libpappsomspp
Library for mass spectrometry
xtandempresetsaxhandler.h
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1 /**
2  * \file pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h
3  * \date 06/02/2020
4  * \author Olivier Langella
5  * \brief read tandem preset file to get centroid parameters and number of
6  * threads
7  */
8 
9 /*******************************************************************************
10  * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
11  *
12  * This file is part of PAPPSOms-tools.
13  *
14  * PAPPSOms-tools is free software: you can redistribute it and/or modify
15  * it under the terms of the GNU General Public License as published by
16  * the Free Software Foundation, either version 3 of the License, or
17  * (at your option) any later version.
18  *
19  * PAPPSOms-tools is distributed in the hope that it will be useful,
20  * but WITHOUT ANY WARRANTY; without even the implied warranty of
21  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22  * GNU General Public License for more details.
23  *
24  * You should have received a copy of the GNU General Public License
25  * along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
26  *
27  ******************************************************************************/
28 
29 #pragma once
30 
31 #include <QDebug>
32 #include <QXmlDefaultHandler>
33 #include <QXmlStreamWriter>
34 /**
35  * @todo write docs
36  */
37 namespace pappso
38 {
39 class XtandemPresetSaxHandler : public QXmlDefaultHandler
40 {
41  public:
42  /**
43  * Default constructor
44  */
46 
47  /**
48  * Destructor
49  */
51 
52  bool startElement(const QString &namespaceURI,
53  const QString &localName,
54  const QString &qName,
55  const QXmlAttributes &attributes) override;
56 
57  bool endElement(const QString &namespaceURI,
58  const QString &localName,
59  const QString &qName) override;
60 
61  bool startDocument() override;
62 
63  bool endDocument() override;
64 
65  bool characters(const QString &str) override;
66 
67  bool fatalError(const QXmlParseException &exception) override;
68  bool error(const QXmlParseException &exception) override;
69 
70  QString errorString() const;
71 
72  int getNumberOfThreads() const;
73  const QString &getCentroidOptions() const;
74 
75  private:
76  bool startElement_note(QXmlAttributes attributes);
77  bool endElement_note();
78 
79  private:
80  QString m_errorString;
81  std::vector<QString> m_tagStack;
82  QString m_currentText;
83  bool m_isTandemParameter = false;
84  QString m_currentLabel;
85  QString m_centroidOptions;
86  int m_threads = -1;
87 };
88 } // namespace pappso
pappso::XtandemPresetSaxHandler::m_isTandemParameter
bool m_isTandemParameter
Definition: xtandempresetsaxhandler.h:119
pappso::XtandemPresetSaxHandler::m_centroidOptions
QString m_centroidOptions
Definition: xtandempresetsaxhandler.h:121
pappso::XtandemPresetSaxHandler::endDocument
bool endDocument() override
Definition: xtandempresetsaxhandler.cpp:173
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::XtandemPresetSaxHandler::getCentroidOptions
const QString & getCentroidOptions() const
Definition: xtandempresetsaxhandler.cpp:267
pappso::XtandemPresetSaxHandler::m_currentLabel
QString m_currentLabel
Definition: xtandempresetsaxhandler.h:120
pappso::XtandemPresetSaxHandler::~XtandemPresetSaxHandler
~XtandemPresetSaxHandler()
Definition: xtandempresetsaxhandler.cpp:56
pappso::XtandemPresetSaxHandler::startDocument
bool startDocument() override
Definition: xtandempresetsaxhandler.cpp:167
pappso::XtandemPresetSaxHandler::errorString
QString errorString() const
Definition: xtandempresetsaxhandler.cpp:214
pappso::XtandemPresetSaxHandler::getNumberOfThreads
int getNumberOfThreads() const
Definition: xtandempresetsaxhandler.cpp:260
pappso::XtandemPresetSaxHandler::XtandemPresetSaxHandler
XtandemPresetSaxHandler()
Definition: xtandempresetsaxhandler.cpp:52
pappso::XtandemPresetSaxHandler::characters
bool characters(const QString &str) override
Definition: xtandempresetsaxhandler.cpp:179
pappso::XtandemPresetSaxHandler::endElement_note
bool endElement_note()
Definition: xtandempresetsaxhandler.cpp:240
pappso::XtandemPresetSaxHandler::m_threads
int m_threads
Definition: xtandempresetsaxhandler.h:122
pappso::XtandemPresetSaxHandler::error
bool error(const QXmlParseException &exception) override
Definition: xtandempresetsaxhandler.cpp:187
pappso::XtandemPresetSaxHandler::endElement
bool endElement(const QString &namespaceURI, const QString &localName, const QString &qName) override
Definition: xtandempresetsaxhandler.cpp:122
pappso::XtandemPresetSaxHandler::m_currentText
QString m_currentText
Definition: xtandempresetsaxhandler.h:118
pappso::XtandemPresetSaxHandler::startElement_note
bool startElement_note(QXmlAttributes attributes)
Definition: xtandempresetsaxhandler.cpp:221
pappso::XtandemPresetSaxHandler::m_errorString
QString m_errorString
Definition: xtandempresetsaxhandler.h:116
pappso::XtandemPresetSaxHandler::m_tagStack
std::vector< QString > m_tagStack
Definition: xtandempresetsaxhandler.h:117
pappso::XtandemPresetSaxHandler::startElement
bool startElement(const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override
Definition: xtandempresetsaxhandler.cpp:62
pappso::XtandemPresetSaxHandler::fatalError
bool fatalError(const QXmlParseException &exception) override
Definition: xtandempresetsaxhandler.cpp:201