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 
30  virtual std::size_t spectrumListSize() const override;
31 
32  protected:
33  QString m_fileName;
34  virtual void initialize() override;
35  virtual bool accept(const QString &file_name) const override;
36 
39 };
40 
41 } // namespace pappso
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:76
pappso::MsRunReader
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:179
pappso::XyMsRunReader::massSpectrumCstSPtr
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
Definition: xymsrunreader.cpp:111
pappso::XyMsRunReader::XyMsRunReader
XyMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
Definition: xymsrunreader.cpp:25
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
Definition: aa.cpp:39
pappso::XyMsRunReader::initialize
virtual void initialize() override
Definition: xymsrunreader.cpp:35
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition: msrunid.h:65
pappso::XyMsRunReader::massSpectrumSPtr
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Definition: xymsrunreader.cpp:104
pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile
QualifiedMassSpectrum qualifiedMassSpectrumFromXyMSDataFile(MassSpectrumId mass_spectrum_id) const
Definition: xymsrunreader.cpp:118
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::MsFileAccessor
Definition: msfileaccessor.h:35
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:86
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:214
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:242
pappso::XyMsRunReader
Definition: xymsrunreader.h:11
pappso::XyMsRunReader::m_fileName
QString m_fileName
Definition: xymsrunreader.h:33
pappso::MassSpectrumId
Definition: massspectrumid.h:59
pappso::XyMsRunReader::~XyMsRunReader
virtual ~XyMsRunReader()
Definition: xymsrunreader.cpp:46
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:267
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:80
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:75