libpappsomspp
Library for mass spectrometry
msrunxicextractordiskbuffer.h
Go to the documentation of this file.
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/**
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* \file pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.h
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* \date 18/05/2018
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* \author Olivier Langella
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* \brief proteowizard based XIC extractor featuring disk cache + write buffer
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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 "
msrunxicextractordisk.h
"
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class
MsRunXicExtractorFactory;
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namespace
pappso
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{
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class
MsRunXicExtractorDiskBuffer
:
public
MsRunXicExtractorDisk
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{
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friend
MsRunXicExtractorFactory
;
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public
:
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MsRunXicExtractorDiskBuffer
(
const
MsRunXicExtractorDiskBuffer
&other);
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virtual
~MsRunXicExtractorDiskBuffer
();
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protected
:
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MsRunXicExtractorDiskBuffer
(
MsRunReaderSPtr
&msrun_reader,
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const
QDir &temporary_dir);
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virtual
void
storeSlices
(std::map<unsigned int, MassSpectrum> &slice_vector,
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std::size_t ipos)
override
;
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void
appendSliceInBuffer
(
unsigned
int
slice_number,
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MassSpectrum
&spectrum,
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std::size_t ipos);
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void
flushBufferOnDisk
();
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virtual
void
endPwizRead
()
override
;
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protected
:
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std::map<unsigned int, QByteArray>
m_sliceBufferMap
;
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std::size_t
m_bufferSize
= 0;
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std::size_t
m_bufferMaxSize
= 150;
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};
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}
// namespace pappso
pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk
void flushBufferOnDisk()
Definition:
msrunxicextractordiskbuffer.cpp:130
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition:
aa.cpp:39
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition:
massspectrum.h:71
pappso::MsRunReaderSPtr
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition:
msrunreader.h:151
pappso::MsRunXicExtractorDiskBuffer::m_bufferMaxSize
std::size_t m_bufferMaxSize
Definition:
msrunxicextractordiskbuffer.h:69
pappso::MsRunXicExtractorDiskBuffer::appendSliceInBuffer
void appendSliceInBuffer(unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
Definition:
msrunxicextractordiskbuffer.cpp:78
pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorFactory
friend MsRunXicExtractorFactory
Definition:
msrunxicextractordiskbuffer.h:45
pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer
MsRunXicExtractorDiskBuffer(const MsRunXicExtractorDiskBuffer &other)
Definition:
msrunxicextractordiskbuffer.cpp:48
pappso::MsRunXicExtractorDiskBuffer::~MsRunXicExtractorDiskBuffer
virtual ~MsRunXicExtractorDiskBuffer()
Definition:
msrunxicextractordiskbuffer.cpp:56
pappso::MsRunXicExtractorDisk
Definition:
msrunxicextractordisk.h:45
msrunxicextractordisk.h
MsRunReader based XIC extractor featuring disk cache.
pappso::MsRunXicExtractorDiskBuffer::storeSlices
virtual void storeSlices(std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos) override
store MassSpectrum slices (by daltons) for a given retention time
Definition:
msrunxicextractordiskbuffer.cpp:61
pappso::MsRunXicExtractorDiskBuffer::m_bufferSize
std::size_t m_bufferSize
Definition:
msrunxicextractordiskbuffer.h:68
pappso::MsRunXicExtractorDiskBuffer
Definition:
msrunxicextractordiskbuffer.h:44
pappso::MsRunXicExtractorDiskBuffer::m_sliceBufferMap
std::map< unsigned int, QByteArray > m_sliceBufferMap
Definition:
msrunxicextractordiskbuffer.h:66
pappso::MsRunXicExtractorDiskBuffer::endPwizRead
virtual void endPwizRead() override
Definition:
msrunxicextractordiskbuffer.cpp:206
pappsomspp
xicextractor
private
msrunxicextractordiskbuffer.h
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