libpappsomspp
Library for mass spectrometry
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fastafileindexer.h
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1/**
2 * \file pappsomspp/fasta/fastafileindexer.h
3 * \date 22/06/2109
4 * \author Olivier Langella
5 * \brief Quick random access to sequences in a fasta file using an index
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27
28#pragma once
29
30#include <QFileInfo>
31#include <QTextStream>
32#include <memory>
34
35namespace pappso
36{
38{
39
40 public:
41 virtual void open() = 0;
42 virtual void getSequenceByIndex(FastaHandlerInterface &fasta_handler,
43 std::size_t index) = 0;
44
45 virtual void close() = 0;
46};
47
49typedef std::shared_ptr<FastaFileIndexer> FastaFileIndexerSPtr;
50
52{
53
54 public:
55 FastaFileIndexer(const QFileInfo &fastaFile);
57 virtual ~FastaFileIndexer();
58
59 void getSequenceByIndex(FastaHandlerInterface &fasta_handler,
60 std::size_t index) override;
61 void open() override;
62 void close() override;
63
64
65 FastaFileIndexerSPtr makeFastaFileIndexerSPtr() const;
66
67 std::size_t size() const;
68
69 private:
70 void parseFastaFile();
71
72 private:
74 std::vector<qint64> m_indexArray;
75 QTextStream *mpa_sequenceTxtIn = nullptr;
76};
77} // namespace pappso
virtual void getSequenceByIndex(FastaHandlerInterface &fasta_handler, std::size_t index)=0
std::vector< qint64 > m_indexArray
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
std::shared_ptr< FastaFileIndexer > FastaFileIndexerSPtr