36 #include <pwiz/data/msdata/DefaultReaderList.hpp>
39 #include "../../utils.h"
40 #include "../../pappsoexception.h"
41 #include "../../exception/exceptionnotfound.h"
42 #include "../../exception/exceptionnotpossible.h"
67 std::string file_name_std =
71 std::string env_backup = setlocale(LC_ALL,
"");
80 pwiz::msdata::DefaultReaderList defaultReaderList;
82 std::vector<pwiz::msdata::MSDataPtr> msDataPtrVector;
86 defaultReaderList.read(file_name_std, msDataPtrVector);
88 catch(std::exception &error)
90 qDebug() << QString(
"Failed to read the data from file %1")
91 .arg(QString::fromStdString(file_name_std));
106 if(msDataPtrVector.size() != 1)
108 ExceptionNotPossible(
"For the kind of file at hand there can only be "
109 "one run in the file."));
120 for(
auto &msDataPtr : msDataPtrVector)
122 if(msDataPtr->run.id ==
mcsp_msRunId->getRunId().toStdString())
136 throw(ExceptionNotPossible(
137 "Could not find a MSDataPtr matching the requested run id."));
143 pwiz::cv::CVID native_id_format =
144 pwiz::msdata::id::getDefaultNativeIDFormat(*
msp_msData.get());
148 if(native_id_format == pwiz::cv::CVID::MS_Thermo_nativeID_format)
169 pwiz::msdata::SpectrumPtr
171 std::size_t spectrum_index,
172 bool want_binary_data)
const
174 pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp;
178 native_pwiz_spectrum_sp =
179 p_spectrum_list->spectrum(spectrum_index, want_binary_data);
181 catch(std::runtime_error &error)
183 qDebug() <<
"getPwizSpectrumPtr error " << error.what() <<
" "
184 <<
typeid(error).name();
187 "MS file std::runtime_error :\n%2")
191 catch(std::exception &error)
193 qDebug() <<
"getPwizSpectrumPtr error " << error.what()
194 <<
typeid(error).name();
197 QObject::tr(
"Pwiz spectrum index %1 not found in MS file :\n%2")
202 if(native_pwiz_spectrum_sp.get() ==
nullptr)
206 "Pwiz spectrum index %1 not found in MS file : null pointer")
207 .arg(spectrum_index));
210 return native_pwiz_spectrum_sp;
214 QualifiedMassSpectrum
216 const MassSpectrumId &massSpectrumId,
217 pwiz::msdata::Spectrum *spectrum_p,
218 bool want_binary_data,
224 env = setlocale(LC_ALL,
"");
225 setlocale(LC_ALL,
"C");
227 QualifiedMassSpectrum qualified_mass_spectrum(massSpectrumId);
235 (spectrum_p->cvParam(pwiz::msdata::MS_ms_level).valueAs<
int>());
237 qualified_mass_spectrum.setMsLevel(msLevel);
246 if(spectrum_p->precursors.size() > 0)
253 qDebug() <<
"Going to throw.";
256 "msLevel cannot be less than two for "
257 "a spectrum that has items in its Precursor list."));
264 pwiz::msdata::Precursor &precursor = spectrum_p->precursors.front();
269 std::size_t precursor_spectrum_index =
270 std::numeric_limits<std::size_t>::max();
274 if(precursor.spectrumID.empty())
294 if(!massSpectrumId.getSpectrumIndex())
296 qDebug() <<
"This MS2 sprectrum is at index 0."
