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  // Now let the loading handler know that the loading of the data has ended.
114  // The handler might need this "signal" to perform additional tasks or to
115  // cleanup cruft.
116 
117  // qDebug() << "Loading ended";
118 
119  // Now let the loading handler know that the loading of the data has ended.
120  // The handler might need this "signal" to perform additional tasks or to
121  // cleanup cruft.
122 
123  // qDebug() << "Loading ended";
124  handler.loadingEnded();
125 }
126 
127 
128 std::size_t
130 {
131  return msp_timsData->getTotalNumberOfScans();
132 }
133 
134 
135 bool
137 {
138  return false;
139 }
140 
141 
142 bool
144 {
145  msp_timsData = nullptr;
146  return true;
147 }
148 
149 bool
151 {
152  if(msp_timsData == nullptr)
153  {
154  initialize();
155  }
156  return true;
157 }
158 
159 
162  [[maybe_unused]],
163  pappso::PrecisionPtr precision
164  [[maybe_unused]]) const
165 {
166  throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
167  .arg(__FILE__)
168  .arg(__FUNCTION__)
169  .arg(__LINE__));
170 }
171 
174  const pappso::QualifiedMassSpectrum &mass_spectrum [[maybe_unused]],
175  pappso::PrecisionPtr precision [[maybe_unused]]) const
176 {
177  throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
178  .arg(__FILE__)
179  .arg(__FUNCTION__)
180  .arg(__LINE__));
181 }
182 
185 {
186  acquireDevice();
187  return msp_timsData;
188 }
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:173
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
virtual void initialize() override
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 TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
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 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
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.