Loading...
Searching...
No Matches
psmfeatures.h
Go to the documentation of this file.
/**
* \file pappsomspp/processing/cbor/psm/evalscan/psmfeatures.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 "pappsomspp/core/processing/cbor/psm/psmfilescanprocessandcopy.h"
#include "pappsomspp/core/psm/xtandem/xtandemspectrumprocess.h"
#include "pappsomspp/core/psm/features/psmfeatures.h"
#include <QJsonObject>
#include "pappsomspp/export-import-config.h"
namespace pappso
{
namespace cbor
{
namespace psm
{
/**
* @todo write docs
*/
class PMSPP_LIB_DECL PsmFeatures : public PsmFileScanProcessAndCopy
{
public:
/**
* Default constructor
*/
PsmFeatures(std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p);
PsmFeatures(std::size_t buffer_scan_size,
CborStreamWriter *cbor_output_p,
const QJsonObject &parameters);
/**
* Destructor
*/
virtual ~PsmFeatures();
protected:
CborScanMapBase *newCborScanMap() override;
void parameterMapReady(pappso::UiMonitorInterface &monitor) override;
private:
pappso::XtandemSpectrumProcess m_tandemSpectrumProcess;
double m_minimumMz = 150;
std::list<pappso::Enums::PeptideIon> m_ionList;
pappso::PrecisionPtr m_fragmentTolerance;
pappso::PsmFeatures *mpa_psmFeatures;
};
} // namespace psm
} // namespace cbor
} // namespace pappso
pappso::PsmFeatures
Definition psmfeatures.h:46
pappso::UiMonitorInterface
Definition uimonitorinterface.h:50
pappso::XtandemSpectrumProcess
Definition xtandemspectrumprocess.h:42
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::PsmFeatures::newCborScanMap
CborScanMapBase * newCborScanMap() override
Definition psmfeatures.cpp:134
pappso::cbor::psm::PsmFeatures::m_tandemSpectrumProcess
pappso::XtandemSpectrumProcess m_tandemSpectrumProcess
Definition psmfeatures.h:69
pappso::cbor::psm::PsmFeatures::parameterMapReady
void parameterMapReady(pappso::UiMonitorInterface &monitor) override
Definition psmfeatures.cpp:109
pappso::cbor::psm::PsmFeatures::mpa_psmFeatures
pappso::PsmFeatures * mpa_psmFeatures
Definition psmfeatures.h:73
pappso::cbor::psm::PsmFeatures::m_fragmentTolerance
pappso::PrecisionPtr m_fragmentTolerance
Definition psmfeatures.h:72
pappso::cbor::psm::PsmFeatures::m_minimumMz
double m_minimumMz
Definition psmfeatures.h:70
pappso::cbor::psm::PsmFeatures::PsmFeatures
PsmFeatures(std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p)
Definition psmfeatures.cpp:39
pappso::cbor::psm::PsmFeatures::m_ionList
std::list< pappso::Enums::PeptideIon > m_ionList
Definition psmfeatures.h:71
pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy
PsmFileScanProcessAndCopy(std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QString &operation)
Definition psmfilescanprocessandcopy.cpp:41
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::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition precision.h:122
psmfeatures.h
psmfilescanprocessandcopy.h
xtandemspectrumprocess.h