libpappsomspp
Library for mass spectrometry
timsmsrunreaderms2selected.h
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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
38namespace pappso
39{
40
42{
43 friend class MsFileAccessor;
44 /**
45 * @todo write docs
46 */
47 public:
50
51 virtual MassSpectrumSPtr
52 massSpectrumSPtr(std::size_t spectrum_index) override;
54 massSpectrumCstSPtr(std::size_t spectrum_index) override;
55
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:45
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.