void do_it(t_truck *b, int sock)
{
while ((b->i = read(0, b->line, 2048)) > 0)
{
b->line[b->i] = '\0';
ft_send(sock, 0, b->line, ft_strlen(b->line));
if ((ft_strnstr(b->line, "quit", 4)) != NULL)
break ;
b->r = c_trans(b, sock);
if (b->r == 0)
{
ft_recv(sock, &b->buff);
printf("%s\n", b->buff);
}
ft_strdel(&b->buff);
ft_bzero(b->line, 2048);
write(1, "client$$$:", 10);
}
return ;
}
void FeatureFinderAlgorithmIsotopeWavelet::run()
{
double max_mz = this->map_->getMax()[1];
double min_mz = this->map_->getMin()[1];
Size max_size = 0;
//Check for useless RT_votes_cutoff_ parameter
if (RT_votes_cutoff_ > this->map_->size())
{
real_RT_votes_cutoff_ = 0;
}
else
{
real_RT_votes_cutoff_ = RT_votes_cutoff_;
}
this->ff_->setLogType(ProgressLogger::CMD);
progress_counter_ = 0;
this->ff_->startProgress(0, 2 * this->map_->size() * max_charge_, "analyzing spectra");
IsotopeWaveletTransform<PeakType>* iwt = new IsotopeWaveletTransform<PeakType>(min_mz, max_mz, max_charge_, max_size, hr_data_, intensity_type_);
for (UInt i = 0; i < this->map_->size(); ++i)
{
const MSSpectrum<PeakType>& c_ref((*this->map_)[i]);
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << ::std::fixed << ::std::setprecision(6) << "Spectrum " << i + 1 << " (" << (*this->map_)[i].getRT() << ") of " << this->map_->size() << " ... ";
std::cout.flush();
#endif
if (c_ref.size() <= 1) //unable to do transform anything
{
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << "scan empty or consisting of a single data point. Skipping." << std::endl;
#endif
this->ff_->setProgress(progress_counter_ += 2);
continue;
}
if (!hr_data_) //LowRes data
{
iwt->initializeScan((*this->map_)[i]);
for (UInt c = 0; c < max_charge_; ++c)
{
MSSpectrum<PeakType> c_trans(c_ref);
iwt->getTransform(c_trans, c_ref, c);
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::stringstream stream;
stream << "cpu_lowres_" << c_ref.getRT() << "_" << c + 1 << ".trans\0";
std::ofstream ofile(stream.str().c_str());
for (UInt k = 0; k < c_ref.size(); ++k)
{
ofile << ::std::setprecision(8) << std::fixed << c_trans[k].getMZ() << "\t" << c_trans[k].getIntensity() << "\t" << c_ref[k].getIntensity() << std::endl;
}
ofile.close();
#endif
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << "transform O.K. ... "; std::cout.flush();
#endif
this->ff_->setProgress(++progress_counter_);
iwt->identifyCharge(c_trans, c_ref, i, c, intensity_threshold_, check_PPMs_);
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << "charge recognition O.K. ... "; std::cout.flush();
#endif
this->ff_->setProgress(++progress_counter_);
}
}
else //HighRes data
{
for (UInt c = 0; c < max_charge_; ++c)
{
MSSpectrum<PeakType>* new_spec = createHRData(i);
iwt->initializeScan(*new_spec, c);
MSSpectrum<PeakType> c_trans(*new_spec);
iwt->getTransformHighRes(c_trans, *new_spec, c);
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::stringstream stream;
stream << "cpu_highres_" << new_spec->getRT() << "_" << c + 1 << ".trans\0";
std::ofstream ofile(stream.str().c_str());
for (UInt k = 0; k < new_spec->size(); ++k)
{
ofile << ::std::setprecision(8) << std::fixed << c_trans[k].getMZ() << "\t" << c_trans[k].getIntensity() << "\t" << (*new_spec)[k].getIntensity() << std::endl;
}
ofile.close();
#endif
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << "transform O.K. ... "; std::cout.flush();
#endif
this->ff_->setProgress(++progress_counter_);
iwt->identifyCharge(c_trans, *new_spec, i, c, intensity_threshold_, check_PPMs_);
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << "charge recognition O.K. ... "; std::cout.flush();
#endif
this->ff_->setProgress(++progress_counter_);
delete (new_spec); new_spec = NULL;
}
}
iwt->updateBoxStates(*this->map_, i, RT_interleave_, real_RT_votes_cutoff_);
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << "updated box states." << std::endl;
#endif
std::cout.flush();
}
this->ff_->endProgress();
//Forces to empty OpenBoxes_ and to synchronize ClosedBoxes_
iwt->updateBoxStates(*this->map_, INT_MAX, RT_interleave_, real_RT_votes_cutoff_);
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::cout << "Final mapping."; std::cout.flush();
#endif
*this->features_ = iwt->mapSeeds2Features(*this->map_, real_RT_votes_cutoff_);
delete (iwt);
}
