libpappsomspp
Library for mass spectrometry
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msrunreader.cpp
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1/**
2 * \file pappsomspp/msrun/msrunreader.cpp
3 * \date 29/05/2018
4 * \author Olivier Langella
5 * \brief base interface to read MSrun files
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2018 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 <QDebug>
29#include <QObject>
30
31#include "msrunreader.h"
32#include "../../pappsomspp/exception/exceptionnotfound.h"
33
34
36 qRegisterMetaType<pappso::MsRunReaderSPtr>("pappso::MsRunReaderSPtr");
37
38
39namespace pappso
40{
41
42
43MsRunReader::MsRunReader(MsRunIdCstSPtr &ms_run_id) : mcsp_msRunId(ms_run_id)
44{
45}
46
48 : mcsp_msRunId(other.mcsp_msRunId)
49{
50 mpa_multiMapScanNumber = nullptr;
52}
53
54
55const MsRunIdCstSPtr &
57{
58 return mcsp_msRunId;
59}
60
61
67
68void
69MsRunReader::setMonoThread(bool is_mono_thread)
70{
71 m_isMonoThread = is_mono_thread;
72}
73
74bool
76{
77 return m_isMonoThread;
78}
79
80
81std::size_t
83{
84 qDebug() << " " << mpa_multiMapScanNumber;
85
86 if(mpa_multiMapScanNumber == nullptr)
87 {
90 }
91 try
92 {
94 scan_number);
95 }
96
97 catch(ExceptionNotFound &error)
98 {
99 throw ExceptionNotFound(QObject::tr("error reading file %1 : %2")
100 .arg(mcsp_msRunId.get()->getFileName())
101 .arg(error.qwhat()));
102 }
103 catch(PappsoException &error)
104 {
105 throw PappsoException(QObject::tr("error reading file %1 : %2")
106 .arg(mcsp_msRunId.get()->getFileName())
107 .arg(error.qwhat()));
108 }
109}
110
111
112bool
114{
115 return false;
116}
117
118std::vector<double>
120{
121 qDebug();
122
123 try
124 {
125
126 MsRunReaderRetentionTimeLine reader_timeline;
127 MsRunReadConfig config;
128 config.setMsLevels({1});
129 config.setNeedPeakList(false);
130 // readSpectrumCollectionByMsLevel(reader_timeline, 1);
131 readSpectrumCollection2(config, reader_timeline);
132
133 return reader_timeline.getRetentionTimeLine();
134 }
135
136 catch(ExceptionNotFound &error)
137 {
138 throw ExceptionNotFound(QObject::tr("error reading file %1 : %2")
139 .arg(mcsp_msRunId.get()->getFileName())
140 .arg(error.qwhat()));
141 }
142 catch(PappsoException &error)
143 {
144 throw PappsoException(QObject::tr("error reading file %1 : %2")
145 .arg(mcsp_msRunId.get()->getFileName())
146 .arg(error.qwhat()));
147 }
148}
149
150
151Trace
153{
154 qDebug();
155
156 try
157 {
158 MsRunReaderTicChromatogram ms_run_reader;
159
160 readSpectrumCollection(ms_run_reader);
161
162 return ms_run_reader.getTicChromatogram();
163 }
164
165 catch(ExceptionNotFound &error)
166 {
167 throw ExceptionNotFound(QObject::tr("error reading file %1 : %2")
168 .arg(mcsp_msRunId.get()->getFileName())
169 .arg(error.qwhat()));
170 }
171 catch(PappsoException &error)
172 {
173 throw PappsoException(QObject::tr("error reading file %1 : %2")
174 .arg(mcsp_msRunId.get()->getFileName())
175 .arg(error.qwhat()));
176 }
177}
178
179
180} // namespace pappso
void setNeedPeakList(bool need_peak_list)
void setMsLevels(std::vector< std::size_t > ms_levels)
const std::vector< double > & getRetentionTimeLine() const
provides a multimap to find quickly spectrum index from scan number
std::size_t getSpectrumIndexFromScanNumber(std::size_t scan_number) const
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition msrunreader.h:63
MsRunIdCstSPtr mcsp_msRunId
MsRunReaderScanNumberMultiMap * mpa_multiMapScanNumber
virtual bool hasScanNumbers() const
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
void setMonoThread(bool is_mono_thread)
set only one is_mono_thread to true
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)=0
virtual std::vector< double > getRetentionTimeLine()
retention timeline get retention times along the MSrun in seconds
virtual std::size_t scanNumber2SpectrumIndex(std::size_t scan_number)
if possible, converts a scan number into a spectrum index This is a convenient function to help trans...
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler)=0
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
bool isMonoThread() const
virtual Trace getTicChromatogram()
get a TIC chromatogram
MsRunReader(MsRunIdCstSPtr &ms_run_id)
const MsRunIdCstSPtr & getMsRunId() const
virtual const QString & qwhat() const
A simple container of DataPoint instances.
Definition trace.h:148
int msRunReaderSPtrMetaTypeId
base interface to read MSrun files
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:46