libpappsomspp
Library for mass spectrometry
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fastafileindexer.h
Go to the documentation of this file.
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/**
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* \file pappsomspp/fasta/fastafileindexer.h
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* \date 22/06/2109
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* \author Olivier Langella
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* \brief Quick random access to sequences in a fasta file using an index
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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 <QFileInfo>
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#include <QTextStream>
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#include <memory>
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#include "
fastahandlerinterface.h
"
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namespace
pappso
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{
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class
PMSPP_LIB_DECL
FastaFileIndexerInterface
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{
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public
:
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virtual
void
open
() = 0;
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virtual
void
getSequenceByIndex
(
FastaHandlerInterface
&fasta_handler,
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std::size_t index) = 0;
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virtual
void
close
() = 0;
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};
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class
FastaFileIndexer
;
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typedef
std::shared_ptr<FastaFileIndexer>
FastaFileIndexerSPtr
;
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class
PMSPP_LIB_DECL
FastaFileIndexer
:
public
FastaFileIndexerInterface
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{
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public
:
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FastaFileIndexer
(
const
QFileInfo &fastaFile);
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FastaFileIndexer
(
const
FastaFileIndexer
&other);
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virtual
~FastaFileIndexer
();
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void
getSequenceByIndex(
FastaHandlerInterface
&fasta_handler,
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std::size_t index)
override
;
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void
open()
override
;
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void
close()
override
;
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FastaFileIndexerSPtr
makeFastaFileIndexerSPtr()
const
;
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private
:
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void
parseFastaFile();
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private
:
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QFile
m_fasta_file
;
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std::vector<qint64>
m_indexArray
;
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QTextStream *mpa_sequenceTxtIn =
nullptr
;
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};
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}
// namespace pappso
pappso::FastaFileIndexerInterface
Definition
fastafileindexer.h:38
pappso::FastaFileIndexerInterface::close
virtual void close()=0
pappso::FastaFileIndexerInterface::getSequenceByIndex
virtual void getSequenceByIndex(FastaHandlerInterface &fasta_handler, std::size_t index)=0
pappso::FastaFileIndexerInterface::open
virtual void open()=0
pappso::FastaFileIndexer
Definition
fastafileindexer.h:52
pappso::FastaFileIndexer::m_fasta_file
QFile m_fasta_file
Definition
fastafileindexer.h:71
pappso::FastaFileIndexer::m_indexArray
std::vector< qint64 > m_indexArray
Definition
fastafileindexer.h:72
pappso::FastaHandlerInterface
Definition
fastahandlerinterface.h:32
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition
exportinmportconfig.h:14
fastahandlerinterface.h
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition
aa.cpp:39
pappso::FastaFileIndexerSPtr
std::shared_ptr< FastaFileIndexer > FastaFileIndexerSPtr
Definition
fastafileindexer.h:49
pappsomspp
fasta
fastafileindexer.h
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