libpappsomspp
Library for mass spectrometry
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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 "timsmsrunreaderbase.h"
32
33namespace pappso
34{
35
37{
38 friend class MsFileAccessor;
39 /**
40 * @todo write docs
41 */
42 public:
43 TimsMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
44 TimsMsRunReader(const TimsMsRunReaderBase &msrun_reader_base);
45
46 virtual ~TimsMsRunReader();
47
48 virtual MassSpectrumSPtr
49 massSpectrumSPtr(std::size_t spectrum_index) override;
51 massSpectrumCstSPtr(std::size_t spectrum_index) override;
52
54 qualifiedMassSpectrum(std::size_t spectrum_index,
55 bool want_binary_data = true) const override;
56
57 virtual void
58 readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
59
60 virtual void
61 readSpectrumCollection2(const MsRunReadConfig &config,
62 SpectrumCollectionHandlerInterface &handler) override;
63 virtual void
64 readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
65 unsigned int ms_level) override;
66
67
68 virtual std::size_t spectrumListSize() const override;
69
70
71};
72
73} // namespace pappso
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
#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:46
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Base class for all tims ms run reader objects.