Loading...
Searching...
No Matches
psmspecglob.h
Go to the documentation of this file.
/**
* \file pappsomspp/processing/cbor/psm/evalscan/psmspecglob.h
* \date 19/07/2025
* \author Olivier Langella
* \brief compute specglob alignment on scan's PSM
*/
/*******************************************************************************
* 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 "../psmfilescanprocessandcopy.h"
#include <QJsonObject>
#include "pappsomspp/export-import-config.h"
namespace pappso::cbor::psm
{
class PsmSpecGlobScan;
/**
* @todo write docs
*/
class PMSPP_LIB_DECL PsmSpecGlob : public PsmFileScanProcessAndCopy
{
friend PsmSpecGlobScan;
public:
/**
* Default constructor
*/
PsmSpecGlob(std::size_t buffer_scan_size,
CborStreamWriter *cbor_output_p,
const QJsonObject &parameters);
/**
* Destructor
*/
virtual ~PsmSpecGlob();
void filterMassSpectrum(pappso::MassSpectrum &mass_spectrum) const;
protected:
pappso::cbor::psm::CborScanMapBase *newCborScanMap() override;
void parameterMapReady(pappso::UiMonitorInterface &monitor) override;
virtual void processBufferScanDone(pappso::UiMonitorInterface &monitor) override;
protected:
QJsonObject m_specglobParameters;
pappso::PrecisionPtr m_fragmentTolerance;
double m_minimumMz;
std::size_t m_nMostIntense;
bool m_deisotope = true;
bool m_isProteinMatcherResult = false;
std::size_t m_countScanProcessed = 0;
};
} // namespace pappso::cbor::psm
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition massspectrum.h:70
pappso::UiMonitorInterface
Definition uimonitorinterface.h:50
pappso::cbor::CborStreamWriter
overrides QCborStreamWriter base class to provide convenient functions
Definition cborstreamwriter.h:45
pappso::cbor::psm::CborScanMapBase
Definition cborscanmapbase.h:48
pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy
PsmFileScanProcessAndCopy(std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QString &operation)
Definition psmfilescanprocessandcopy.cpp:41
pappso::cbor::psm::PsmSpecGlobScan
Definition psmspecglobscan.h:38
pappso::cbor::psm::PsmSpecGlob::m_isProteinMatcherResult
bool m_isProteinMatcherResult
Definition psmspecglob.h:73
pappso::cbor::psm::PsmSpecGlob::m_minimumMz
double m_minimumMz
Definition psmspecglob.h:70
pappso::cbor::psm::PsmSpecGlob::newCborScanMap
pappso::cbor::psm::CborScanMapBase * newCborScanMap() override
Definition psmspecglob.cpp:99
pappso::cbor::psm::PsmSpecGlob::m_fragmentTolerance
pappso::PrecisionPtr m_fragmentTolerance
Definition psmspecglob.h:69
pappso::cbor::psm::PsmSpecGlob::m_specglobParameters
QJsonObject m_specglobParameters
Definition psmspecglob.h:68
pappso::cbor::psm::PsmSpecGlob::processBufferScanDone
virtual void processBufferScanDone(pappso::UiMonitorInterface &monitor) override
Definition psmspecglob.cpp:107
pappso::cbor::psm::PsmSpecGlob::filterMassSpectrum
void filterMassSpectrum(pappso::MassSpectrum &mass_spectrum) const
Definition psmspecglob.cpp:89
pappso::cbor::psm::PsmSpecGlob::parameterMapReady
void parameterMapReady(pappso::UiMonitorInterface &monitor) override
Definition psmspecglob.cpp:67
pappso::cbor::psm::PsmSpecGlob::PsmSpecGlob
PsmSpecGlob(std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QJsonObject &parameters)
Definition psmspecglob.cpp:35
pappso::cbor::psm::PsmSpecGlob::m_deisotope
bool m_deisotope
Definition psmspecglob.h:72
pappso::cbor::psm::PsmSpecGlob::m_countScanProcessed
std::size_t m_countScanProcessed
Definition psmspecglob.h:74
pappso::cbor::psm::PsmSpecGlob::m_nMostIntense
std::size_t m_nMostIntense
Definition psmspecglob.h:71
pappso::cbor::psm::PsmSpecGlob::PsmSpecGlobScan
friend PsmSpecGlobScan
Definition psmspecglob.h:42
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::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition precision.h:122
psmfilescanprocessandcopy.h