xymsrunreader.h
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#pragma once
#include "../msfile/msfileaccessor.h"
namespace pappso
{
class 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 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:35
pappso::MsRunReader
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:191
pappso::PrecisionBase
Definition: precision.h:44
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:85
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
pappso::XyMsRunReader
Definition: xymsrunreader.h:11
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:326
pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile
QualifiedMassSpectrum qualifiedMassSpectrumFromXyMSDataFile(MassSpectrumId mass_spectrum_id) const
Definition: xymsrunreader.cpp:119
pappso::XyMsRunReader::m_fileName
QString m_fileName
Definition: xymsrunreader.h:50
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:243
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:53
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:268
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:36
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:105
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:215
pappso::XyMsRunReader::~XyMsRunReader
virtual ~XyMsRunReader()
Definition: xymsrunreader.cpp:47
pappso::XyMsRunReader::massSpectrumCstSPtr
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
Definition: xymsrunreader.cpp:112
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:44
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:41