libpappsomspp
Library for mass spectrometry
timsmsrunreaderms2selected.h
Go to the documentation of this file.
1 /**
2  * \file pappsomspp/msrun/private/timsmsrunreaderms2.h
3  * \date 10/09/2019
4  * \author Olivier Langella
5  * \brief MSrun file reader for native Bruker TimsTOF specialized for MS2
6  * purpose
7  */
8 
9 /*******************************************************************************
10  * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
11  *
12  * This file is part of the PAPPSOms++ library.
13  *
14  * PAPPSOms++ is free software: you can redistribute it and/or modify
15  * it under the terms of the GNU General Public License as published by
16  * the Free Software Foundation, either version 3 of the License, or
17  * (at your option) any later version.
18  *
19  * PAPPSOms++ is distributed in the hope that it will be useful,
20  * but WITHOUT ANY WARRANTY; without even the implied warranty of
21  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22  * GNU General Public License for more details.
23  *
24  * You should have received a copy of the GNU General Public License
25  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26  *
27  ******************************************************************************/
28 
29 
30 #pragma once
31 
32 #include "timsmsrunreaderms2.h"
33 #include "../../types.h"
34 #include "../../msfile/msfileaccessor.h"
35 #include "../../msfile/msfilereader.h"
36 #include "../../vendors/tims/timsdata.h"
37 
38 namespace pappso
39 {
40 
42 {
43  friend class MsFileAccessor;
44  /**
45  * @todo write docs
46  */
47  public:
49  virtual ~TimsMsRunReaderMs2Selected();
50 
51  virtual MassSpectrumSPtr
52  massSpectrumSPtr(std::size_t spectrum_index) override;
53  virtual MassSpectrumCstSPtr
54  massSpectrumCstSPtr(std::size_t spectrum_index) override;
55 
56  virtual QualifiedMassSpectrum
57  qualifiedMassSpectrum(std::size_t spectrum_index,
58  bool want_binary_data = true) const override;
59 
60  virtual void
61  readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
62 
63  virtual std::size_t spectrumListSize() const override;
64 
65  virtual bool hasScanNumbers() const override;
66 
67  void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
68  void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
69 
70  protected:
71  virtual void initialize() override;
72  virtual bool accept(const QString &file_name) const override;
73 
74  private:
75  TimsData *mpa_timsData = nullptr;
76 };
77 
78 
79 } // namespace pappso
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
#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:44
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
MSrun file reader for native Bruker TimsTOF specialized for MS2 purpose.