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timsmsrunreaderms2selected.h
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/**
* \file pappsomspp/msrun/private/timsmsrunreaderms2.h
* \date 10/09/2019
* \author Olivier Langella
* \brief MSrun file reader for native Bruker TimsTOF specialized for MS2
* purpose
*/
/*******************************************************************************
* Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.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/msrun/private/timsmsrunreaderms2.h"
#include "../../types.h"
#include "pappsomspp/core/msfile/msfileaccessor.h"
#include "pappsomspp/core/msfile/msfilereader.h"
#include "../../vendors/tims/timsdata.h"
namespace pappso
{
class PMSPP_LIB_DECL TimsMsRunReaderMs2Selected : public TimsMsRunReaderMs2
{
friend class MsFileAccessor;
/**
* @todo write docs
*/
public:
TimsMsRunReaderMs2Selected(MsRunIdCstSPtr &msrun_id_csp);
virtual ~TimsMsRunReaderMs2Selected();
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override;
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override;
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index,
bool want_binary_data = true) const override;
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override;
virtual void readSpectrumCollection2(const MsRunReadConfig &config,
SpectrumCollectionHandlerInterface &handler) override;
virtual std::size_t spectrumListSize() const override;
virtual bool hasScanNumbers() const override;
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
virtual std::size_t
spectrumStringIdentifier2SpectrumIndex(const QString &spectrum_identifier) override;
protected:
virtual void initialize() override;
virtual bool accept(const QString &file_name) const override;
private:
TimsData *mpa_timsData = nullptr;
};
} // namespace pappso
pappso::MsRunReadConfig
Definition msrunreadconfig.h:62
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition qualifiedmassspectrum.h:99
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition spectrumcollectionhandlerinterface.h:52
pappso::TimsData
Definition timsdata.h:68
pappso::TimsMsRunReaderMs2Selected::massSpectrumCstSPtr
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
Definition timsmsrunreaderms2selected.cpp:107
pappso::TimsMsRunReaderMs2Selected::spectrumListSize
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
Definition timsmsrunreaderms2selected.cpp:306
pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection2
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Definition timsmsrunreaderms2selected.cpp:299
pappso::TimsMsRunReaderMs2Selected::MsFileAccessor
friend class MsFileAccessor
Definition timsmsrunreaderms2selected.h:43
pappso::TimsMsRunReaderMs2Selected::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 timsmsrunreaderms2selected.cpp:91
pappso::TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter)
Definition timsmsrunreaderms2selected.cpp:61
pappso::TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter)
Definition timsmsrunreaderms2selected.cpp:76
pappso::TimsMsRunReaderMs2Selected::mpa_timsData
TimsData * mpa_timsData
Definition timsmsrunreaderms2selected.h:77
pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
Definition timsmsrunreaderms2selected.cpp:115
pappso::TimsMsRunReaderMs2Selected::massSpectrumSPtr
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Definition timsmsrunreaderms2selected.cpp:99
pappso::TimsMsRunReaderMs2Selected::TimsMsRunReaderMs2Selected
TimsMsRunReaderMs2Selected(MsRunIdCstSPtr &msrun_id_csp)
Definition timsmsrunreaderms2selected.cpp:38
pappso::TimsMsRunReaderMs2Selected::hasScanNumbers
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
Definition timsmsrunreaderms2selected.cpp:313
pappso::TimsMsRunReaderMs2Selected::spectrumStringIdentifier2SpectrumIndex
virtual std::size_t spectrumStringIdentifier2SpectrumIndex(const QString &spectrum_identifier) override
if possible, get the spectrum index given a string identifier throw a not found exception if spectrum...
Definition timsmsrunreaderms2selected.cpp:320
pappso::TimsMsRunReaderMs2Selected::initialize
virtual void initialize() override
Definition timsmsrunreaderms2selected.cpp:53
pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Definition timsmsrunreaderms2selected.cpp:160
pappso::TimsMsRunReaderMs2::TimsMsRunReaderMs2
TimsMsRunReaderMs2(MsRunIdCstSPtr &msrun_id_csp)
Definition timsmsrunreaderms2.cpp:39
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
msfileaccessor.h
msfilereader.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::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition massspectrum.h:54
pappso::FilterInterfaceCstSPtr
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
Definition filterinterface.h:47
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition massspectrum.h:53
timsdata.h
timsmsrunreaderms2.h
types.h