Loading...
Searching...
No Matches
timsframesmsrunreader.h
Go to the documentation of this file.
/**
* \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 "../../msfile/msfileaccessor.h"
#include "../../vendors/tims/timsdata.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 TimsFramesMsRunReader : public MsRunReader
{
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 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 std::size_t spectrumListSize() const override;
virtual bool hasScanNumbers() const override;
virtual bool releaseDevice() override;
virtual bool acquireDevice() override;
/** @brief give an access to the underlying raw data pointer
*/
virtual TimsDataSp getTimsDataSPtr();
virtual Trace getTicChromatogram() override;
virtual Trace computeTicChromatogram();
protected:
virtual void initialize() override;
virtual bool accept(const QString &file_name) const override;
private:
TimsDataSp msp_timsData = nullptr;
};
} // namespace pappso
pappso::MsFileAccessor
Definition msfileaccessor.h:27
pappso::MsRunReadConfig
Definition msrunreadconfig.h:52
pappso::MsRunReader
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition msrunreader.h:63
pappso::PrecisionBase
Definition precision.h:44
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition qualifiedmassspectrum.h:93
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition spectrumcollectionhandlerinterface.h:56
pappso::TimsFramesMsRunReader
Definition timsframesmsrunreader.h:44
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:401
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:102
pappso::TimsFramesMsRunReader::massSpectrumCstSPtr
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
Definition timsframesmsrunreader.cpp:82
pappso::TimsFramesMsRunReader::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 timsframesmsrunreader.cpp:444
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:89
pappso::TimsFramesMsRunReader::massSpectrumSPtr
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
Definition timsframesmsrunreader.cpp:70
pappso::TimsFramesMsRunReader::getTicChromatogram
virtual Trace getTicChromatogram() override
get a TIC chromatogram
Definition timsframesmsrunreader.cpp:463
pappso::TimsFramesMsRunReader::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 timsframesmsrunreader.cpp:415
pappso::TimsFramesMsRunReader::initialize
virtual void initialize() override
Definition timsframesmsrunreader.cpp:48
pappso::TimsFramesMsRunReader::readSpectrumCollection2
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
Definition timsframesmsrunreader.cpp:112
pappso::TimsFramesMsRunReader::computeTicChromatogram
virtual Trace computeTicChromatogram()
Definition timsframesmsrunreader.cpp:475
pappso::TimsFramesMsRunReader::getTimsDataSPtr
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
Definition timsframesmsrunreader.cpp:455
pappso::TimsFramesMsRunReader::hasScanNumbers
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
Definition timsframesmsrunreader.cpp:408
pappso::TimsFramesMsRunReader::acquireDevice
virtual bool acquireDevice() override
acquire data back end device
Definition timsframesmsrunreader.cpp:422
pappso::TimsFramesMsRunReader::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 timsframesmsrunreader.cpp:62
pappso::TimsFramesMsRunReader::~TimsFramesMsRunReader
virtual ~TimsFramesMsRunReader()
Definition timsframesmsrunreader.cpp:42
pappso::TimsFramesMsRunReader::msp_timsData
TimsDataSp msp_timsData
Definition timsframesmsrunreader.h:103
pappso::TimsFramesMsRunReader::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 timsframesmsrunreader.cpp:433
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:392
pappso::Trace
A simple container of DataPoint instances.
Definition trace.h:148
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:50
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition massspectrum.h:57
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition massspectrum.h:56
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:43