libpappsomspp
Library for mass spectrometry
pwizmsrunreader.h
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1 /**
2  * \file pappsomspp/msrun/private/pwizmsrunreader.h
3  * \date 29/05/2018
4  * \author Olivier Langella
5  * \brief MSrun file reader base on proteowizard library
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  * Contributors:
27  * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
31 
32 #pragma once
33 
34 #include <pwiz/data/msdata/MSData.hpp>
35 #include <pwiz/data/msdata/MSDataFile.hpp>
36 
37 #include "../../types.h"
38 #include "../../msfile/msfileaccessor.h"
39 #include "../../msfile/msfilereader.h"
40 
41 
42 namespace pappso
43 {
44 
46 {
47  friend class MsFileAccessor;
48 
49  public:
50  PwizMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
51  virtual ~PwizMsRunReader();
52 
53  virtual MassSpectrumSPtr
54  massSpectrumSPtr(std::size_t spectrum_index) override;
55  virtual MassSpectrumCstSPtr
56  massSpectrumCstSPtr(std::size_t spectrum_index) override;
57 
58  virtual QualifiedMassSpectrum
59  qualifiedMassSpectrum(std::size_t spectrum_index,
60  bool want_binary_data = true) const override;
61 
62  virtual void
64 
66  std::size_t spectrum_index, pappso::PrecisionPtr precision) const override;
67 
69  const pappso::QualifiedMassSpectrum &mass_spectrum,
70  pappso::PrecisionPtr precision) const override;
71 
72 
73  virtual void
75  unsigned int ms_level) override;
76 
77 
78  virtual std::size_t spectrumListSize() const override;
79 
80  virtual bool hasScanNumbers() const override;
81 
82  virtual bool releaseDevice() override;
83 
84  virtual bool acquireDevice() override;
85 
86  protected:
87  pwiz::msdata::MSDataPtr msp_msData = nullptr;
88 
89  virtual void initialize() override;
90  virtual bool accept(const QString &file_name) const override;
91 
92  bool
93  processRetentionTime(pwiz::msdata::Spectrum *spectrum_p,
94  QualifiedMassSpectrum &qualified_mass_spectrum) const;
95  bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p,
96  QualifiedMassSpectrum &qualified_mass_spectrum) const;
97 
99  std::size_t spectrum_index, bool want_binary_data, bool &ok) const;
100 
103  pwiz::msdata::Spectrum *spectrum_p,
104  bool want_binary_data,
105  bool &ok) const;
106 
107  pwiz::msdata::SpectrumPtr
108  getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list,
109  std::size_t spectrum_index,
110  bool want_binary_data) const;
111 
112  private:
113  bool m_hasScanNumbers = false;
114 };
115 
116 } // namespace pappso
117 
118 
119 // Q_DECLARE_METATYPE(pappso::PwizMsRunReader);
120 // extern int pwizMsRunReaderMetaTypeId;
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:192
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
pwiz::msdata::MSDataPtr msp_msData
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
bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizMSData(std::size_t spectrum_index, bool want_binary_data, bool &ok) const
PwizMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizSpectrumPtr(const MassSpectrumId &massSpectrumId, pwiz::msdata::Spectrum *spectrum_p, bool want_binary_data, bool &ok) const
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
bool processRetentionTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
virtual bool acquireDevice() override
acquire data back end device
virtual void initialize() override
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
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
pwiz::msdata::SpectrumPtr getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list, std::size_t spectrum_index, bool want_binary_data) const
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
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