libpappsomspp
Library for mass spectrometry
msrunxicextractorfactory.h
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1 /**
2  * \file pappsomspp/xicextractor/msrunxicextractorfactory.h
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 
31 #pragma once
32 
34 
35 
36 namespace pappso
37 {
38 
39 
40 /** \def MsRunXicExtractorFactoryType the kind of xic extractor you want
41  * this may be usefull to choose if you want a direct extraction (no buffer, no
42  * temporary file) or an optimized xic extraction to save memory or cpu
43  *
44  */
45 enum class MsRunXicExtractorFactoryType : std::int8_t
46 {
47  nose = 0, ///< default factory
48  direct = 1, ///< build a simple XIC extractor that directly uses Proeowizard
49  ///< library to read and extract XICs building the xic extractor
50  ///< is fast, but extracting each XIC is slow
51  disk = 2, ///< build Xic extractor that first read the whole MsRun, put it on
52  ///< disk and extract XICs more quickly This needs some space on
53  ///< disk to store slices (1 dalton each) building the XIC extractor
54  ///< is slow extracting XIC from slices is a very quick operation
55  diskbuffer =
56  3, ///< build Xic extractor that first read the whole MsRun, put it on disk
57  ///< using a write cache and extract XICs more quickly This needs some
58  ///< space on disk to store slices (1 dalton each) building the XIC
59  ///< extractor is slower than buildMsRunXicExtractorPwizSp, but faster
60  ///< than buildMsRunXicExtractorDiskSp extracting XIC from slices is a
61  ///< very quick operation
62 };
63 
64 
65 /** @brief factory to build different kinds of XIC extractors
66  */
68 {
69  public:
70  /** @brief singleton to get the only instance of the factory
71  */
72  static MsRunXicExtractorFactory &getInstance();
73 
74  /** @brief build a simple XIC extractor that directly uses Proeowizard library
75  * to read and extract XICs building the xic extractor is fast, but extracting
76  * each XIC is slow
77  * @param msrun_reader the MsRun reader on which the XIC extractor will run
78  */
80  buildMsRunXicExtractorSp(MsRunReaderSPtr &msrun_reader) const;
81 
82  /// set the temporary working directory
83  void setTmpDir(const QString &dir_name);
84 
85  /** @brief sets the xic extractor type
86  * @param type see the documentation of enumerations
87  */
88  void
89  setMsRunXicExtractorFactoryType(pappso::MsRunXicExtractorFactoryType type);
90 
91  private:
93  virtual ~MsRunXicExtractorFactory();
94 
95 
96  private:
98  QString m_tmpDirName;
100 };
101 
102 } // namespace pappso
factory to build different kinds of XIC extractors
static MsRunXicExtractorFactory m_instance
#define PMSPP_LIB_DECL
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