libpappsomspp
Library for mass spectrometry
timsmsfilereader.cpp
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1 /**
2  * \file pappsomspp/msfile/timsmsfilereader.cpp
3  * \date 06/09/2019
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 "timsmsfilereader.h"
29 #include "../vendors/tims/timsdata.h"
30 #include "../pappsoexception.h"
31 #include "../exception/exceptionnotimplemented.h"
32 #include <QDebug>
33 #include <QFileInfo>
34 
35 namespace pappso
36 {
37 
38 
39 TimsMsFileReader::TimsMsFileReader(const QString &file_name)
40  : MsFileReader(file_name)
41 {
42  qDebug() << " " << m_fileName;
43  initialize();
44 }
45 
46 
48 {
49 }
50 
51 
52 std::size_t
54 {
55 
57  try
58  {
59  TimsData tims_data(m_fileName);
61  }
62  catch(ExceptionNotImplemented &error)
63  {
66  QObject::tr("Error reading Bruker tims data in %1 :\n%2")
67  .arg(m_fileName)
68  .arg(error.qwhat()));
69  }
70  catch(PappsoException &error)
71  {
72  return 0;
73  }
74 
75  return 1;
76 }
77 
78 
81 {
82  return m_fileFormat;
83 }
84 
85 
86 std::vector<MsRunIdCstSPtr>
87 TimsMsFileReader::getMsRunIds(const QString &run_prefix)
88 {
89  std::vector<MsRunIdCstSPtr> ms_run_ids;
90 
91  if(!initialize())
92  return ms_run_ids;
93 
94  // Finally create the MsRunId with the file name.
95  MsRunId ms_run_id(m_fileName);
96  ms_run_id.setMzFormat(m_fileFormat);
97 
98  // We need to set the unambiguous xmlId string.
99  ms_run_id.setXmlId(QString("%1a1").arg(run_prefix));
100 
101  ms_run_id.setRunId("a1");
102 
103  // Now set the sample name to the run id:
104 
105  ms_run_id.setSampleName(QFileInfo(m_fileName).baseName());
106 
107  qDebug() << "Current ms_run_id:" << ms_run_id.toString();
108 
109  // Finally make a shared pointer out of it and append it to the vector.
110  ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
111 
112  return ms_run_ids;
113 }
114 
115 
116 } // namespace pappso
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informa...
Definition: msrunid.h:53
QString toString() const
Definition: msrunid.cpp:193
void setRunId(const QString &run_id)
Definition: msrunid.cpp:123
void setMzFormat(MzFormat format)
Definition: msrunid.cpp:158
void setXmlId(const QString &xml_id)
set an XML unique identifier for this MsRunId
Definition: msrunid.cpp:137
void setSampleName(const QString &name)
set a sample name for this MsRunId
Definition: msrunid.cpp:79
virtual const QString & qwhat() const
virtual std::size_t initialize()
virtual std::vector< MsRunIdCstSPtr > getMsRunIds(const QString &run_prefix) override
virtual MzFormat getFileFormat() override
TimsMsFileReader(const QString &file_name)
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
MzFormat
Definition: types.h:108
@ unknown
unknown format
MSrun file reader for native Bruker TimsTOF raw data.