libpappsomspp
Library for mass spectrometry
timsmsrunreader.cpp
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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 #include "timsmsrunreader.h"
29 #include "../../exception/exceptionnotimplemented.h"
30 #include <QDebug>
31 
32 using namespace pappso;
33 
35  : MsRunReader(msrun_id_csp)
36 {
37  initialize();
38 }
39 
41 {
42  msp_timsData = nullptr;
43 }
44 
45 void
47 {
48  msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
49  if(msp_timsData == nullptr)
50  {
51  throw PappsoException(QObject::tr("ERROR in TimsMsRunReader::initialize "
52  "msp_timsData is null for MsRunId %1")
53  .arg(mcsp_msRunId.get()->toString()));
54  }
55 }
56 
57 
58 bool
59 TimsMsRunReader::accept(const QString &file_name) const
60 {
61  qDebug() << file_name;
62  return true;
63 }
64 
65 
67 TimsMsRunReader::massSpectrumSPtr([[maybe_unused]] std::size_t spectrum_index)
68 {
70  QObject::tr("Not yet implemented in TimsMsRunReader %1.\n").arg(__LINE__));
71  return pappso::MassSpectrumSPtr();
72 }
73 
74 
76 TimsMsRunReader::massSpectrumCstSPtr(std::size_t spectrum_index)
77 {
78  return msp_timsData->getMassSpectrumCstSPtrByRawIndex(spectrum_index);
79 }
80 
81 
83 TimsMsRunReader::qualifiedMassSpectrum(std::size_t spectrum_index,
84  bool want_binary_data) const
85 {
86 
87  QualifiedMassSpectrum mass_spectrum;
88 
89  msp_timsData->getQualifiedMassSpectrumByRawIndex(
90  getMsRunId(), mass_spectrum, spectrum_index, want_binary_data);
91  return mass_spectrum;
92 }
93 
94 
95 void
98 {
100 }
101 
102 
103 void
105  SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)
106 {
107 
108  qDebug();
109 
110 
111  msp_timsData.get()->rawReaderSpectrumCollectionByMsLevel(
112  getMsRunId(), handler, ms_level);
113 
114  // Now let the loading handler know that the loading of the data has ended.
115  // The handler might need this "signal" to perform additional tasks or to
116  // cleanup cruft.
117 
118  // qDebug() << "Loading ended";
119  handler.loadingEnded();
120 }
121 
122 
123 std::size_t
125 {
126  return msp_timsData->getTotalNumberOfScans();
127 }
128 
129 
130 bool
132 {
133  return false;
134 }
135 
136 
137 bool
139 {
140  msp_timsData = nullptr;
141  return true;
142 }
143 
144 bool
146 {
147  if(msp_timsData == nullptr)
148  {
149  initialize();
150  }
151  return true;
152 }
153 
154 
157  [[maybe_unused]],
158  pappso::PrecisionPtr precision
159  [[maybe_unused]]) const
160 {
161  throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
162  .arg(__FILE__)
163  .arg(__FUNCTION__)
164  .arg(__LINE__));
165 }
166 
169  const pappso::QualifiedMassSpectrum &mass_spectrum [[maybe_unused]],
170  pappso::PrecisionPtr precision [[maybe_unused]]) const
171 {
172  throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
173  .arg(__FILE__)
174  .arg(__FUNCTION__)
175  .arg(__LINE__));
176 }
177 
180 {
181  acquireDevice();
182  return msp_timsData;
183 }
184 
185 
186 Trace
188 {
189  // Use the Sqlite database to fetch the total ion current chromatogram (TIC
190  // chromatogram).
191 
192  acquireDevice();
193 
194  return msp_timsData->getTicChromatogram();
195 }
196 
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:191
MsRunIdCstSPtr mcsp_msRunId
Definition: msrunreader.h:298
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
TimsMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
virtual bool acquireDevice() override
acquire data back end device
virtual bool accept(const QString &file_name) const override
tells if the reader is able to handle this file must be implemented by private MS run reader,...
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
virtual void initialize() override
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
virtual Trace getTicChromatogram() override
get a TIC chromatogram
A simple container of DataPoint instances.
Definition: trace.h:38
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< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:41
MSrun file reader for native Bruker TimsTOF raw data.