libpappsomspp
Library for mass spectrometry
msrunxicextractor.h
Go to the documentation of this file.
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/**
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* \file pappsomspp/xicextractor/private/msrunxicextractorpwiz.h
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* \date 07/05/2018
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* \author Olivier Langella
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* \brief simple proteowizard based XIC extractor
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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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#pragma once
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#include "../msrunxicextractorinterface.h"
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class
MsRunXicExtractorFactory;
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namespace
pappso
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{
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class
MsRunXicExtractor
:
public
MsRunXicExtractorInterface
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{
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friend
MsRunXicExtractorFactory
;
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public
:
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MsRunXicExtractor
(
const
MsRunXicExtractor
&other);
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virtual
~MsRunXicExtractor
();
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virtual
XicCstSPtr
getXicCstSPtr
(
const
MzRange
&mz_range,
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pappso::pappso_double
rt_begin,
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pappso::pappso_double
rt_end)
override
;
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virtual
std::vector<XicCstSPtr>
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getXicCstSPtrList
(
const
std::vector<MzRange> &mz_range_list)
override
;
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protected
:
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MsRunXicExtractor
(
MsRunReaderSPtr
&msrun_reader);
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virtual
void
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getXicFromPwizMSDataFile
(std::vector<Xic *> &xic_list,
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const
std::vector<MzRange> &mass_range_list,
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pappso::pappso_double
rt_begin,
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pappso::pappso_double
rt_end);
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protected
:
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std::vector<MsRunXicExtractorPoints>
m_msrun_points
;
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};
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}
// namespace pappso
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition:
types.h:48
pappso::MsRunXicExtractor::MsRunXicExtractor
MsRunXicExtractor(const MsRunXicExtractor &other)
Definition:
msrunxicextractor.cpp:64
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::MsRunXicExtractorInterface
Definition:
msrunxicextractorinterface.h:46
pappso::MzRange
Definition:
mzrange.h:46
pappso::XicCstSPtr
std::shared_ptr< const Xic > XicCstSPtr
Definition:
xic.h:37
pappso::MsRunXicExtractor::getXicCstSPtr
virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) override
get a XIC on this MsRun at the given mass range
Definition:
msrunxicextractor.cpp:71
pappso::MsRunXicExtractor::getXicCstSPtrList
virtual std::vector< XicCstSPtr > getXicCstSPtrList(const std::vector< MzRange > &mz_range_list) override
extract a list of XIC given a list of mass to extract
Definition:
msrunxicextractor.cpp:128
pappso::MsRunXicExtractor::MsRunXicExtractorFactory
friend MsRunXicExtractorFactory
Definition:
msrunxicextractor.h:43
pappso::MsRunXicExtractor::~MsRunXicExtractor
virtual ~MsRunXicExtractor()
Definition:
msrunxicextractor.cpp:59
pappso::MsRunXicExtractor
Definition:
msrunxicextractor.h:42
pappso::MsRunXicExtractor::getXicFromPwizMSDataFile
virtual void getXicFromPwizMSDataFile(std::vector< Xic * > &xic_list, const std::vector< MzRange > &mass_range_list, pappso::pappso_double rt_begin, pappso::pappso_double rt_end)
Definition:
msrunxicextractor.cpp:149
pappso::MsRunXicExtractor::m_msrun_points
std::vector< MsRunXicExtractorPoints > m_msrun_points
Definition:
msrunxicextractor.h:65
pappsomspp
xicextractor
private
msrunxicextractor.h
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