libpappsomspp
Library for mass spectrometry
timsmsrunreaderms2.h
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/**
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* \file pappsomspp/msrun/private/timsmsrunreaderms2.h
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* \date 10/09/2019
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* \author Olivier Langella
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* \brief MSrun file reader for native Bruker TimsTOF specialized for MS2
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* purpose
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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 "../../types.h"
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#include "../../msfile/msfileaccessor.h"
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#include "../../msfile/msfilereader.h"
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#include "../../vendors/tims/timsdata.h"
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namespace
pappso
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{
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class
PMSPP_LIB_DECL
TimsMsRunReaderMs2
:
public
MsRunReader
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{
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friend
class
MsFileAccessor
;
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/**
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* @todo write docs
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*/
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public
:
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TimsMsRunReaderMs2
(
MsRunIdCstSPtr
&msrun_id_csp);
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virtual
~
TimsMsRunReaderMs2
();
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virtual
MassSpectrumSPtr
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massSpectrumSPtr(std::size_t spectrum_index)
override
;
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virtual
MassSpectrumCstSPtr
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massSpectrumCstSPtr(std::size_t spectrum_index)
override
;
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virtual
QualifiedMassSpectrum
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qualifiedMassSpectrum(std::size_t spectrum_index,
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bool
want_binary_data =
true
)
const override
;
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virtual
void
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readSpectrumCollection(
SpectrumCollectionHandlerInterface
&handler)
override
;
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virtual
std::size_t spectrumListSize()
const override
;
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virtual
bool
hasScanNumbers()
const override
;
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void
setMs2FilterCstSPtr(
pappso::FilterInterfaceCstSPtr
filter);
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void
setMs1FilterCstSPtr(
pappso::FilterInterfaceCstSPtr
filter);
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protected
:
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virtual
void
initialize()
override
;
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virtual
bool
accept(
const
QString &file_name)
const override
;
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private
:
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TimsData
*mpa_timsData =
nullptr
;
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};
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}
// namespace pappso
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition:
massspectrum.h:55
pappso::MsRunReader
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition:
msrunreader.h:158
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition:
exportinmportconfig.h:14
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
Definition:
aa.cpp:39
pappso::FilterInterfaceCstSPtr
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
Definition:
filterinterface.h:46
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition:
msrunid.h:44
pappso::TimsData
Definition:
timsdata.h:65
pappso::MsFileAccessor
Definition:
msfileaccessor.h:35
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition:
qualifiedmassspectrum.h:68
pappso::TimsMsRunReaderMs2
Definition:
timsmsrunreaderms2.h:41
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition:
msrunreader.h:59
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition:
massspectrum.h:54
pappsomspp
msrun
private
timsmsrunreaderms2.h
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