libpappsomspp
Library for mass spectrometry
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timsframesmsrunreader.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
36// This class is aimed at processing the frames in a Bruker timsTOF data set. In
37// this processing of the data, we skip the ion mobility scans altogether. One
38// main aim of this processing is to compute the TIC chromatogram from the
39// binary data file and not using the TIC chromatogram that is stored in the DB
40// file.
41
43{
44 friend class MsFileAccessor;
45 /**
46 * @todo write docs
47 */
48 public:
50 virtual ~TimsFramesMsRunReader();
51
52 virtual MassSpectrumSPtr
53 massSpectrumSPtr(std::size_t spectrum_index) override;
55 massSpectrumCstSPtr(std::size_t spectrum_index) override;
56
58 qualifiedMassSpectrum(std::size_t spectrum_index,
59 bool want_binary_data = true) const override;
60
61 virtual void
62 readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
63
64 virtual void
65 readSpectrumCollection2(const MsRunReadConfig &config,
66 SpectrumCollectionHandlerInterface &handler) override;
67 virtual void
68 readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
69 unsigned int ms_level) override;
70
71
72
73
74 virtual std::size_t spectrumListSize() const override;
75
76
77 virtual Trace computeTicChromatogram();
78
79
80
81};
82
83typedef std::shared_ptr<TimsFramesMsRunReader> TimsFramesMsRunReaderSPtr;
84typedef std::shared_ptr<const TimsFramesMsRunReader>
86
87} // namespace pappso
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
A simple container of DataPoint instances.
Definition trace.h:148
#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< TimsFramesMsRunReader > TimsFramesMsRunReaderSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
std::shared_ptr< const TimsFramesMsRunReader > TimsFramesMsRunReaderCstSPtr
Base class for all tims ms run reader objects.