libpappsomspp
Library for mass spectrometry
timsmsrunreaderms2.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 "../../types.h"
33#include "../../msfile/msfileaccessor.h"
34#include "../../msfile/msfilereader.h"
35#include "../../vendors/tims/timsdata.h"
36
37namespace pappso
38{
39
41{
42 friend class MsFileAccessor;
43 /**
44 * @todo write docs
45 */
46 public:
48 virtual ~TimsMsRunReaderMs2();
49
50 virtual MassSpectrumSPtr
51 massSpectrumSPtr(std::size_t spectrum_index) override;
53 massSpectrumCstSPtr(std::size_t spectrum_index) override;
54
56 qualifiedMassSpectrum(std::size_t spectrum_index,
57 bool want_binary_data = true) const override;
58
59 virtual void
60 readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
61
62
63 virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(
64 std::size_t spectrum_index, pappso::PrecisionPtr precision) const override;
65
66 virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(
67 const pappso::QualifiedMassSpectrum &mass_spectrum,
68 pappso::PrecisionPtr precision) const override;
69
70
71 virtual void
72 readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
73 unsigned int ms_level) override;
74
75 virtual std::size_t spectrumListSize() const override;
76
77 virtual bool hasScanNumbers() const override;
78
79 void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
80 void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
81
82 /** @brief enable or disable simple centroid filter on raw tims data for MS2
83 */
84 void setMs2BuiltinCentroid(bool centroid);
85
86 /** @brief Get all the precursors id which match the values
87 * @return list of precursors Ids
88 */
89 virtual std::vector<std::size_t>
90 getPrecursorsIDFromMzRt(int charge, double mz_val, double rt_sec, double k0);
91
92
93 virtual bool releaseDevice() override;
94
95 virtual bool acquireDevice() override;
96
97 /** @brief give an access to the underlying raw data pointer
98 */
99 virtual TimsDataSp getTimsDataSPtr();
100
101
102 /** @brief retention timeline
103 * get retention times along the MSrun in seconds
104 * @return vector of retention times (seconds)
105 */
106 virtual std::vector<double> getRetentionTimeLine() override;
107
108 virtual Trace getTicChromatogram() override;
109
110 protected:
111 virtual void initialize() override;
112 virtual bool accept(const QString &file_name) const override;
113
114 private:
115 TimsDataSp msp_timsData = nullptr;
116
119 /** @brief enable builtin centroid on raw tims integers by default
120 */
121 bool m_builtinMs2Centroid = true;
122};
123
124
125} // namespace pappso
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:191
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
pappso::FilterInterfaceCstSPtr msp_ms2Filter
pappso::FilterInterfaceCstSPtr msp_ms1Filter
A simple container of DataPoint instances.
Definition: trace.h:147
#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< TimsData > TimsDataSp
shared pointer on a TimsData object
Definition: timsdata.h:50
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
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:43