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 "../../vendors/tims/timsdata.h"
35
36namespace pappso
37{
38
40{
41 friend class MsFileAccessor;
42 /**
43 * @todo write docs
44 */
45 public:
47 virtual ~TimsMsRunReaderMs2();
48
49 virtual MassSpectrumSPtr
50 massSpectrumSPtr(std::size_t spectrum_index) override;
52 massSpectrumCstSPtr(std::size_t spectrum_index) override;
53
55 qualifiedMassSpectrum(std::size_t spectrum_index,
56 bool want_binary_data = true) const override;
57
58 virtual void
59 readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
60
61
62 virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(
63 std::size_t spectrum_index, pappso::PrecisionPtr precision) const override;
64
65 virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(
66 const pappso::QualifiedMassSpectrum &mass_spectrum,
67 pappso::PrecisionPtr precision) const override;
68
69
70 virtual void
71 readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
72 unsigned int ms_level) override;
73
74 virtual std::size_t spectrumListSize() const override;
75
76 virtual bool hasScanNumbers() const override;
77
78 void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
79 void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
80
81 /** @brief enable or disable simple centroid filter on raw tims data for MS2
82 */
83 void setMs2BuiltinCentroid(bool centroid);
84
85 /** @brief Get all the precursors id which match the values
86 * @return list of precursors Ids
87 */
88 virtual std::vector<std::size_t>
89 getPrecursorsIDFromMzRt(int charge, double mz_val, double rt_sec, double k0);
90
91
92 virtual bool releaseDevice() override;
93
94 virtual bool acquireDevice() override;
95
96 /** @brief give an access to the underlying raw data pointer
97 */
98 virtual TimsDataSp getTimsDataSPtr();
99
100
101 /** @brief retention timeline
102 * get retention times along the MSrun in seconds
103 * @return vector of retention times (seconds)
104 */
105 virtual std::vector<double> getRetentionTimeLine() override;
106
107 virtual Trace getTicChromatogram() override;
108
109 protected:
110 virtual void initialize() override;
111 virtual bool accept(const QString &file_name) const override;
112
113 private:
114 TimsDataSp msp_timsData = nullptr;
115
118 /** @brief enable builtin centroid on raw tims integers by default
119 */
120 bool m_builtinMs2Centroid = true;
121};
122
123
124} // namespace pappso
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:192
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: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: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