libpappsomspp
Library for mass spectrometry
msrunxicextractorinterface.cpp
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/**
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* \file pappsomspp/xicextractor/msrunxicextractor.cpp
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* \date 07/05/2018
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* \author Olivier Langella
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* \brief base interface to build XICs on an MsRun file
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*/
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/*******************************************************************************
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* Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
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*
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* This file is part of the PAPPSOms++ library.
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*
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* PAPPSOms++ 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++ 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++. If not, see <http://www.gnu.org/licenses/>.
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*
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* Contributors:
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* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
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*implementation
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******************************************************************************/
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#include "
msrunxicextractorinterface.h
"
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namespace
pappso
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{
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MsRunXicExtractorInterface::MsRunXicExtractorInterface
(
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MsRunReaderSPtr
&msrun_reader)
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: msp_msrun_reader(msrun_reader)
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{
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}
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MsRunXicExtractorInterface::MsRunXicExtractorInterface
(
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const
MsRunXicExtractorInterface
&other)
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: msp_msrun_reader(other.msp_msrun_reader)
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{
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m_xicExtractMethod
= other.
m_xicExtractMethod
;
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}
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MsRunXicExtractorInterface::~MsRunXicExtractorInterface
()
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{
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}
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XicCstSPtr
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MsRunXicExtractorInterface::getXicCstSPtr
(
const
MzRange
&mz_range)
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{
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return
getXicCstSPtr
(mz_range, 0, 100000000);
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}
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void
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MsRunXicExtractorInterface::setXicExtractMethod
(
XicExtractMethod
method)
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{
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m_xicExtractMethod
= method;
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}
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const
MsRunIdCstSPtr
&
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MsRunXicExtractorInterface::getMsRunId
()
const
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{
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return
msp_msrun_reader
.get()->getMsRunId();
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}
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}
// namespace pappso
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition:
aa.cpp:39
pappso::MsRunReaderSPtr
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition:
msrunreader.h:151
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition:
msrunid.h:44
pappso::MsRunXicExtractorInterface
Definition:
msrunxicextractorinterface.h:46
msrunxicextractorinterface.h
pappso::MzRange
Definition:
mzrange.h:46
pappso::XicExtractMethod
XicExtractMethod
Definition:
types.h:200
pappso::MsRunXicExtractorInterface::m_xicExtractMethod
XicExtractMethod m_xicExtractMethod
Definition:
msrunxicextractorinterface.h:124
pappso::MsRunXicExtractorInterface::~MsRunXicExtractorInterface
virtual ~MsRunXicExtractorInterface()
Definition:
msrunxicextractorinterface.cpp:51
pappso::XicCstSPtr
std::shared_ptr< const Xic > XicCstSPtr
Definition:
xic.h:37
pappso::MsRunXicExtractorInterface::setXicExtractMethod
void setXicExtractMethod(XicExtractMethod method)
set the XIC extraction method
Definition:
msrunxicextractorinterface.cpp:62
pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface
MsRunXicExtractorInterface(MsRunReaderSPtr &msrun_reader)
constructor is private, use the MsRunXicExtractorFactory
Definition:
msrunxicextractorinterface.cpp:37
pappso::MsRunXicExtractorInterface::msp_msrun_reader
MsRunReaderSPtr msp_msrun_reader
Definition:
msrunxicextractorinterface.h:123
pappso::MsRunXicExtractorInterface::getMsRunId
const MsRunIdCstSPtr & getMsRunId() const
Definition:
msrunxicextractorinterface.cpp:67
pappso::MsRunXicExtractorInterface::getXicCstSPtr
virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range) final
get a XIC on this MsRun at the given mass range
Definition:
msrunxicextractorinterface.cpp:56
pappsomspp
xicextractor
msrunxicextractorinterface.cpp
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