libpappsomspp
Library for mass spectrometry
msrunxicextractordiskbuffer.h
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1 /**
2  * \file pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.h
3  * \date 18/05/2018
4  * \author Olivier Langella
5  * \brief proteowizard based XIC extractor featuring disk cache + write buffer
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 
32 #pragma once
33 
34 
35 #include "msrunxicextractordisk.h"
36 
37 
38 class MsRunXicExtractorFactory;
39 
40 namespace pappso
41 {
42 
44 {
46 
47  protected:
48  std::map<unsigned int, QByteArray> m_sliceBufferMap;
49 
50  std::size_t m_bufferSize = 0;
51  std::size_t m_bufferMaxSize = 150;
52 
54  const QDir &temporary_dir);
55 
56  virtual void storeSlices(std::map<unsigned int, MassSpectrum> &slice_vector,
57  std::size_t ipos) override;
58  void appendSliceInBuffer(unsigned int slice_number,
59  MassSpectrum &spectrum,
60  std::size_t ipos);
61 
62  void flushBufferOnDisk();
63  virtual void endPwizRead() override;
64 
65  public:
68 };
69 
70 
71 } // namespace pappso
pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk
void flushBufferOnDisk()
Definition: msrunxicextractordiskbuffer.cpp:151
pappso
Definition: aa.cpp:38
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition: massspectrum.h:91
pappso::MsRunReaderSPtr
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition: msrunreader.h:172
pappso::MsRunXicExtractorDiskBuffer::m_bufferMaxSize
std::size_t m_bufferMaxSize
Definition: msrunxicextractordiskbuffer.h:51
pappso::MsRunXicExtractorDiskBuffer::appendSliceInBuffer
void appendSliceInBuffer(unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
Definition: msrunxicextractordiskbuffer.cpp:99
pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorFactory
friend MsRunXicExtractorFactory
Definition: msrunxicextractordiskbuffer.h:45
pappso::MsRunXicExtractorDiskBuffer::~MsRunXicExtractorDiskBuffer
virtual ~MsRunXicExtractorDiskBuffer()
Definition: msrunxicextractordiskbuffer.cpp:77
pappso::MsRunXicExtractorDisk
Definition: msrunxicextractordisk.h:44
msrunxicextractordisk.h
MsRunReader based XIC extractor featuring disk cache.
pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer
MsRunXicExtractorDiskBuffer(MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)
Definition: msrunxicextractordiskbuffer.cpp:61
pappso::MsRunXicExtractorDiskBuffer::storeSlices
virtual void storeSlices(std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos) override
store MassSpectrum slices (by daltons) for a given retention time
Definition: msrunxicextractordiskbuffer.cpp:82
pappso::MsRunXicExtractorDiskBuffer::m_bufferSize
std::size_t m_bufferSize
Definition: msrunxicextractordiskbuffer.h:50
pappso::MsRunXicExtractorDiskBuffer
Definition: msrunxicextractordiskbuffer.h:43
pappso::MsRunXicExtractorDiskBuffer::m_sliceBufferMap
std::map< unsigned int, QByteArray > m_sliceBufferMap
Definition: msrunxicextractordiskbuffer.h:48
pappso::MsRunXicExtractorDiskBuffer::endPwizRead
virtual void endPwizRead() override
Definition: msrunxicextractordiskbuffer.cpp:227