libpappsomspp
Library for mass spectrometry
timsmsrunreader.h
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1 /**
2  * \file pappsomspp/msrun/private/timsmsrunreader.h
3  * \date 05/09/2019
4  * \author Olivier Langella
5  * \brief MSrun file reader for native Bruker TimsTOF raw data
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2019 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  ******************************************************************************/
27 
28 
29 #pragma once
30 
31 #include "../../msfile/msfileaccessor.h"
32 #include "../../msfile/msfilereader.h"
33 #include "../../vendors/tims/timsdata.h"
34 
35 namespace pappso
36 {
37 
39 {
40  friend class MsFileAccessor;
41  /**
42  * @todo write docs
43  */
44  public:
45  TimsMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
46  virtual ~TimsMsRunReader();
47 
48  virtual MassSpectrumSPtr
49  massSpectrumSPtr(std::size_t spectrum_index) override;
50  virtual MassSpectrumCstSPtr
51  massSpectrumCstSPtr(std::size_t spectrum_index) override;
52 
53  virtual QualifiedMassSpectrum
54  qualifiedMassSpectrum(std::size_t spectrum_index,
55  bool want_binary_data = true) const override;
56 
57  virtual void
59 
60  virtual void
62  unsigned int ms_level) override;
63 
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 std::size_t spectrumListSize() const override;
74 
75  virtual bool hasScanNumbers() const override;
76 
77  virtual bool releaseDevice() override;
78 
79  virtual bool acquireDevice() override;
80 
81 
82  /** @brief give an access to the underlying raw data pointer
83  */
84  virtual TimsDataSp getTimsDataSPtr();
85 
86 
87 
88  protected:
89  virtual void initialize() override;
90  virtual bool accept(const QString &file_name) const override;
91 
92  private:
94 };
95 
96 } // namespace pappso
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:173
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
virtual void initialize() override
TimsMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
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 MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
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 QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
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 pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
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< TimsData > TimsDataSp
shared pointer on a TimsData object
Definition: timsdata.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:41