libpappsomspp
Library for mass spectrometry
xymsrunreader.h
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1 
2 #pragma once
3 
4 #include "../msfile/msfileaccessor.h"
5 
6 
7 namespace pappso
8 {
9 
10 class XyMsRunReader : public MsRunReader
11 {
12  friend class MsFileAccessor;
13 
14  public:
15  XyMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
16  virtual ~XyMsRunReader();
17 
18  virtual MassSpectrumSPtr
19  massSpectrumSPtr(std::size_t spectrum_index) override;
20  virtual MassSpectrumCstSPtr
21  massSpectrumCstSPtr(std::size_t spectrum_index) override;
22 
23  virtual QualifiedMassSpectrum
24  qualifiedMassSpectrum(std::size_t spectrum_index,
25  bool want_binary_data = true) const override;
26 
27  virtual void
29 
31  std::size_t spectrum_index, pappso::PrecisionPtr precision) const override;
32 
34  const pappso::QualifiedMassSpectrum &mass_spectrum,
35  pappso::PrecisionPtr precision) const override;
36 
37  virtual void
39  unsigned int ms_level) override;
40 
41 
42  virtual std::size_t spectrumListSize() const override;
43 
44  virtual bool releaseDevice() override;
45 
46  virtual bool acquireDevice() override;
47 
48 
49  protected:
50  QString m_fileName;
51  virtual void initialize() override;
52  virtual bool accept(const QString &file_name) const override;
53 
56 };
57 
58 } // namespace pappso
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:192
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
QualifiedMassSpectrum qualifiedMassSpectrumFromXyMSDataFile(MassSpectrumId mass_spectrum_id) const
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
virtual bool acquireDevice() override
acquire data back end device
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
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
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
XyMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
virtual void initialize() override
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition: msrunid.h:44
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:41