32#include "../../exception/exceptionnotfound.h"
33#include "../../exception/exceptionnotimplemented.h"
63 if(msp_timsData ==
nullptr)
65 std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
67 if(msp_timsData.get() ==
nullptr)
70 QObject::tr(
"ERROR in TimsMsRunReaderDia::initialize "
71 "msp_timsData is null for MsRunId %1")
72 .arg(mcsp_msRunId.get()->toString()));
75 qDebug() << msp_timsData.get();
76 mp_timsDiaSlices = msp_timsData.get()->getTimsDiaSlicesPtr();
113 bool want_binary_data)
const
119 getMsRunId(), q_dia_spectrum, spectrum_index, want_binary_data);
120 return q_dia_spectrum;
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
void getMs2QualifiedSpectrumByGlobalSliceIndex(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_slice_index, bool want_binary_data) const
std::size_t getTotalSlicesCount() const
get the number of DIA MS2 slices analyzed by PASEF
virtual bool acquireDevice() override
acquire data back end device
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
TimsDiaSlices * mp_timsDiaSlices
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
virtual XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
virtual void initialize() override
virtual XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const QualifiedMassSpectrum &mass_spectrum, PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
TimsMsRunReaderDia(MsRunIdCstSPtr &msrun_id_csp)
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
virtual bool acquireDevice() override
acquire data back end device
virtual ~TimsMsRunReaderDia()
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
MSrun file reader for native Bruker TimsTOF specialized for DIA purpose.