libpappsomspp
Library for mass spectrometry
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psmfilescanprocess.h
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1/**
2 * \file pappsomspp/processing/cbor/psm/psmfilescanprocess.h
3 * \date 12/07/2025
4 * \author Olivier Langella
5 * \brief PSM file reader designed to parallelize scan process
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.fr>.
10 *
11 * This file is part of PAPPSOms-tools.
12 *
13 * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27#pragma once
28
29#include "psmfilereaderbase.h"
30#include <QTemporaryDir>
31#include <QCborMap>
32#include "cborscanmapbase.h"
34
35namespace pappso
36{
37namespace cbor
38{
39namespace psm
40{
41
42
43/**
44 * @brief Basic PSM file reader to process scan (parallelized scan processing)
45 */
47
48{
50
51 public:
52 /**
53 * Default constructor
54 */
55 PsmFileScanProcess(std::size_t buffer_scan_size);
56
57 /**
58 * Destructor
59 */
60 virtual ~PsmFileScanProcess();
61
62 protected:
63 void readScan(pappso::UiMonitorInterface &monitor) override;
64 void scanFinished(pappso::UiMonitorInterface &monitor) override;
65 void sampleFinished(pappso::UiMonitorInterface &monitor) override;
66 virtual void processBufferScan(pappso::UiMonitorInterface &monitor);
69 void clearScanBuffer();
70
71
72 protected:
73 std::size_t m_bufferScanSize = 1000;
74 std::vector<CborScanMapBase *> m_cborScanList;
75};
76
77} // namespace psm
78} // namespace cbor
79} // namespace pappso
std::vector< CborScanMapBase * > m_cborScanList
void scanFinished(pappso::UiMonitorInterface &monitor) override
void readScan(pappso::UiMonitorInterface &monitor) override
void sampleFinished(pappso::UiMonitorInterface &monitor) override
virtual void processBufferScanDone(pappso::UiMonitorInterface &monitor)
PsmFileScanProcess(std::size_t buffer_scan_size)
virtual void processBufferScan(pappso::UiMonitorInterface &monitor)
virtual CborScanMapBase * newCborScanMap()=0
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39