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psmfeaturesscan.h
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/**
* \file pappsomspp/processing/cbor/psm/evalscan/psmfeaturesscan.h
* \date 15/07/2025
* \author Olivier Langella
* \brief compute features 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 "../cborscanmapbase.h"
#include "../../../../psm/xtandem/xtandemspectrumprocess.h"
#include "../../../../psm/features/psmfeatures.h"
namespace pappso
{
namespace cbor
{
namespace psm
{
/**
* @todo write docs
*/
class PsmFeaturesScan : public CborScanMapBase
{
public:
/**
* Default constructor
*/
PsmFeaturesScan(const PsmFileScanProcess &psm_file_scan_process,
pappso::XtandemSpectrumProcess &tandem_spectrum_process,
std::list<pappso::Enums::PeptideIon> &ion_list,
pappso::PsmFeatures &psm_features,
pappso::PrecisionPtr fragment_tolerance);
/**
* Destructor
*/
virtual ~PsmFeaturesScan();
protected:
void process() override;
double checkInf(double input) const;
private:
pappso::XtandemSpectrumProcess &m_tandemSpectrumProcess;
std::list<pappso::Enums::PeptideIon> &m_ionList;
pappso::PsmFeatures m_psmFeatures;
pappso::PrecisionPtr m_fragmentTolerance;
};
} // namespace psm
} // namespace cbor
} // namespace pappso
cborscanmapbase.h
pappso::PsmFeatures
Definition psmfeatures.h:46
pappso::XtandemSpectrumProcess
Definition xtandemspectrumprocess.h:42
pappso::cbor::psm::CborScanMapBase::CborScanMapBase
CborScanMapBase(const PsmFileScanProcess &psm_file_scan_process)
Definition cborscanmapbase.cpp:40
pappso::cbor::psm::PsmFeaturesScan::process
void process() override
Definition psmfeaturesscan.cpp:68
pappso::cbor::psm::PsmFeaturesScan::PsmFeaturesScan
PsmFeaturesScan(const PsmFileScanProcess &psm_file_scan_process, pappso::XtandemSpectrumProcess &tandem_spectrum_process, std::list< pappso::Enums::PeptideIon > &ion_list, pappso::PsmFeatures &psm_features, pappso::PrecisionPtr fragment_tolerance)
Definition psmfeaturesscan.cpp:42
pappso::cbor::psm::PsmFeaturesScan::~PsmFeaturesScan
virtual ~PsmFeaturesScan()
Definition psmfeaturesscan.cpp:55
pappso::cbor::psm::PsmFeaturesScan::m_tandemSpectrumProcess
pappso::XtandemSpectrumProcess & m_tandemSpectrumProcess
Definition psmfeaturesscan.h:66
pappso::cbor::psm::PsmFeaturesScan::m_ionList
std::list< pappso::Enums::PeptideIon > & m_ionList
Definition psmfeaturesscan.h:67
pappso::cbor::psm::PsmFeaturesScan::checkInf
double checkInf(double input) const
Definition psmfeaturesscan.cpp:60
pappso::cbor::psm::PsmFeaturesScan::m_fragmentTolerance
pappso::PrecisionPtr m_fragmentTolerance
Definition psmfeaturesscan.h:69
pappso::cbor::psm::PsmFeaturesScan::m_psmFeatures
pappso::PsmFeatures m_psmFeatures
Definition psmfeaturesscan.h:68
pappso::cbor::psm::PsmFileScanProcess
Basic PSM file reader to process scan (parallelized scan processing).
Definition psmfilescanprocess.h:48
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
pappso::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition precision.h:122
psmfeatures.h
xtandemspectrumprocess.h