Loading...
Searching...
No Matches
pwizmsrunreader.h
Go to the documentation of this file.
/**
* \file pappsomspp/msrun/private/pwizmsrunreader.h
* \date 29/05/2018
* \author Olivier Langella
* \brief MSrun file reader base on proteowizard library
*/
/*******************************************************************************
* Copyright (c) 2018 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/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
*implementation
******************************************************************************/
#pragma once
#include <pwiz/data/msdata/MSData.hpp>
#include <pwiz/data/msdata/MSDataFile.hpp>
#include "../../types.h"
#include "../../msfile/msfileaccessor.h"
#include "../../msfile/msfilereader.h"
namespace pappso
{
class PMSPP_LIB_DECL PwizMsRunReader : public MsRunReader
{
friend class MsFileAccessor;
public:
PwizMsRunReader(MsRunIdCstSPtr &msrun_id_csp);
virtual ~PwizMsRunReader();
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 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;
virtual bool releaseDevice() override;
virtual bool acquireDevice() override;
/** @brief get OboPsiModTerm corresponding to the nativeID format format of mz
* data
*/
const OboPsiModTerm getOboPsiModTermNativeIDFormat() const;
protected:
virtual void readSpectrumCollectionWithMsrunReadConfig(
const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler);
virtual void initialize() override;
virtual bool accept(const QString &file_name) const override;
bool
processRetentionTime(pwiz::msdata::Spectrum *spectrum_p,
QualifiedMassSpectrum &qualified_mass_spectrum) const;
bool processDriftTime(pwiz::msdata::Spectrum *spectrum_p,
QualifiedMassSpectrum &qualified_mass_spectrum) const;
QualifiedMassSpectrum qualifiedMassSpectrumFromPwizMSData(
std::size_t spectrum_index, bool want_binary_data, bool &ok) const;
QualifiedMassSpectrum
qualifiedMassSpectrumFromPwizSpectrumPtr(const MassSpectrumId &massSpectrumId,
pwiz::msdata::Spectrum *spectrum_p,
bool want_binary_data,
bool &ok) const;
pwiz::msdata::SpectrumPtr
getPwizSpectrumPtr(pwiz::msdata::SpectrumList *p_spectrum_list,
std::size_t spectrum_index,
bool want_binary_data) const;
static std::string setGlobalLocaleToEnglish();
static void setGlobalLocaleToCurrentOs(const std::string &environment_locale);
protected:
static QMutex m_mutex;
pwiz::msdata::MSDataPtr msp_msData = nullptr;
private:
bool m_hasScanNumbers = false;
};
} // namespace pappso
// Q_DECLARE_METATYPE(pappso::PwizMsRunReader);
// extern int pwizMsRunReaderMetaTypeId;
pappso::MassSpectrumId
Definition massspectrumid.h:40
pappso::MsFileAccessor
Definition msfileaccessor.h:28
pappso::MsRunReadConfig
Definition msrunreadconfig.h:62
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::OboPsiModTerm
Definition obopsimodterm.h:32
pappso::PrecisionBase
Definition precision.h:44
pappso::PwizMsRunReader
Definition pwizmsrunreader.h:46
pappso::PwizMsRunReader::m_mutex
static QMutex m_mutex
Definition pwizmsrunreader.h:128
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:56
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:46
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