void AlignementGet::run()
{
try
{
if(Alignement_init)
{
if( (Alignement_identity->at(Alignement_hit_b->id())).first == -1)
{
FastaThread seqa(*Alignement_fasta_a, *Alignement_hit_a);
FastaThread seqb(*Alignement_fasta_b, *Alignement_hit_b);
Alignement_first_seq = seqa.find();
Alignement_second_seq = seqb.find();
pair<long int, long int> identity = compute_identity(false);
if((Alignement_first_seq->length() - identity.second) > 0)
{
if( (identity.first/(Alignement_first_seq->length() - identity.second)) >= 0.5)
{
delete Alignement_first_seq;
delete Alignement_second_seq;
Alignement_first_seq = seqa.find();
Alignement_second_seq = seqb.find();
Alignement_identity->at(Alignement_hit_b->id()) = compute_identity(true);
}
if( (Alignement_identity->at(Alignement_hit_b->id())).first > identity.first || (Alignement_identity->at(Alignement_hit_b->id())).first == -1)
{
Alignement_identity->at(Alignement_hit_b->id()) = identity;
}
}
delete Alignement_first_seq;
delete Alignement_second_seq;
}
}
}
catch(exception const& e)
{
cerr << "ERROR : " << e.what() << " in : void AlignementGet::run()" << endl;
exit(-1);
}
}
RcppExport SEXP rthxpos(SEXP m)
{
Rcpp::NumericMatrix tmpm = Rcpp::NumericMatrix(m);
int nr = tmpm.nrow();
int nc = tmpm.ncol();
thrust::device_vector<double> dmat(tmpm.begin(),tmpm.end());
// make space for the transpose
thrust::device_vector<double> dxp(nr*nc);
// iterator to march through the matrix elements
thrust::counting_iterator<int> seqb(0);
thrust::counting_iterator<int> seqe = seqb + nr*nc;
// for each i in seq, copy the matrix elt to its spot in the
// transpose
thrust::for_each(seqb,seqe,
copyelt2xp(dmat.begin(),dxp.begin(),nr,nc));
// prepare the R output, and return it
Rcpp::NumericVector routmat(nc*nr);
thrust::copy(dxp.begin(),dxp.end(),routmat.begin());
return routmat;
}
