34 #include <pwiz/data/msdata/MSData.hpp>
35 #include <pwiz/data/msdata/MSDataFile.hpp>
37 #include "../../types.h"
38 #include "../../msfile/msfileaccessor.h"
39 #include "../../msfile/msfilereader.h"
60 bool want_binary_data =
true)
const override;
75 unsigned int ms_level)
override;
90 virtual bool accept(
const QString &file_name)
const override;
99 std::size_t spectrum_index,
bool want_binary_data,
bool &ok)
const;
103 pwiz::msdata::Spectrum *spectrum_p,
104 bool want_binary_data,
107 pwiz::msdata::SpectrumPtr
109 std::size_t spectrum_index,
110 bool want_binary_data)
const;
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
pwiz::msdata::MSDataPtr msp_msData
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
bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizMSData(std::size_t spectrum_index, bool want_binary_data, bool &ok) const
PwizMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizSpectrumPtr(const MassSpectrumId &massSpectrumId, pwiz::msdata::Spectrum *spectrum_p, bool want_binary_data, bool &ok) const
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
bool processRetentionTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
virtual bool acquireDevice() override
acquire data back end device
virtual ~PwizMsRunReader()
virtual void initialize() override
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
virtual bool accept(const QString &file_name) const override
tells if the reader is able to handle this file must be implemented by private MS run reader,...
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
pwiz::msdata::SpectrumPtr getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list, std::size_t spectrum_index, bool want_binary_data) const
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
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