libpappsomspp
Library for mass spectrometry
timsxicextractorinterface.h
Go to the documentation of this file.
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/**
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* \file pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.h
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* \date 21/09/2019
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* \author Olivier Langella
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* \brief minimum functions to extract XICs from Tims Data
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*/
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/*******************************************************************************
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* Copyright (c) 2019 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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******************************************************************************/
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#pragma once
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#include "../../../mzrange.h"
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#include "../../../xic/xic.h"
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#include "../timsdata.h"
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namespace
pappso
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{
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/**
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* @todo set of minimum functions to build XICs using Tims data
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*/
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class
TimsXicExtractorInterface
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{
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friend
TimsData
;
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public
:
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TimsXicExtractorInterface
(
const
TimsData
*mp_tims_data);
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virtual
~TimsXicExtractorInterface
();
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/** @brief set the XIC extraction method
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*/
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void
setXicExtractMethod
(
XicExtractMethod
method);
// sum or max
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protected
:
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/** @brief extract XICs for given coordinates
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* XICs are extracted given their coordinates : retention time target,
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* mobility range, mz range
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* @param timsXicList list of TIMS XIC structures (XIC coordinates)
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* @param rtRange the range in seconds that will be applied before and after
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* XIC rtTarget to extract signal
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*/
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virtual
void
extractTimsXicList
(std::vector<TimsXicStructure> &timsXicList,
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double
rtRange)
const
= 0;
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protected
:
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const
TimsData
*
mp_timsData
;
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XicExtractMethod
m_xicExtractMethod
=
XicExtractMethod::max
;
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};
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}
// namespace pappso
pappso::TimsXicExtractorInterface::~TimsXicExtractorInterface
virtual ~TimsXicExtractorInterface()
Definition:
timsxicextractorinterface.cpp:38
pappso::TimsXicExtractorInterface
Definition:
timsxicextractorinterface.h:42
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition:
aa.cpp:39
pappso::TimsData
Definition:
timsdata.h:71
pappso::XicExtractMethod
XicExtractMethod
Definition:
types.h:200
pappso::TimsXicExtractorInterface::TimsXicExtractorInterface
TimsXicExtractorInterface(const TimsData *mp_tims_data)
Definition:
timsxicextractorinterface.cpp:32
pappso::TimsXicExtractorInterface::mp_timsData
const TimsData * mp_timsData
Definition:
timsxicextractorinterface.h:66
pappso::TimsXicExtractorInterface::setXicExtractMethod
void setXicExtractMethod(XicExtractMethod method)
set the XIC extraction method
Definition:
timsxicextractorinterface.cpp:43
pappso::XicExtractMethod::sum
@ sum
sum of intensities
pappso::TimsXicExtractorInterface::m_xicExtractMethod
XicExtractMethod m_xicExtractMethod
Definition:
timsxicextractorinterface.h:67
pappso::TimsXicExtractorInterface::extractTimsXicList
virtual void extractTimsXicList(std::vector< TimsXicStructure > &timsXicList, double rtRange) const =0
extract XICs for given coordinates XICs are extracted given their coordinates : retention time target...
pappso::TimsXicExtractorInterface::TimsData
friend TimsData
Definition:
timsxicextractorinterface.h:43
pappsomspp
vendors
tims
xicextractor
timsxicextractorinterface.h
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