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cborscanmapbase.h
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/**
* \file pappsomspp/processing/cbor/psm/cborscanmapbase.h
* \date 13/07/2025
* \author Olivier Langella
* \brief Base class to handle scan cbor map
*/
/*******************************************************************************
* 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 <QCborMap>
#include "pappsomspp/core/massspectrum/qualifiedmassspectrum.h"
#include "pappsomspp/core/processing/cbor/psm/psmproteinmap.h"
#include "pappsomspp/export-import-config.h"
namespace pappso
{
namespace cbor
{
namespace psm
{
class PsmFileScanProcess;
/**
* @todo write docs
*/
class PMSPP_LIB_DECL CborScanMapBase : public QCborMap
{
public:
/**
* Default constructor
*/
CborScanMapBase(const PsmFileScanProcess &psm_file_scan_process);
/**
* Destructor
*/
virtual ~CborScanMapBase();
virtual void process();
virtual void filterAndSortPsmList();
void filterPsmListUniqueUniqueProforma();
/** @brief add a new eval key and double values (from a vector) to each PSM
*/
std::vector<double>::iterator addPsmEvalVectorDouble(const QString &eval_name,
const QString &eval_value_key,
std::vector<double>::iterator begin,
std::vector<double>::const_iterator end);
QCborMap getCborScanId() const;
QCborMap getCborScanPrecursor() const;
QCborArray getCborPsmList() const;
void populateProteinMapUsingOldProteinMap(const PsmProteinMap &old_protein_map,
PsmProteinMap &new_protein_map) const;
protected:
pappso::QualifiedMassSpectrumSPtr getCurrentQualifiedMassSpectrumSPtr() const;
protected:
const PsmFileScanProcess &m_PsmFileScanProcess;
};
} // namespace psm
} // namespace cbor
} // namespace pappso
pappso::cbor::psm::CborScanMapBase::getCborScanPrecursor
QCborMap getCborScanPrecursor() const
Definition cborscanmapbase.cpp:65
pappso::cbor::psm::CborScanMapBase::process
virtual void process()
Definition cborscanmapbase.cpp:50
pappso::cbor::psm::CborScanMapBase::filterAndSortPsmList
virtual void filterAndSortPsmList()
Definition cborscanmapbase.cpp:261
pappso::cbor::psm::CborScanMapBase::filterPsmListUniqueUniqueProforma
void filterPsmListUniqueUniqueProforma()
Definition cborscanmapbase.cpp:268
pappso::cbor::psm::CborScanMapBase::addPsmEvalVectorDouble
std::vector< double >::iterator addPsmEvalVectorDouble(const QString &eval_name, const QString &eval_value_key, std::vector< double >::iterator begin, std::vector< double >::const_iterator end)
add a new eval key and double values (from a vector) to each PSM
Definition cborscanmapbase.cpp:86
pappso::cbor::psm::CborScanMapBase::m_PsmFileScanProcess
const PsmFileScanProcess & m_PsmFileScanProcess
Definition cborscanmapbase.h:85
pappso::cbor::psm::CborScanMapBase::getCborPsmList
QCborArray getCborPsmList() const
Definition cborscanmapbase.cpp:75
pappso::cbor::psm::CborScanMapBase::CborScanMapBase
CborScanMapBase(const PsmFileScanProcess &psm_file_scan_process)
Definition cborscanmapbase.cpp:40
pappso::cbor::psm::CborScanMapBase::populateProteinMapUsingOldProteinMap
void populateProteinMapUsingOldProteinMap(const PsmProteinMap &old_protein_map, PsmProteinMap &new_protein_map) const
Definition cborscanmapbase.cpp:230
pappso::cbor::psm::CborScanMapBase::getCborScanId
QCborMap getCborScanId() const
Definition cborscanmapbase.cpp:55
pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr
pappso::QualifiedMassSpectrumSPtr getCurrentQualifiedMassSpectrumSPtr() const
Definition cborscanmapbase.cpp:136
pappso::cbor::psm::PsmFileScanProcess
Basic PSM file reader to process scan (parallelized scan processing).
Definition psmfilescanprocess.h:48
pappso::cbor::psm::PsmProteinMap
store PsmProtein in a map with accession as key
Definition psmproteinmap.h:56
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
pappso::QualifiedMassSpectrumSPtr
std::shared_ptr< QualifiedMassSpectrum > QualifiedMassSpectrumSPtr
Definition qualifiedmassspectrum.h:43
psmproteinmap.h
qualifiedmassspectrum.h