libpappsomspp
Library for mass spectrometry
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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"
58 virtual QualifiedMassSpectrum
60 bool want_binary_data =
true)
const override;
77 virtual bool accept(
const QString &file_name)
const override;
86 std::size_t spectrum_index,
bool want_binary_data,
bool &ok)
const;
90 pwiz::msdata::Spectrum *spectrum_p,
91 bool want_binary_data,
94 pwiz::msdata::SpectrumPtr
96 std::size_t spectrum_index,
97 bool want_binary_data)
const;
virtual void initialize() override
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizMSData(std::size_t spectrum_index, bool want_binary_data, bool &ok) const
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizSpectrumPtr(const MassSpectrumId &massSpectrumId, pwiz::msdata::Spectrum *spectrum_p, bool want_binary_data, bool &ok) const
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
virtual ~PwizMsRunReader()
virtual bool acquireDevice() override
acquire data back end device
bool processRetentionTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
Class representing a fully specified mass spectrum.
friend class MsFileAccessor
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
class PMSPP_LIB_DECL MsRunReader
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 QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
PwizMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
pwiz::msdata::MSDataPtr msp_msData
pwiz::msdata::SpectrumPtr getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list, std::size_t spectrum_index, bool want_binary_data) const
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler