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timsmsrunreaderbase.h
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/**
* \file pappsomspp/msrun/private/timsmsrunreaderbase.h
* \date 15/07/2024
* \author Olivier Langella
* \brief Base class for all tims ms run reader objects
*/
/*******************************************************************************
* Copyright (c) 2024 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ 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++ 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++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include "pappsomspp/core/msfile/msfileaccessor.h"
#include "../../vendors/tims/timsdata.h"
namespace pappso
{
class PMSPP_LIB_DECL TimsMsRunReaderBase : public MsRunReader
{
friend class MsFileAccessor;
public:
/**
* Default constructor
*/
TimsMsRunReaderBase(MsRunIdCstSPtr &msrun_id_csp);
TimsMsRunReaderBase(const TimsMsRunReaderBase &msrun_reader_base);
/**
* Destructor
*/
virtual ~TimsMsRunReaderBase();
/** @brief give an access to the underlying raw data pointer
*/
virtual TimsDataSp getTimsDataSPtr();
virtual bool hasScanNumbers() const override;
virtual bool releaseDevice() override;
virtual bool acquireDevice() override;
virtual Trace getTicChromatogram() override;
/** @brief retention timeline
* get retention times along the MSrun in seconds
* @return vector of retention times (seconds)
*/
virtual std::vector<double> getRetentionTimeLine() override;
virtual pappso::XicCoordSPtr
newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index,
pappso::PrecisionPtr precision) const override;
virtual pappso::XicCoordSPtr
newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum,
pappso::PrecisionPtr precision) const override;
virtual const OboPsiModTerm getOboPsiModTermInstrumentModelName() const override;
protected:
virtual void initialize() override;
virtual bool accept(const QString &file_name) const override;
protected:
TimsDataSp msp_timsData = nullptr;
};
} // namespace pappso
pappso::MsRunReader::MsRunReader
MsRunReader(const MsRunIdCstSPtr &ms_run_id)
Definition msrunreader.cpp:43
pappso::OboPsiModTerm
Definition obopsimodterm.h:34
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition qualifiedmassspectrum.h:99
pappso::TimsMsRunReaderBase::TimsMsRunReaderBase
TimsMsRunReaderBase(MsRunIdCstSPtr &msrun_id_csp)
Definition timsmsrunreaderbase.cpp:38
pappso::TimsMsRunReaderBase::getTicChromatogram
virtual Trace getTicChromatogram() override
get a TIC chromatogram
Definition timsmsrunreaderbase.cpp:111
pappso::TimsMsRunReaderBase::MsFileAccessor
friend class MsFileAccessor
Definition timsmsrunreaderbase.h:39
pappso::TimsMsRunReaderBase::releaseDevice
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
Definition timsmsrunreaderbase.cpp:86
pappso::TimsMsRunReaderBase::initialize
virtual void initialize() override
Definition timsmsrunreaderbase.cpp:57
pappso::TimsMsRunReaderBase::getOboPsiModTermInstrumentModelName
virtual const OboPsiModTerm getOboPsiModTermInstrumentModelName() const override
get OboPsiModTerm corresponding to the instrument model name child of : [Term] id: MS:1000031 name: i...
Definition timsmsrunreaderbase.cpp:152
pappso::TimsMsRunReaderBase::newXicCoordSPtrFromSpectrumIndex
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
Definition timsmsrunreaderbase.cpp:131
pappso::TimsMsRunReaderBase::getRetentionTimeLine
virtual std::vector< double > getRetentionTimeLine() override
retention timeline get retention times along the MSrun in seconds
Definition timsmsrunreaderbase.cpp:124
pappso::TimsMsRunReaderBase::msp_timsData
TimsDataSp msp_timsData
Definition timsmsrunreaderbase.h:87
pappso::TimsMsRunReaderBase::hasScanNumbers
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
Definition timsmsrunreaderbase.cpp:79
pappso::TimsMsRunReaderBase::newXicCoordSPtrFromQualifiedMassSpectrum
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
Definition timsmsrunreaderbase.cpp:140
pappso::TimsMsRunReaderBase::acquireDevice
virtual bool acquireDevice() override
acquire data back end device
Definition timsmsrunreaderbase.cpp:93
pappso::TimsMsRunReaderBase::accept
virtual bool accept(const QString &file_name) const override
tells if the reader is able to handle this file must be implemented by private MS run reader,...
Definition timsmsrunreaderbase.cpp:72
pappso::TimsMsRunReaderBase::getTimsDataSPtr
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
Definition timsmsrunreaderbase.cpp:103
pappso::Trace
A simple container of DataPoint instances.
Definition trace.h:152
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
msfileaccessor.h
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition msrunid.h:46
pappso::TimsDataSp
std::shared_ptr< TimsData > TimsDataSp
shared pointer on a TimsData object
Definition timsdata.h:54
pappso::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition precision.h:122
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:44
timsdata.h