Loading...
Searching...
No Matches
msrun.h
Go to the documentation of this file.
/**
* \file pappsomspp/masschroq/core/msrun.h
* \date 24/09/2024
* \author Olivier Langella
* \brief msrun 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 "../peptide/peptide.h"
#include "pappsomspp/core/msrun/msrunreader.h"
#include "../xicextractor/msrunxicextractorinterface.h"
#include "precursor.h"
#include "input/precursorparser.h"
namespace pappso::masschroq
{
class MsRun;
typedef std::shared_ptr<MsRun> MsRunSp;
/**
* @description group together an msrun reader object and list of precursors
* (MS1 peak chosen for fragmentation)
*/
class MsRun
{
public:
/**
* Default constructor
*/
MsRun(pappso::MsRunReaderSPtr msrun_reader);
/**
* Destructor
*/
virtual ~MsRun();
const pappso::MsRunReaderSPtr &getMsRunReaderSPtr() const;
pappso::MsRunReaderSPtr &getMsRunReaderSPtr();
const PrecursorSp &getPrecursorSPtrBySpectrumIndex(std::size_t spectrum_index) const;
const PrecursorSp &getPrecursorSPtrByScanNumber(std::size_t scan_number) const;
const std::vector<double> &getRetentionTimeLine() const;
bool hasTimsTofMobilityIndex() const;
private:
pappso::MsRunReaderSPtr msp_msRunReader;
/** @brief new map dedicated to spectrum index to replace obsolete scan number
*/
std::map<std::size_t, PrecursorSp> m_spectrumIndex2precursorMap;
pappso::MsRunXicExtractorInterfaceSp msp_msRunXicExtractorInterfaceSp;
PrecursorParser *mpa_precursorParser;
std::vector<double> m_retentionTimeLine;
bool m_hasTimsTofMobilityIndex = false;
};
} // namespace pappso::masschroq
pappso::masschroq::MsRun
Definition msrun.h:50
pappso::masschroq::MsRun::MsRun
MsRun(pappso::MsRunReaderSPtr msrun_reader)
Definition msrun.cpp:35
pappso::masschroq::MsRun::msp_msRunXicExtractorInterfaceSp
pappso::MsRunXicExtractorInterfaceSp msp_msRunXicExtractorInterfaceSp
Definition msrun.h:81
pappso::masschroq::MsRun::getMsRunReaderSPtr
const pappso::MsRunReaderSPtr & getMsRunReaderSPtr() const
Definition msrun.cpp:63
pappso::masschroq::MsRun::hasTimsTofMobilityIndex
bool hasTimsTofMobilityIndex() const
Definition msrun.cpp:94
pappso::masschroq::MsRun::mpa_precursorParser
PrecursorParser * mpa_precursorParser
Definition msrun.h:83
pappso::masschroq::MsRun::getPrecursorSPtrBySpectrumIndex
const PrecursorSp & getPrecursorSPtrBySpectrumIndex(std::size_t spectrum_index) const
Definition msrun.cpp:82
pappso::masschroq::MsRun::m_retentionTimeLine
std::vector< double > m_retentionTimeLine
Definition msrun.h:85
pappso::masschroq::MsRun::getPrecursorSPtrByScanNumber
const PrecursorSp & getPrecursorSPtrByScanNumber(std::size_t scan_number) const
Definition msrun.cpp:76
pappso::masschroq::MsRun::~MsRun
virtual ~MsRun()
Definition msrun.cpp:57
pappso::masschroq::MsRun::m_hasTimsTofMobilityIndex
bool m_hasTimsTofMobilityIndex
Definition msrun.h:87
pappso::masschroq::MsRun::msp_msRunReader
pappso::MsRunReaderSPtr msp_msRunReader
Definition msrun.h:75
pappso::masschroq::MsRun::getRetentionTimeLine
const std::vector< double > & getRetentionTimeLine() const
Definition msrun.cpp:88
pappso::masschroq::MsRun::m_spectrumIndex2precursorMap
std::map< std::size_t, PrecursorSp > m_spectrumIndex2precursorMap
new map dedicated to spectrum index to replace obsolete scan number
Definition msrun.h:79
pappso::masschroq::PrecursorParser
Definition precursorparser.h:41
precursor.h
msrunreader.h
msrunxicextractorinterface.h
pappso::masschroq
Definition alignmentmethod.h:38
pappso::masschroq::PrecursorSp
std::shared_ptr< Precursor > PrecursorSp
Definition precursor.h:39
pappso::masschroq::MsRunSp
std::shared_ptr< MsRun > MsRunSp
Definition msrun.h:44
pappso::MsRunReaderSPtr
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition msrunreader.h:57
pappso::MsRunXicExtractorInterfaceSp
std::shared_ptr< MsRunXicExtractorInterface > MsRunXicExtractorInterfaceSp
Definition msrunxicextractorinterface.h:42
peptide.h
precursorparser.h