libpappsomspp
Library for mass spectrometry
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mzcborreaderbase.h
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1/**
2 * \file pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.h
3 * \date 19/11/2025
4 * \author Olivier Langella
5 * \brief read mzcbor stream or file
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.fr>.
10 *
11 * This file is part of PAPPSOms-tools.
12 *
13 * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27
28
29#pragma once
32#include "cvparam.h"
33namespace pappso
34{
35namespace cbor
36{
37namespace mzcbor
38{
39/**
40 * @todo write docs
41 */
43{
44 public:
45 /**
46 * Default constructor
47 */
49
50 /**
51 * Destructor
52 */
53 virtual ~MzcborReaderBase();
54 virtual void readCbor(QFile *cborp, pappso::UiMonitorInterface &monitor);
55 virtual void readCbor(QIODevice *cborp, pappso::UiMonitorInterface &monitor);
56
57 virtual void close();
58
59 bool isMzcbor() const;
60
61 const QStringList &getMsrunIdList() const;
62
63
64 protected:
66
67 virtual void readMsrun();
69
70 /** @brief read the array containing cvParams to give accessions and values
71 */
72 std::map<QString, CvParam> getCvParamsMap();
73
74 protected:
75 bool m_stopParsing = false;
76
77 private:
78 bool m_isMzcbor = false;
79 QStringList m_msrunIdList;
80};
81} // namespace mzcbor
82} // namespace cbor
83} // namespace pappso
virtual void readCbor(QFile *cborp, pappso::UiMonitorInterface &monitor)
void readRoot(pappso::UiMonitorInterface &monitor)
std::map< QString, CvParam > getCvParamsMap()
read the array containing cvParams to give accessions and values
const QStringList & getMsrunIdList() const
PSI cvParam object for mzML/mzCBOR.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39