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 
45 class PwizMsRunReader : public MsRunReader
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
63  readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
64 
65  virtual std::size_t spectrumListSize() const override;
66 
67  virtual bool hasScanNumbers() const override;
68 
69  virtual bool releaseDevice() override;
70 
71  virtual bool acquireDevice() override;
72 
73  protected:
74  pwiz::msdata::MSDataPtr msp_msData = nullptr;
75 
76  virtual void initialize() override;
77  virtual bool accept(const QString &file_name) const override;
78 
79  bool
80  processRetentionTime(pwiz::msdata::Spectrum *spectrum_p,
81  QualifiedMassSpectrum &qualified_mass_spectrum) const;
82  bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p,
83  QualifiedMassSpectrum &qualified_mass_spectrum) const;
84 
86  std::size_t spectrum_index, bool want_binary_data, bool &ok) const;
87 
90  pwiz::msdata::Spectrum *spectrum_p,
91  bool want_binary_data,
92  bool &ok) const;
93 
94  pwiz::msdata::SpectrumPtr
95  getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list,
96  std::size_t spectrum_index,
97  bool want_binary_data) const;
98 
99  private:
100  bool m_hasScanNumbers = false;
101 };
102 
103 } // namespace pappso
104 
105 
106 // Q_DECLARE_METATYPE(pappso::PwizMsRunReader);
107 // extern int pwizMsRunReaderMetaTypeId;
pappso::PwizMsRunReader::initialize
virtual void initialize() override
Definition: pwizmsrunreader.cpp:86
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:76
pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizMSData
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizMSData(std::size_t spectrum_index, bool want_binary_data, bool &ok) const
Definition: pwizmsrunreader.cpp:699
pappso::PwizMsRunReader::m_hasScanNumbers
bool m_hasScanNumbers
Definition: pwizmsrunreader.h:142
pappso::PwizMsRunReader::hasScanNumbers
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
Definition: pwizmsrunreader.cpp:943
pappso::PwizMsRunReader::massSpectrumSPtr
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Definition: pwizmsrunreader.cpp:768
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizSpectrumPtr(const MassSpectrumId &massSpectrumId, pwiz::msdata::Spectrum *spectrum_p, bool want_binary_data, bool &ok) const
Definition: pwizmsrunreader.cpp:379
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition: msrunid.h:65
pappso::PwizMsRunReader::~PwizMsRunReader
virtual ~PwizMsRunReader()
Definition: pwizmsrunreader.cpp:192
pappso::PwizMsRunReader::acquireDevice
virtual bool acquireDevice() override
acquire data back end device
Definition: pwizmsrunreader.cpp:956
pappso::PwizMsRunReader::processRetentionTime
bool processRetentionTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
Definition: pwizmsrunreader.cpp:243
pappso::PwizMsRunReader::processDriftTime
bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
Definition: pwizmsrunreader.cpp:311
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:103
pappso::PwizMsRunReader::MsFileAccessor
friend class MsFileAccessor
Definition: pwizmsrunreader.h:89
pappso::PwizMsRunReader::massSpectrumCstSPtr
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
Definition: pwizmsrunreader.cpp:775
pappso::MsRunReader
class PMSPP_LIB_DECL MsRunReader
Definition: msrunreader.h:171
pappso::MassSpectrumId
Definition: massspectrumid.h:59
pappso::PwizMsRunReader::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: pwizmsrunreader.cpp:753
pappso::PwizMsRunReader::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: pwizmsrunreader.cpp:782
pappso::PwizMsRunReader::PwizMsRunReader
PwizMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
Definition: pwizmsrunreader.cpp:74
pappso::PwizMsRunReader::releaseDevice
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
Definition: pwizmsrunreader.cpp:949
pappso::PwizMsRunReader::msp_msData
pwiz::msdata::MSDataPtr msp_msData
Definition: pwizmsrunreader.h:116
pappso::PwizMsRunReader::getPwizSpectrumPtr
pwiz::msdata::SpectrumPtr getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list, std::size_t spectrum_index, bool want_binary_data) const
Definition: pwizmsrunreader.cpp:198
pappso::PwizMsRunReader::spectrumListSize
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
Definition: pwizmsrunreader.cpp:937
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:75
pappso::PwizMsRunReader::readSpectrumCollection
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Definition: pwizmsrunreader.cpp:808