297 "This might indicate a fragmentation "
298 "experiment performed in Tune mode.";
306 qDebug() <<
"This MS2 spectrum has no precursor's "
325 qualified_mass_spectrum.setPrecursorNativeId(
326 QString::fromStdString(precursor.spectrumID));
328 if(qualified_mass_spectrum.getPrecursorNativeId().isEmpty())
337 precursor_spectrum_index =
338 msp_msData->run.spectrumListPtr->find(precursor.spectrumID);
342 if(precursor_spectrum_index ==
349 "precursor ion's spectrum."));
353 qualified_mass_spectrum.setPrecursorSpectrumIndex(
354 precursor_spectrum_index);
363 if(!precursor.selectedIons.size())
365 qDebug() <<
"Going to throw.";
369 "precursor ions's selected ions "
373 pwiz::msdata::SelectedIon &ion = *(precursor.selectedIons.begin());
378 QString(ion.cvParam(pwiz::cv::MS_selected_ion_m_z).value.c_str())
381 qualified_mass_spectrum.setPrecursorMz(selected_ion_mz);
386 QString(ion.cvParam(pwiz::cv::MS_peak_intensity).value.c_str())
389 qualified_mass_spectrum.setPrecursorIntensity(
390 selected_ion_peak_intensity);
398 unsigned int selected_ion_charge_state =
399 QString(ion.cvParam(pwiz::cv::MS_charge_state).value.c_str())
402 if(selected_ion_charge_state > 0)
404 qualified_mass_spectrum.setPrecursorCharge(
405 selected_ion_charge_state);
431 "there is not a single precursor ion."));
439 if(!spectrum_p->scanList.scans[0].hasCVParam(
440 pwiz::msdata::MS_scan_start_time))
444 qualified_mass_spectrum.setRtInSeconds(-1);
448 throw(ExceptionNotPossible(
449 "The spectrum has no scan start time value set."));
454 pwiz::data::CVParam retention_time_cv_param =
455 spectrum_p->scanList.scans[0].cvParam(
456 pwiz::msdata::MS_scan_start_time);
460 std::string unit_name = retention_time_cv_param.unitsName();
465 if(unit_name ==
"second")
467 qualified_mass_spectrum.setRtInSeconds(
468 retention_time_cv_param.valueAs<
double>());
470 else if(unit_name ==
"minute")
472 qualified_mass_spectrum.setRtInSeconds(
473 retention_time_cv_param.valueAs<
double>() * 60);
476 throw(ExceptionNotPossible(
477 "Could not determine the unit for the scan start time value."));
497 if(spectrum_p->scanList.scans[0].hasCVParam(
498 pwiz::msdata::MS_ion_mobility_drift_time))
508 spectrum_p->scanList.scans[0]
509 .cvParam(pwiz::msdata::MS_ion_mobility_drift_time)
530 if(std::isnan(driftTime) || std::isinf(driftTime))
536 return qualified_mass_spectrum;
542 qualified_mass_spectrum.setDtInMilliSeconds(driftTime);
552 qualified_mass_spectrum.setDtInMilliSeconds(-1);
570 std::vector<pwiz::msdata::MZIntensityPair> pairs;
571 spectrum_p->getMZIntensityPairs(pairs);
573 MassSpectrum spectrum;
578 for(std::vector<pwiz::msdata::MZIntensityPair>::const_iterator
590 spectrum.push_back(DataPoint(it->mz, it->intensity));
591 tic += it->intensity;
607 qualified_mass_spectrum.setMassSpectrumSPtr(spectrum_sp);
618 qualified_mass_spectrum.setMassSpectrumSPtr(
nullptr);
620 catch(PappsoException &errorp)
622 qDebug() <<
"Going to throw";
625 QObject::tr(
"Error reading data using the proteowizard library: %1")
626 .arg(errorp.qwhat()));
628 catch(std::exception &error)
630 qDebug() <<
"Going to throw";
633 QObject::tr(
"Error reading data using the proteowizard library: %1")
640 return qualified_mass_spectrum;
644 QualifiedMassSpectrum
646 bool want_binary_data,
651 env = setlocale(LC_ALL,
"");
658 setlocale(LC_ALL,
"C");
664 setlocale(LC_ALL, env.c_str());
665 return (QualifiedMassSpectrum(massSpectrumId));
670 pwiz::msdata::SpectrumListPtr spectrum_list_p =
673 if(spectrum_index == spectrum_list_p.get()->size())
675 setlocale(LC_ALL, env.c_str());
677 QObject::tr(
"The spectrum index cannot be equal to the size of the "
683 massSpectrumId.setSpectrumIndex(spectrum_index);
685 pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp =
688 setlocale(LC_ALL, env.c_str());
690 massSpectrumId.setNativeId(
691 QString::fromStdString(native_pwiz_spectrum_sp->id));
694 massSpectrumId, native_pwiz_spectrum_sp.get(), want_binary_data, ok);
702 pwiz::msdata::ReaderList reader_list;
704 std::string reader_type = reader_list.identify(file_name.toStdString());
706 if(!reader_type.empty())
729 bool want_binary_data)
const
773 env = setlocale(LC_ALL,
"");
774 setlocale(LC_ALL,
"C");
780 pwiz::msdata::SpectrumListPtr spectrum_list_p =
784 std::size_t spectrum_list_size = spectrum_list_p.get()->size();
794 for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
801 qDebug() <<
"The operation was cancelled. Breaking the loop.";
808 pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp =
833 QString native_id = QString::fromStdString(native_pwiz_spectrum_sp->id);
844 massSpectrumId, native_pwiz_spectrum_sp.get(), want_binary_data, ok);
860 !native_pwiz_spectrum_sp->defaultArrayLength);
867 setlocale(LC_ALL, env.c_str());
883 return msp_msData->run.spectrumListPtr.get()->size();