libpappsomspp
Library for mass spectrometry
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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
36
37
38class MsRunXicExtractorFactory;
39
40namespace pappso
41{
42
44{
46
47 public:
50
51 protected:
53 const QDir &temporary_dir);
54
55 virtual void storeSlices(std::map<unsigned int, MassSpectrum> &slice_vector,
56 std::size_t ipos) override;
57 void appendSliceInBuffer(unsigned int slice_number,
58 MassSpectrum &spectrum,
59 std::size_t ipos);
60
61 void flushBufferOnDisk();
62 virtual void endPwizRead() override;
63
64
65 protected:
66 std::map<unsigned int, QByteArray> m_sliceBufferMap;
67
68 std::size_t m_bufferSize = 0;
69 std::size_t m_bufferMaxSize = 150;
70};
71
72
73} // namespace pappso
Class to represent a mass spectrum.
void appendSliceInBuffer(unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
std::map< unsigned int, QByteArray > m_sliceBufferMap
MsRunXicExtractorDiskBuffer(const MsRunXicExtractorDiskBuffer &other)
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
MsRunReader based XIC extractor featuring disk cache.
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:56