Loading...
Searching...
No Matches
xymsrunreader.h
Go to the documentation of this file.
#pragma once
#include "../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;
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:40
pappso::MsFileAccessor
Definition msfileaccessor.h:28
pappso::MsRunReadConfig
Definition msrunreadconfig.h:62
pappso::MsRunReader
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition msrunreader.h:63
pappso::PrecisionBase
Definition precision.h:44
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:56
pappso::XyMsRunReader
Definition xymsrunreader.h:11
pappso::XyMsRunReader::m_fileName
QString m_fileName
Definition xymsrunreader.h:54
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition exportinmportconfig.h:14
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:57
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition massspectrum.h:56
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:43