timsmsrunreaderms2.h
Go to the documentation of this file.
/**
* \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 "../../types.h"
#include "../../msfile/msfileaccessor.h"
#include "../../msfile/msfilereader.h"
#include "../../vendors/tims/timsdata.h"
namespace pappso
{
class PMSPP_LIB_DECL TimsMsRunReaderMs2 : public MsRunReader
{
friend class MsFileAccessor;
/**
* @todo write docs
*/
public:
TimsMsRunReaderMs2(MsRunIdCstSPtr &msrun_id_csp);
virtual ~TimsMsRunReaderMs2();
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 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 void
readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler,
unsigned int ms_level) override;
virtual std::size_t spectrumListSize() const override;
virtual bool hasScanNumbers() const override;
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
/** @brief enable or disable simple centroid filter on raw tims data for MS2
*/
void setMs2BuiltinCentroid(bool centroid);
/** @brief Get all the precursors id which match the values
* @return list of precursors Ids
*/
virtual std::vector<std::size_t>
getPrecursorsIDFromMzRt(int charge, double mz_val, double rt_sec, double k0);
virtual bool releaseDevice() override;
virtual bool acquireDevice() override;
/** @brief give an access to the underlying raw data pointer
*/
virtual TimsDataSp getTimsDataSPtr();
/** @brief retention timeline
* get retention times along the MSrun in seconds
* @return vector of retention times (seconds)
*/
virtual std::vector<double> getRetentionTimeLine() override;
virtual Trace getTicChromatogram() override;
protected:
virtual void initialize() override;
virtual bool accept(const QString &file_name) const override;
private:
TimsDataSp msp_timsData = nullptr;
pappso::FilterInterfaceCstSPtr msp_ms1Filter;
pappso::FilterInterfaceCstSPtr msp_ms2Filter;
/** @brief enable builtin centroid on raw tims integers by default
*/
bool m_builtinMs2Centroid = true;
};
} // namespace pappso
pappso::MsFileAccessor
Definition: msfileaccessor.h:35
pappso::MsRunReader
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:191
pappso::PrecisionBase
Definition: precision.h:44
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:85
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
pappso::TimsMsRunReaderMs2
Definition: timsmsrunreaderms2.h:41
pappso::TimsMsRunReaderMs2::msp_ms2Filter
pappso::FilterInterfaceCstSPtr msp_ms2Filter
Definition: timsmsrunreaderms2.h:118
pappso::TimsMsRunReaderMs2::msp_ms1Filter
pappso::FilterInterfaceCstSPtr msp_ms1Filter
Definition: timsmsrunreaderms2.h:117
pappso::Trace
A simple container of DataPoint instances.
Definition: trace.h:148
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition: exportinmportconfig.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:44
pappso::TimsDataSp
std::shared_ptr< TimsData > TimsDataSp
shared pointer on a TimsData object
Definition: timsdata.h:46
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
pappso::FilterInterfaceCstSPtr
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
Definition: filterinterface.h:47
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:41