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mzcborbuildindexreader.h
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/**
* \file pappsomspp/core/processing/cbor/mzcbor/mzcborbuildindexreader.h
* \date 24/11/2025
* \author Olivier Langella
* \brief read mzcbor to build an index
*/
/*******************************************************************************
* Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of PAPPSOms-tools.
*
* PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include "pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.h"
#include "pappsomspp/core/msrun/spectrumcollectionhandlerinterface.h"
#include "pappsomspp/core/msrun/msrunreadconfig.h"
#include "pappsomspp/core/msrun/msrunid.h"
namespace pappso
{
namespace cbor
{
namespace mzcbor
{
/**
* @todo write docs
*/
class PMSPP_LIB_DECL MzcborBuildIndexReader : public MzcborReaderBase
{
public:
/**
* Default constructor
*/
MzcborBuildIndexReader(const MsRunIdCstSPtr &msrun_id);
/**
* Destructor
*/
virtual ~MzcborBuildIndexReader();
virtual void readCbor(QFile *cborp, pappso::UiMonitorInterface &monitor)override;
const std::vector<qint64> &getSpectrumIndexPositionInFile() const;
const std::map<QString, std::size_t> &getNativeId2SpectrumIndexMap() const;
protected:
/** @brief read only the targeted msrun
*/
virtual void readMsrun() override;
/** @brief only the spectrum list of targeted msrun, then stop parsing
*/
void readSpectrumListAndLeave();
/** @brief read each spectrum in the targeted msrun (msrunId)
*/
void readSpectrum(qint64 position_of_spectrum_in_file, std::size_t index_count);
private:
MsRunIdCstSPtr mcsp_msRunId;
QString m_xmlMzMlRunId;
std::vector<qint64> m_spectrumIndexPositionInFile;
std::map<QString, std::size_t> m_nativeId2SpectrumIndexMap;
};
} // namespace mzcbor
} // namespace cbor
} // namespace pappso
pappso::UiMonitorInterface
Definition uimonitorinterface.h:50
pappso::cbor::mzcbor::MzcborBuildIndexReader::readSpectrumListAndLeave
void readSpectrumListAndLeave()
only the spectrum list of targeted msrun, then stop parsing
Definition mzcborbuildindexreader.cpp:121
pappso::cbor::mzcbor::MzcborBuildIndexReader::mcsp_msRunId
MsRunIdCstSPtr mcsp_msRunId
Definition mzcborbuildindexreader.h:82
pappso::cbor::mzcbor::MzcborBuildIndexReader::m_spectrumIndexPositionInFile
std::vector< qint64 > m_spectrumIndexPositionInFile
Definition mzcborbuildindexreader.h:85
pappso::cbor::mzcbor::MzcborBuildIndexReader::m_nativeId2SpectrumIndexMap
std::map< QString, std::size_t > m_nativeId2SpectrumIndexMap
Definition mzcborbuildindexreader.h:86
pappso::cbor::mzcbor::MzcborBuildIndexReader::getSpectrumIndexPositionInFile
const std::vector< qint64 > & getSpectrumIndexPositionInFile() const
Definition mzcborbuildindexreader.cpp:70
pappso::cbor::mzcbor::MzcborBuildIndexReader::m_xmlMzMlRunId
QString m_xmlMzMlRunId
Definition mzcborbuildindexreader.h:83
pappso::cbor::mzcbor::MzcborBuildIndexReader::readMsrun
virtual void readMsrun() override
read only the targeted msrun
Definition mzcborbuildindexreader.cpp:81
pappso::cbor::mzcbor::MzcborBuildIndexReader::readCbor
virtual void readCbor(QFile *cborp, pappso::UiMonitorInterface &monitor) override
read mzCBOR file
Definition mzcborbuildindexreader.cpp:51
pappso::cbor::mzcbor::MzcborBuildIndexReader::getNativeId2SpectrumIndexMap
const std::map< QString, std::size_t > & getNativeId2SpectrumIndexMap() const
Definition mzcborbuildindexreader.cpp:76
pappso::cbor::mzcbor::MzcborBuildIndexReader::MzcborBuildIndexReader
MzcborBuildIndexReader(const MsRunIdCstSPtr &msrun_id)
Definition mzcborbuildindexreader.cpp:39
pappso::cbor::mzcbor::MzcborBuildIndexReader::readSpectrum
void readSpectrum(qint64 position_of_spectrum_in_file, std::size_t index_count)
read each spectrum in the targeted msrun (msrunId)
Definition mzcborbuildindexreader.cpp:178
pappso::cbor::mzcbor::MzcborReaderBase::MzcborReaderBase
MzcborReaderBase()
Definition mzcborreaderbase.cpp:31
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
msrunid.h
msrunreadconfig.h
mzcborreaderbase.h
read mzcbor stream or file
pappso::cbor::mzcbor
Definition binarydataarray.h:41
pappso::cbor
Definition cborstreamreader.cpp:35
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
spectrumcollectionhandlerinterface.h
base interface to read MSrun files