libpappsomspp
Library for mass spectrometry
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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
28 readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
29
30 virtual void
31 readSpectrumCollection2(const MsRunReadConfig &config,
32 SpectrumCollectionHandlerInterface &handler) override;
33
34 virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(
35 std::size_t spectrum_index, pappso::PrecisionPtr precision) const override;
36
37 virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(
38 const pappso::QualifiedMassSpectrum &mass_spectrum,
39 pappso::PrecisionPtr precision) const override;
40
41 virtual void
42 readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
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
59 qualifiedMassSpectrumFromXyMSDataFile(MassSpectrumId mass_spectrum_id) const;
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
#define PMSPP_LIB_DECL
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
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:43