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precursor.h
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/**
* \file pappsomspp/masschroq/precursor.h
* \date 04/11/2024
* \author Olivier Langella
* \brief MS1 precursor information
*/
/*******************************************************************************
* 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 <memory>
#include "pappsomspp/core/msrun/xiccoord/xiccoord.h"
namespace pappso::masschroq
{
class Precursor;
typedef std::shared_ptr<Precursor> PrecursorSp;
/**
* \class Precursor
* \brief A Precursor object represents the parent/precursor of the MS level 2
* scan with number _scan_num in the mzxml file.
* In mzxml files, MS scans of level 2 have each a precursor object
* representing their MS level 1 parent/precursor. A Precursor object has :
* - a spectrum index
* - a retention time value
* - an intensity value
* - an mz value
* - Xic coordinates
*/
class Precursor
{
public:
/**
* Default constructor
*/
Precursor(std::size_t spectrum_index,
double mz,
double intensity,
pappso::XicCoordSPtr xic_coord);
/**
* Destructor
*/
virtual ~Precursor();
double getIntensity() const;
std::size_t getSpectrumIndex() const;
const pappso::XicCoordSPtr &getXicCoordSPtr() const;
private:
///< MS level 2 scan number whome this Precursor is parent
std::size_t m_spectrumIndex;
/// intensity of this precursor
double m_intensity;
/// selected m/z of this precursor
double m_mz;
/// Xic coordinates
pappso::XicCoordSPtr msp_xicCoord;
};
} // namespace pappso::masschroq
pappso::masschroq::Precursor
A Precursor object represents the parent/precursor of the MS level 2 scan with number _scan_num in th...
Definition precursor.h:56
pappso::masschroq::Precursor::~Precursor
virtual ~Precursor()
Definition precursor.cpp:54
pappso::masschroq::Precursor::msp_xicCoord
pappso::XicCoordSPtr msp_xicCoord
Xic coordinates.
Definition precursor.h:84
pappso::masschroq::Precursor::getSpectrumIndex
std::size_t getSpectrumIndex() const
Definition precursor.cpp:65
pappso::masschroq::Precursor::m_mz
double m_mz
selected m/z of this precursor
Definition precursor.h:82
pappso::masschroq::Precursor::getXicCoordSPtr
const pappso::XicCoordSPtr & getXicCoordSPtr() const
Definition precursor.cpp:71
pappso::masschroq::Precursor::Precursor
Precursor(std::size_t spectrum_index, double mz, double intensity, pappso::XicCoordSPtr xic_coord)
Definition precursor.cpp:33
pappso::masschroq::Precursor::m_intensity
double m_intensity
intensity of this precursor
Definition precursor.h:80
pappso::masschroq::Precursor::getIntensity
double getIntensity() const
Definition precursor.cpp:59
pappso::masschroq::Precursor::m_spectrumIndex
std::size_t m_spectrumIndex
< MS level 2 scan number whome this Precursor is parent
Definition precursor.h:78
pappso::masschroq
Definition alignmentmethod.h:38
pappso::masschroq::PrecursorSp
std::shared_ptr< Precursor > PrecursorSp
Definition precursor.h:39
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:44
xiccoord.h