libpappsomspp
Library for mass spectrometry
msrunxicextractorfactory.cpp
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1 /**
2  * \file pappsomspp/xicextractor/msrunxicextractorfactory.cpp
3  * \date 07/05/2018
4  * \author Olivier Langella
5  * \brief factory to build XIC extractor on an MsRun file
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  * Contributors:
27  * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
35 #include "../vendors/tims/xicextractor/timsdirectxicextractor.h"
36 #include "../msrun/private/timsmsrunreaderms2.h"
37 
38 namespace pappso
39 {
40 
41 
42 MsRunXicExtractorFactory MsRunXicExtractorFactory::m_instance =
43  MsRunXicExtractorFactory();
44 
45 MsRunXicExtractorFactory &
47 {
48  return m_instance;
49 }
50 
51 
53 {
54 }
56 {
57 }
58 
59 void
60 MsRunXicExtractorFactory::setTmpDir(const QString &dir_name)
61 {
62  m_tmpDirName = dir_name;
63 }
64 void
67 {
68  m_type = type;
69 }
70 
73  MsRunReaderSPtr &msrun_reader) const
74 {
75 
76  pappso::TimsMsRunReaderMs2 *tims2_reader =
77  dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader.get());
78  if(tims2_reader == nullptr)
79  {
80  // NO TIMS
83  {
84  std::shared_ptr<MsRunXicExtractor> msrun_xic_extractor_sp =
85  std::make_shared<MsRunXicExtractor>(
86  MsRunXicExtractor(msrun_reader));
87  return (msrun_xic_extractor_sp);
88  }
90  {
91 
92  std::shared_ptr<MsRunXicExtractorDisk> msrun_xic_extractor_sp =
93  std::make_shared<MsRunXicExtractorDisk>(
94  MsRunXicExtractorDisk(msrun_reader, QDir(m_tmpDirName)));
95 
96  msrun_xic_extractor_sp.get()->prepareExtractor();
97  return (msrun_xic_extractor_sp);
98  }
100  {
101 
102  std::shared_ptr<MsRunXicExtractorDiskBuffer> msrun_xic_extractor_sp =
103  std::make_shared<MsRunXicExtractorDiskBuffer>(
104  MsRunXicExtractorDiskBuffer(msrun_reader, QDir(m_tmpDirName)));
105  msrun_xic_extractor_sp.get()->prepareExtractor();
106  return (msrun_xic_extractor_sp);
107  }
108  }
109  else
110  {
111  // TIMS
112  std::shared_ptr<TimsDirectXicExtractor> msrun_xic_extractor_sp =
113  std::make_shared<TimsDirectXicExtractor>(msrun_reader);
114  return (msrun_xic_extractor_sp);
115  }
116  return nullptr;
117 }
118 
119 
120 } // namespace pappso
MsRunXicExtractorFactoryType m_type
void setTmpDir(const QString &dir_name)
set the temporary working directory
MsRunXicExtractorInterfaceSp buildMsRunXicExtractorSp(MsRunReaderSPtr &msrun_reader) const
build a simple XIC extractor that directly uses Proeowizard library to read and extract XICs building...
static MsRunXicExtractorFactory & getInstance()
singleton to get the only instance of the factory
void setMsRunXicExtractorFactoryType(pappso::MsRunXicExtractorFactoryType type)
sets the xic extractor type
static MsRunXicExtractorFactory m_instance
MsRunReader based XIC extractor featuring disk cache.
proteowizard based XIC extractor featuring disk cache + write buffer
factory to build XIC extractor on an MsRun file
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition: msrunreader.h:185
std::shared_ptr< MsRunXicExtractorInterface > MsRunXicExtractorInterfaceSp