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timsframesmsrunreader.h
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/**
* \file pappsomspp/msrun/private/timsmsrunreader.h
* \date 05/09/2019
* \author Olivier Langella
* \brief MSrun file reader for native Bruker TimsTOF raw data
*/
/*******************************************************************************
* 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/timsmsrunreaderbase.h"
namespace pappso
{
// This class is aimed at processing the frames in a Bruker timsTOF data set. In
// this processing of the data, we skip the ion mobility scans altogether. One
// main aim of this processing is to compute the TIC chromatogram from the
// binary data file and not using the TIC chromatogram that is stored in the DB
// file.
class PMSPP_LIB_DECL TimsFramesMsRunReader : public TimsMsRunReaderBase
{
friend class MsFileAccessor;
/**
* @todo write docs
*/
public:
TimsFramesMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
virtual ~TimsFramesMsRunReader();
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 void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
unsigned int ms_level) override;
virtual std::size_t spectrumListSize() const override;
virtual Trace computeTicChromatogram();
virtual std::size_t
spectrumStringIdentifier2SpectrumIndex(const QString &spectrum_identifier) override;
};
typedef std::shared_ptr<TimsFramesMsRunReader> TimsFramesMsRunReaderSPtr;
typedef std::shared_ptr<const TimsFramesMsRunReader> TimsFramesMsRunReaderCstSPtr;
} // 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::TimsFramesMsRunReader::spectrumListSize
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
Definition timsframesmsrunreader.cpp:438
pappso::TimsFramesMsRunReader::readSpectrumCollection
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Definition timsframesmsrunreader.cpp:79
pappso::TimsFramesMsRunReader::MsFileAccessor
friend class MsFileAccessor
Definition timsframesmsrunreader.h:44
pappso::TimsFramesMsRunReader::massSpectrumCstSPtr
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
Definition timsframesmsrunreader.cpp:59
pappso::TimsFramesMsRunReader::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 timsframesmsrunreader.cpp:66
pappso::TimsFramesMsRunReader::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 timsframesmsrunreader.cpp:496
pappso::TimsFramesMsRunReader::massSpectrumSPtr
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Definition timsframesmsrunreader.cpp:49
pappso::TimsFramesMsRunReader::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 timsframesmsrunreader.cpp:89
pappso::TimsFramesMsRunReader::computeTicChromatogram
virtual Trace computeTicChromatogram()
Definition timsframesmsrunreader.cpp:445
pappso::TimsFramesMsRunReader::TimsFramesMsRunReader
TimsFramesMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
Definition timsframesmsrunreader.cpp:37
pappso::TimsFramesMsRunReader::readSpectrumCollectionByMsLevel
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
Definition timsframesmsrunreader.cpp:429
pappso::TimsMsRunReaderBase::TimsMsRunReaderBase
TimsMsRunReaderBase(MsRunIdCstSPtr &msrun_id_csp)
Definition timsmsrunreaderbase.cpp:38
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
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::TimsFramesMsRunReaderSPtr
std::shared_ptr< TimsFramesMsRunReader > TimsFramesMsRunReaderSPtr
Definition timsframesmsrunreader.h:75
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition massspectrum.h:54
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition massspectrum.h:53
pappso::TimsFramesMsRunReaderCstSPtr
std::shared_ptr< const TimsFramesMsRunReader > TimsFramesMsRunReaderCstSPtr
Definition timsframesmsrunreader.h:76
timsmsrunreaderbase.h