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Library for mass spectrometry
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mzcborreaderbase.h
Go to the documentation of this file.
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/**
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* \file pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.h
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* \date 19/11/2025
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* \author Olivier Langella
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* \brief read mzcbor stream or file
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*/
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/*******************************************************************************
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* Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.fr>.
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*
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* This file is part of PAPPSOms-tools.
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*
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* PAPPSOms-tools is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PAPPSOms-tools is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
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*
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******************************************************************************/
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#pragma once
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#include "
pappsomspp/core/processing/cbor/cborstreamreaderinterface.h
"
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#include "
pappsomspp/core/processing/uimonitor/uimonitorinterface.h
"
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#include "
cvparam.h
"
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namespace
pappso
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{
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namespace
cbor
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{
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namespace
mzcbor
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{
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/**
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* @brief base class to initialize mzCBOR file parsing
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*
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* ensures stream read on regular file or any readable device
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*/
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class
PMSPP_LIB_DECL
MzcborReaderBase
:
public
CborStreamReaderInterface
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{
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public
:
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/**
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* Default constructor
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*/
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MzcborReaderBase
();
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/**
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* Destructor
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*/
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virtual
~MzcborReaderBase
();
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/**
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* @brief read mzCBOR file
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* @param cborp file pointer
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* @param monitor monitor read progress and messages
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*/
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virtual
void
readCbor
(QFile *cborp,
pappso::UiMonitorInterface
&monitor);
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/**
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* @brief read mzCBOR from any device (memory buffer or else)
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* @param cborp device pointer
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* @param monitor monitor read progress and messages
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*/
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virtual
void
readCbor
(QIODevice *cborp,
pappso::UiMonitorInterface
&monitor);
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virtual
void
close
();
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bool
isMzcbor
()
const
;
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const
QStringList &
getMsrunIdList
()
const
;
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protected
:
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void
readRoot
(
pappso::UiMonitorInterface
&monitor);
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virtual
void
readMsrun
();
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virtual
void
readReferenceableParamGroupList
();
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/** @brief read the array containing cvParams to give accessions and values
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*/
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std::map<QString, CvParam>
getCvParamsMap
();
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protected
:
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bool
m_stopParsing
=
false
;
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private
:
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bool
m_isMzcbor
=
false
;
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QStringList
m_msrunIdList
;
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};
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}
// namespace mzcbor
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}
// namespace cbor
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}
// namespace pappso
cborstreamreaderinterface.h
pappso::UiMonitorInterface
Definition
uimonitorinterface.h:50
pappso::cbor::CborStreamReaderInterface::CborStreamReaderInterface
CborStreamReaderInterface()
Definition
cborstreamreaderinterface.cpp:30
pappso::cbor::mzcbor::MzcborReaderBase::m_msrunIdList
QStringList m_msrunIdList
Definition
mzcborreaderbase.h:94
pappso::cbor::mzcbor::MzcborReaderBase::MzcborReaderBase
MzcborReaderBase()
Definition
mzcborreaderbase.cpp:31
pappso::cbor::mzcbor::MzcborReaderBase::m_isMzcbor
bool m_isMzcbor
Definition
mzcborreaderbase.h:93
pappso::cbor::mzcbor::MzcborReaderBase::readReferenceableParamGroupList
virtual void readReferenceableParamGroupList()
Definition
mzcborreaderbase.cpp:133
pappso::cbor::mzcbor::MzcborReaderBase::readCbor
virtual void readCbor(QFile *cborp, pappso::UiMonitorInterface &monitor)
read mzCBOR file
Definition
mzcborreaderbase.cpp:45
pappso::cbor::mzcbor::MzcborReaderBase::readMsrun
virtual void readMsrun()
Definition
mzcborreaderbase.cpp:169
pappso::cbor::mzcbor::MzcborReaderBase::isMzcbor
bool isMzcbor() const
Definition
mzcborreaderbase.cpp:120
pappso::cbor::mzcbor::MzcborReaderBase::readRoot
void readRoot(pappso::UiMonitorInterface &monitor)
Definition
mzcborreaderbase.cpp:75
pappso::cbor::mzcbor::MzcborReaderBase::m_stopParsing
bool m_stopParsing
Definition
mzcborreaderbase.h:90
pappso::cbor::mzcbor::MzcborReaderBase::close
virtual void close()
convenient function to clean pointer before leaving
Definition
mzcborreaderbase.cpp:40
pappso::cbor::mzcbor::MzcborReaderBase::getCvParamsMap
std::map< QString, CvParam > getCvParamsMap()
read the array containing cvParams to give accessions and values
Definition
mzcborreaderbase.cpp:190
pappso::cbor::mzcbor::MzcborReaderBase::getMsrunIdList
const QStringList & getMsrunIdList() const
Definition
mzcborreaderbase.cpp:126
cvparam.h
PSI cvParam object for mzML/mzCBOR.
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition
export-import-config.h:14
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
uimonitorinterface.h
pappsomspp
core
processing
cbor
mzcbor
mzcborreaderbase.h
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