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 "timsmsrunreaderms2.h"
#include "../../types.h"
#include "../../msfile/msfileaccessor.h"
#include "../../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 std::size_t spectrumListSize() const override;
virtual bool hasScanNumbers() const override;
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter);
protected:
virtual void initialize() override;
virtual bool accept(const QString &file_name) const override;
private:
TimsData *mpa_timsData = nullptr;
};
} // namespace pappso
pappso::MsFileAccessor
Definition: msfileaccessor.h:35
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::TimsData
Definition: timsdata.h:56
pappso::TimsMsRunReaderMs2Selected
Definition: timsmsrunreaderms2selected.h:42
pappso::TimsMsRunReaderMs2
Definition: timsmsrunreaderms2.h:41
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::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
timsmsrunreaderms2.h
MSrun file reader for native Bruker TimsTOF specialized for MS2 purpose.