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
35namespace pappso
36{
37
38
39TimsMsFileReader::TimsMsFileReader(const QString &file_name)
40 : MsFileReader(file_name)
41{
42 qDebug() << " " << m_fileName;
43 initialize();
44}
45
46
48{
49}
50
51
52std::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
86std::vector<MsRunIdCstSPtr>
87TimsMsFileReader::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:54
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:120
@ unknown
unknown format
MSrun file reader for native Bruker TimsTOF raw data.