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psmspecglobscan.h
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/**
* \file pappsomspp/processing/cbor/psm/evalscan/psmspecglobscan.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.
*https://visio.numerique.gouv.fr/
* 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 "psmspecglob.h"
namespace pappso::cbor::psm
{
/**
* @todo write docs
*/
class PsmSpecGlobScan : public CborScanMapBase
{
public:
/**
* Default constructor
*/
PsmSpecGlobScan(const PsmSpecGlob &psm_specgloc,
pappso::PrecisionPtr fragment_tolerance);
/**
* Destructor
*/
virtual ~PsmSpecGlobScan();
protected:
void process() override;
private:
const PsmSpecGlob *mp_psmSpecGlob;
pappso::PrecisionPtr m_fragmentTolerance;
bool m_checkMutations = false;
};
} // namespace pappso::cbor::psm
cborscanmapbase.h
pappso::cbor::psm::CborScanMapBase::CborScanMapBase
CborScanMapBase(const PsmFileScanProcess &psm_file_scan_process)
Definition cborscanmapbase.cpp:40
pappso::cbor::psm::PsmSpecGlobScan::m_fragmentTolerance
pappso::PrecisionPtr m_fragmentTolerance
Definition psmspecglobscan.h:56
pappso::cbor::psm::PsmSpecGlobScan::m_checkMutations
bool m_checkMutations
Definition psmspecglobscan.h:57
pappso::cbor::psm::PsmSpecGlobScan::mp_psmSpecGlob
const PsmSpecGlob * mp_psmSpecGlob
Definition psmspecglobscan.h:55
pappso::cbor::psm::PsmSpecGlobScan::~PsmSpecGlobScan
virtual ~PsmSpecGlobScan()
Definition psmspecglobscan.cpp:43
pappso::cbor::psm::PsmSpecGlobScan::PsmSpecGlobScan
PsmSpecGlobScan(const PsmSpecGlob &psm_specgloc, pappso::PrecisionPtr fragment_tolerance)
Definition psmspecglobscan.cpp:35
pappso::cbor::psm::PsmSpecGlobScan::process
void process() override
Definition psmspecglobscan.cpp:48
pappso::cbor::psm::PsmSpecGlob
Definition psmspecglob.h:41
pappso::cbor::psm
Definition cborscanmapbase.h:40
pappso::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition precision.h:122
psmspecglob.h