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peptidemeasurements.h
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/**
* \file pappsomspp/masschroq/peptidemeasurements.h
* \date 26/09/2024
* \author Olivier Langella
* \brief peptide extracted measures model in masschroqlite
*/
/*******************************************************************************
* Copyright (c) 2024 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of MassChroQ.
*
* MassChroQ 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.
*
* MassChroQ 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 MassChroQ. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include <cstdint>
#include "pappsomspp/core/msrun/msrunid.h"
#include "peptidebase.h"
#include "peptidemeasurementsbase.h"
namespace pappso::masschroq
{
class PeptideObservation;
typedef std::shared_ptr<PeptideObservation> PeptideObservationSp;
class PeptideMeasurements;
typedef std::shared_ptr<PeptideMeasurements> PeptideMeasurementsSp;
class MsRunGroup;
/**
* group together a peptide and measurements made on this peptide
*/
class PeptideMeasurements : public PeptideMeasurementsBase
{
public:
/**
* Default constructor
*/
PeptideMeasurements(const PeptideObservationSp &peptide_observations);
/**
* Copy constructor
*
* @param other TODO
*/
PeptideMeasurements(const PeptideMeasurements &other);
/**
* Destructor
*/
virtual ~PeptideMeasurements();
void prepareMeasurements(const pappso::MsRunId &targeted_msrun,
const MsRunGroup *msrun_group_p,
const QuantificationMethodSp &quantification_method);
virtual void detectQuantifyPeaks(const QuantificationMethodSp &quantification_method) override;
const PeptideObservationSp &getPeptideObservationSp() const;
private:
PeptideObservationSp msp_peptideObservation;
};
} // namespace pappso::masschroq
pappso::MsRunId
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informa...
Definition msrunid.h:54
pappso::masschroq::MsRunGroup
Definition msrungroup.h:48
pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase
PeptideMeasurementsBase()
Definition peptidemeasurementsbase.cpp:34
pappso::masschroq::PeptideMeasurements
Definition peptidemeasurements.h:58
pappso::masschroq::PeptideMeasurements::msp_peptideObservation
PeptideObservationSp msp_peptideObservation
Definition peptidemeasurements.h:88
pappso::masschroq::PeptideMeasurements::getPeptideObservationSp
const PeptideObservationSp & getPeptideObservationSp() const
Definition peptidemeasurements.cpp:166
pappso::masschroq::PeptideMeasurements::~PeptideMeasurements
virtual ~PeptideMeasurements()
Definition peptidemeasurements.cpp:47
pappso::masschroq::PeptideMeasurements::PeptideMeasurements
PeptideMeasurements(const PeptideObservationSp &peptide_observations)
Definition peptidemeasurements.cpp:35
pappso::masschroq::PeptideMeasurements::detectQuantifyPeaks
virtual void detectQuantifyPeaks(const QuantificationMethodSp &quantification_method) override
Definition peptidemeasurements.cpp:101
pappso::masschroq::PeptideMeasurements::prepareMeasurements
void prepareMeasurements(const pappso::MsRunId &targeted_msrun, const MsRunGroup *msrun_group_p, const QuantificationMethodSp &quantification_method)
Definition peptidemeasurements.cpp:52
pappso::masschroq::PeptideObservation
Definition peptideobservation.h:48
msrunid.h
pappso::masschroq
Definition alignmentmethod.h:38
pappso::masschroq::QuantificationMethodSp
std::shared_ptr< QuantificationMethod > QuantificationMethodSp
Definition quantificationmethod.h:46
pappso::masschroq::PeptideMeasurementsSp
std::shared_ptr< PeptideMeasurements > PeptideMeasurementsSp
Definition peptidemeasurements.h:50
pappso::masschroq::PeptideObservationSp
std::shared_ptr< PeptideObservation > PeptideObservationSp
Definition peptidemeasurements.h:45
peptidebase.h
peptidemeasurementsbase.h