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psmfilescanprocess.h
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/**
* \file pappsomspp/processing/cbor/psm/psmfilescanprocess.h
* \date 12/07/2025
* \author Olivier Langella
* \brief PSM file reader designed to parallelize scan process
*/
/*******************************************************************************
* Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of PAPPSOms-tools.
*
* PAPPSOms-tools is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms-tools is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include "psmfilereaderbase.h"
#include <QTemporaryDir>
#include <QCborMap>
#include "cborscanmapbase.h"
#include "pappsomspp/export-import-config.h"
namespace pappso
{
namespace cbor
{
namespace psm
{
/**
* @brief Basic PSM file reader to process scan (parallelized scan processing)
*/
class PMSPP_LIB_DECL PsmFileScanProcess : public PsmFileReaderBase
{
friend CborScanMapBase;
public:
/**
* Default constructor
*/
PsmFileScanProcess(std::size_t buffer_scan_size);
/**
* Destructor
*/
virtual ~PsmFileScanProcess();
protected:
void readScan(pappso::UiMonitorInterface &monitor) override;
void scanFinished(pappso::UiMonitorInterface &monitor) override;
void sampleFinished(pappso::UiMonitorInterface &monitor) override;
virtual void processBufferScan(pappso::UiMonitorInterface &monitor);
virtual void processBufferScanDone(pappso::UiMonitorInterface &monitor);
virtual CborScanMapBase *newCborScanMap() = 0;
void clearScanBuffer();
protected:
std::size_t m_bufferScanSize = 1000;
std::vector<CborScanMapBase *> m_cborScanList;
};
} // namespace psm
} // namespace cbor
} // namespace pappso
cborscanmapbase.h
pappso::UiMonitorInterface
Definition uimonitorinterface.h:50
pappso::cbor::psm::PsmFileReaderBase::PsmFileReaderBase
PsmFileReaderBase()
Definition psmfilereaderbase.cpp:42
pappso::cbor::psm::PsmFileScanProcess::m_cborScanList
std::vector< CborScanMapBase * > m_cborScanList
Definition psmfilescanprocess.h:74
pappso::cbor::psm::PsmFileScanProcess::scanFinished
void scanFinished(pappso::UiMonitorInterface &monitor) override
Definition psmfilescanprocess.cpp:80
pappso::cbor::psm::PsmFileScanProcess::m_bufferScanSize
std::size_t m_bufferScanSize
Definition psmfilescanprocess.h:73
pappso::cbor::psm::PsmFileScanProcess::CborScanMapBase
friend CborScanMapBase
Definition psmfilescanprocess.h:49
pappso::cbor::psm::PsmFileScanProcess::readScan
void readScan(pappso::UiMonitorInterface &monitor) override
Definition psmfilescanprocess.cpp:62
pappso::cbor::psm::PsmFileScanProcess::sampleFinished
void sampleFinished(pappso::UiMonitorInterface &monitor) override
Definition psmfilescanprocess.cpp:93
pappso::cbor::psm::PsmFileScanProcess::processBufferScanDone
virtual void processBufferScanDone(pappso::UiMonitorInterface &monitor)
Definition psmfilescanprocess.cpp:122
pappso::cbor::psm::PsmFileScanProcess::PsmFileScanProcess
PsmFileScanProcess(std::size_t buffer_scan_size)
Definition psmfilescanprocess.cpp:41
pappso::cbor::psm::PsmFileScanProcess::processBufferScan
virtual void processBufferScan(pappso::UiMonitorInterface &monitor)
Definition psmfilescanprocess.cpp:102
pappso::cbor::psm::PsmFileScanProcess::clearScanBuffer
void clearScanBuffer()
Definition psmfilescanprocess.cpp:51
pappso::cbor::psm::PsmFileScanProcess::newCborScanMap
virtual CborScanMapBase * newCborScanMap()=0
export-import-config.h
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
pappso::cbor::psm
Definition cborscanmapbase.h:40
pappso::cbor
Definition cborstreamreader.cpp:35
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
psmfilereaderbase.h