libpappsomspp
Library for mass spectrometry
Loading...
Searching...
No Matches
bafasciimsrunreader.h
Go to the documentation of this file.
1
2#pragma once
3
5
6
7namespace pappso
8{
9
11 {
12 double retentionTime; // minutes
13 QString ionizationMode; // + or -
14 QString ionSourceType; // MALDI or ESI
16 QString dash;
17 QString peakShapeType; // profile or line
18 std::pair<double,double> mz_range;
19 std::size_t peakCount;
20 QStringList peakList;
21 };
22
24{
25 friend class MsFileAccessor;
26
27 public:
29 virtual ~BafAsciiMsRunReader();
30
31 virtual MassSpectrumSPtr
32 massSpectrumSPtr(std::size_t spectrum_index) override;
34 massSpectrumCstSPtr(std::size_t spectrum_index) override;
35
37 qualifiedMassSpectrum(std::size_t spectrum_index,
38 bool want_binary_data = true) const override;
39
40 virtual void
41 readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
42
43 virtual void
44 readSpectrumCollection2(const MsRunReadConfig &config,
45 SpectrumCollectionHandlerInterface &handler) override;
46
47 virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(
48 std::size_t spectrum_index, pappso::PrecisionPtr precision) const override;
49
50 virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(
51 const pappso::QualifiedMassSpectrum &mass_spectrum,
52 pappso::PrecisionPtr precision) const override;
53
54 virtual void
55 readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
56 unsigned int ms_level) override;
57
58
59 virtual std::size_t spectrumListSize() const override;
60
61 virtual bool releaseDevice() override;
62
63 virtual bool acquireDevice() override;
64
65
66 protected:
67 QString m_fileName;
68
69 // Set when the accept function is called.
70 mutable std::size_t m_spectrumCount = 0;
71
72 QString craftLineParserRegExpPattern() const;
73 QRegularExpression craftLineParserRegExp(QString &pattern) const;
74
75 bool parseMassSpectrumLine(QString &line, MassSpectrumLineData &ms_line_data,
76 QRegularExpression &line_regexp) const;
77
78 virtual void initialize() override;
79 virtual bool accept(const QString &file_name) const override;
80
82 qualifiedMassSpectrumFromBafAsciiMSDataFile(std::size_t spectrum_index,
83 bool want_binary_data) const;
84};
85
86} // 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
std::pair< double, double > mz_range