(), N, &cv_temp[0]);
cv = cv_temp[1];
#endif
free_aln(seqs);
return min_en;
}