Loading...
Searching...
No Matches
mbrpeptidemeasurements.h
Go to the documentation of this file.
/**
* \file pappsomspp/masschroq/mbrpeptidemeasurements.h
* \date 27/10/2024
* \author Olivier Langella
* \brief peptide extracted measures in MBR mode 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 "peptide.h"
#include "peptidemeasurementsbase.h"
#include "pappsomspp/core/msrun/alignment/msrunretentiontime.h"
namespace pappso::masschroq
{
class MbrPeptideMeasurements;
typedef std::shared_ptr<MbrPeptideMeasurements> MbrPeptideMeasurementsSp;
/**
* @todo write docs
*/
class MbrPeptideMeasurements : public PeptideMeasurementsBase
{
public:
/**
* Default constructor
*/
MbrPeptideMeasurements(const PeptideSp &peptide_sp);
MbrPeptideMeasurements(const MbrPeptideMeasurements &other);
/**
* Destructor
*/
virtual ~MbrPeptideMeasurements();
void prepareMeasurements(const pappso::MsRunId &targeted_msrun,
const MsRunGroup *msrun_group_p,
const pappso::MsRunRetentionTime<QString> &msrun_retention_time,
const QuantificationMethodSp &quantification_method);
virtual void detectQuantifyPeaks(const QuantificationMethodSp &quantification_method) override;
const PeptideSp &getPeptideSp() const;
private:
PeptideSp msp_peptide;
double m_consensusMs2RetentionTime = 0;
};
} // 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::MsRunRetentionTime
Definition msrunretentiontime.h:43
pappso::masschroq::MbrPeptideMeasurements
Definition mbrpeptidemeasurements.h:49
pappso::masschroq::MbrPeptideMeasurements::detectQuantifyPeaks
virtual void detectQuantifyPeaks(const QuantificationMethodSp &quantification_method) override
Definition mbrpeptidemeasurements.cpp:121
pappso::masschroq::MbrPeptideMeasurements::MbrPeptideMeasurements
MbrPeptideMeasurements(const PeptideSp &peptide_sp)
Definition mbrpeptidemeasurements.cpp:35
pappso::masschroq::MbrPeptideMeasurements::getPeptideSp
const PeptideSp & getPeptideSp() const
Definition mbrpeptidemeasurements.cpp:172
pappso::masschroq::MbrPeptideMeasurements::m_consensusMs2RetentionTime
double m_consensusMs2RetentionTime
Definition mbrpeptidemeasurements.h:78
pappso::masschroq::MbrPeptideMeasurements::msp_peptide
PeptideSp msp_peptide
Definition mbrpeptidemeasurements.h:76
pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements
void prepareMeasurements(const pappso::MsRunId &targeted_msrun, const MsRunGroup *msrun_group_p, const pappso::MsRunRetentionTime< QString > &msrun_retention_time, const QuantificationMethodSp &quantification_method)
Definition mbrpeptidemeasurements.cpp:61
pappso::masschroq::MbrPeptideMeasurements::~MbrPeptideMeasurements
virtual ~MbrPeptideMeasurements()
Definition mbrpeptidemeasurements.cpp:55
pappso::masschroq::MsRunGroup
Definition msrungroup.h:48
pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase
PeptideMeasurementsBase()
Definition peptidemeasurementsbase.cpp:34
peptide.h
msrunretentiontime.h
pappso::masschroq
Definition alignmentmethod.h:38
pappso::masschroq::QuantificationMethodSp
std::shared_ptr< QuantificationMethod > QuantificationMethodSp
Definition quantificationmethod.h:46
pappso::masschroq::MbrPeptideMeasurementsSp
std::shared_ptr< MbrPeptideMeasurements > MbrPeptideMeasurementsSp
Definition mbrpeptidemeasurements.h:44
pappso::masschroq::PeptideSp
std::shared_ptr< Peptide > PeptideSp
Definition peptide.h:46
peptidemeasurementsbase.h