libpappsomspp
Library for mass spectrometry
xymsrunreader.h
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1
2#pragma once
3
4#include "../msfile/msfileaccessor.h"
5
6
7namespace pappso
8{
9
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;
21 massSpectrumCstSPtr(std::size_t spectrum_index) override;
22
24 qualifiedMassSpectrum(std::size_t spectrum_index,
25 bool want_binary_data = true) const override;
26
27 virtual void
29
30 virtual void
32 SpectrumCollectionHandlerInterface &handler) override;
33
35 std::size_t spectrum_index, pappso::PrecisionPtr precision) const override;
36
38 const pappso::QualifiedMassSpectrum &mass_spectrum,
39 pappso::PrecisionPtr precision) const override;
40
41 virtual void
43 unsigned int ms_level) override;
44
45
46 virtual std::size_t spectrumListSize() const override;
47
48 virtual bool releaseDevice() override;
49
50 virtual bool acquireDevice() override;
51
52
53 protected:
54 QString m_fileName;
55 virtual void initialize() override;
56 virtual bool accept(const QString &file_name) const override;
57
60};
61
62} // namespace pappso
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:63
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
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 void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
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:46
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:43