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xymsrunreader.h
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#pragma once
#include "pappsomspp/core/msfile/msfileaccessor.h"
namespace pappso
{
class PMSPP_LIB_DECL XyMsRunReader : public MsRunReader
{
friend class MsFileAccessor;
public:
XyMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
virtual ~XyMsRunReader();
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override;
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override;
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index,
bool want_binary_data = true) const override;
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
virtual void readSpectrumCollection2(const MsRunReadConfig &config,
SpectrumCollectionHandlerInterface &handler) override;
virtual pappso::XicCoordSPtr
newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index,
pappso::PrecisionPtr precision) const override;
virtual pappso::XicCoordSPtr
newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum,
pappso::PrecisionPtr precision) const override;
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
unsigned int ms_level) override;
virtual std::size_t spectrumListSize() const override;
virtual bool releaseDevice() override;
virtual bool acquireDevice() override;
virtual std::size_t
spectrumStringIdentifier2SpectrumIndex(const QString &spectrum_identifier) override;
protected:
QString m_fileName;
virtual void initialize() override;
virtual bool accept(const QString &file_name) const override;
QualifiedMassSpectrum
qualifiedMassSpectrumFromXyMSDataFile(MassSpectrumId mass_spectrum_id) const;
};
} // namespace pappso
pappso::MassSpectrumId
Definition massspectrumid.h:41
pappso::MsRunReadConfig
Definition msrunreadconfig.h:62
pappso::MsRunReader::MsRunReader
MsRunReader(const MsRunIdCstSPtr &ms_run_id)
Definition msrunreader.cpp:43
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition qualifiedmassspectrum.h:99
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition spectrumcollectionhandlerinterface.h:52
pappso::XyMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
Definition xymsrunreader.cpp:323
pappso::XyMsRunReader::MsFileAccessor
friend class MsFileAccessor
Definition xymsrunreader.h:12
pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile
QualifiedMassSpectrum qualifiedMassSpectrumFromXyMSDataFile(MassSpectrumId mass_spectrum_id) const
Definition xymsrunreader.cpp:117
pappso::XyMsRunReader::m_fileName
QString m_fileName
Definition xymsrunreader.h:52
pappso::XyMsRunReader::readSpectrumCollection
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Definition xymsrunreader.cpp:237
pappso::XyMsRunReader::acquireDevice
virtual bool acquireDevice() override
acquire data back end device
Definition xymsrunreader.cpp:308
pappso::XyMsRunReader::accept
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,...
Definition xymsrunreader.cpp:52
pappso::XyMsRunReader::spectrumStringIdentifier2SpectrumIndex
virtual std::size_t spectrumStringIdentifier2SpectrumIndex(const QString &spectrum_identifier) override
if possible, get the spectrum index given a string identifier throw a not found exception if spectrum...
Definition xymsrunreader.cpp:333
pappso::XyMsRunReader::spectrumListSize
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
Definition xymsrunreader.cpp:296
pappso::XyMsRunReader::readSpectrumCollectionByMsLevel
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
Definition xymsrunreader.cpp:261
pappso::XyMsRunReader::releaseDevice
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
Definition xymsrunreader.cpp:302
pappso::XyMsRunReader::XyMsRunReader
XyMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
Definition xymsrunreader.cpp:26
pappso::XyMsRunReader::initialize
virtual void initialize() override
Definition xymsrunreader.cpp:35
pappso::XyMsRunReader::newXicCoordSPtrFromSpectrumIndex
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
Definition xymsrunreader.cpp:314
pappso::XyMsRunReader::massSpectrumSPtr
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Definition xymsrunreader.cpp:103
pappso::XyMsRunReader::qualifiedMassSpectrum
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
Definition xymsrunreader.cpp:209
pappso::XyMsRunReader::readSpectrumCollection2
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Definition xymsrunreader.cpp:289
pappso::XyMsRunReader::massSpectrumCstSPtr
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
Definition xymsrunreader.cpp:110
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
msfileaccessor.h
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition msrunid.h:46
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition massspectrum.h:54
pappso::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition precision.h:122
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition massspectrum.h:53
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:44