libpappsomspp
Library for mass spectrometry
timsmsrunreaderms2.h
Go to the documentation of this file.
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 
36 namespace pappso
37 {
38 
40 {
41  friend class MsFileAccessor;
42  /**
43  * @todo write docs
44  */
45  public:
46  TimsMsRunReaderMs2(MsRunIdCstSPtr &msrun_id_csp);
47  virtual ~TimsMsRunReaderMs2();
48 
49  virtual MassSpectrumSPtr
50  massSpectrumSPtr(std::size_t spectrum_index) override;
51  virtual MassSpectrumCstSPtr
52  massSpectrumCstSPtr(std::size_t spectrum_index) override;
53 
54  virtual QualifiedMassSpectrum
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:44
std::shared_ptr< TimsData > TimsDataSp
shared pointer on a TimsData object
Definition: timsdata.h:46
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:41