libpappsomspp
Library for mass spectrometry
xtandeminputsaxhandler.h
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1 /**
2  * \file pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h
3  * \date 25/01/2020
4  * \author Olivier Langella
5  * \brief rewrites tandem xml input file with temporary files
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.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 #pragma once
29 
30 #include <QDebug>
31 #include <QXmlDefaultHandler>
32 #include <QXmlStreamWriter>
33 /**
34  * @todo write docs
35  */
36 namespace pappso
37 {
38 class XtandemInputSaxHandler : public QXmlDefaultHandler
39 {
40  public:
41  /**
42  * Default constructor
43  */
44  XtandemInputSaxHandler(const QString &destinationMzXmlFile,
45  const QString &destinationTandemInputFile,
46  const QString &destinationTandemOutputFile);
47 
48  /**
49  * Destructor
50  */
52 
53 
54  bool startElement(const QString &namespaceURI,
55  const QString &localName,
56  const QString &qName,
57  const QXmlAttributes &attributes) override;
58 
59  bool endElement(const QString &namespaceURI,
60  const QString &localName,
61  const QString &qName) override;
62 
63  bool startDocument() override;
64 
65  bool endDocument() override;
66 
67  bool characters(const QString &str) override;
68 
69  bool fatalError(const QXmlParseException &exception) override;
70  bool error(const QXmlParseException &exception) override;
71 
72  QString errorString() const;
73 
74  const QString &getOriginalMsDataFileName() const;
75  const QString &getOriginalTandemOutputFileName() const;
76 
77  const QString &getOriginalTandemPresetFileName() const;
78 
79  private:
80  bool startElement_note(QXmlAttributes attributes);
81  bool endElement_note();
82  void writeOpenTag(const QString &qName, const QXmlAttributes &attributes);
83 
84 
85  private:
93  QXmlStreamWriter *p_writeXmlTandemInput;
94  std::vector<QString> m_tagStack;
95  bool m_isTandemParameter = false;
96  QString m_errorString;
97  QString m_currentText;
98  QString m_currentLabel;
99  QString m_labelName;
100 };
101 } // namespace pappso
pappso::XtandemInputSaxHandler::m_currentText
QString m_currentText
Definition: xtandeminputsaxhandler.h:97
pappso::XtandemInputSaxHandler::errorString
QString errorString() const
Definition: xtandeminputsaxhandler.cpp:265
pappso::XtandemInputSaxHandler
Definition: xtandeminputsaxhandler.h:39
pappso::XtandemInputSaxHandler::fatalError
bool fatalError(const QXmlParseException &exception) override
Definition: xtandeminputsaxhandler.cpp:252
pappso::XtandemInputSaxHandler::XtandemInputSaxHandler
XtandemInputSaxHandler(const QString &destinationMzXmlFile, const QString &destinationTandemInputFile, const QString &destinationTandemOutputFile)
Definition: xtandeminputsaxhandler.cpp:34
pappso::XtandemInputSaxHandler::m_destinationTandemInputFile
QFile m_destinationTandemInputFile
Definition: xtandeminputsaxhandler.h:92
pappso::XtandemInputSaxHandler::startDocument
bool startDocument() override
Definition: xtandeminputsaxhandler.cpp:210
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::XtandemInputSaxHandler::endElement_note
bool endElement_note()
Definition: xtandeminputsaxhandler.cpp:292
pappso::XtandemInputSaxHandler::startElement
bool startElement(const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override
Definition: xtandeminputsaxhandler.cpp:84
pappso::XtandemInputSaxHandler::~XtandemInputSaxHandler
~XtandemInputSaxHandler()
Definition: xtandeminputsaxhandler.cpp:62
pappso::XtandemInputSaxHandler::m_labelName
QString m_labelName
Definition: xtandeminputsaxhandler.h:99
pappso::XtandemInputSaxHandler::m_currentLabel
QString m_currentLabel
Definition: xtandeminputsaxhandler.h:98
pappso::XtandemInputSaxHandler::p_writeXmlTandemInput
QXmlStreamWriter * p_writeXmlTandemInput
Definition: xtandeminputsaxhandler.h:93
pappso::XtandemInputSaxHandler::m_originTandemOutpuFileName
QString m_originTandemOutpuFileName
Definition: xtandeminputsaxhandler.h:90
pappso::XtandemInputSaxHandler::writeOpenTag
void writeOpenTag(const QString &qName, const QXmlAttributes &attributes)
Definition: xtandeminputsaxhandler.cpp:72
pappso::XtandemInputSaxHandler::characters
bool characters(const QString &str) override
Definition: xtandeminputsaxhandler.cpp:230
pappso::XtandemInputSaxHandler::endElement
bool endElement(const QString &namespaceURI, const QString &localName, const QString &qName) override
Definition: xtandeminputsaxhandler.cpp:164
pappso::XtandemInputSaxHandler::getOriginalTandemOutputFileName
const QString & getOriginalTandemOutputFileName() const
Definition: xtandeminputsaxhandler.cpp:331
pappso::XtandemInputSaxHandler::startElement_note
bool startElement_note(QXmlAttributes attributes)
Definition: xtandeminputsaxhandler.cpp:272
pappso::XtandemInputSaxHandler::error
bool error(const QXmlParseException &exception) override
Definition: xtandeminputsaxhandler.cpp:238
pappso::XtandemInputSaxHandler::m_destinationMzXmlFileName
QString m_destinationMzXmlFileName
Definition: xtandeminputsaxhandler.h:86
pappso::XtandemInputSaxHandler::m_originMzDataFileName
QString m_originMzDataFileName
Definition: xtandeminputsaxhandler.h:87
pappso::XtandemInputSaxHandler::getOriginalTandemPresetFileName
const QString & getOriginalTandemPresetFileName() const
Definition: xtandeminputsaxhandler.cpp:337
pappso::XtandemInputSaxHandler::endDocument
bool endDocument() override
Definition: xtandeminputsaxhandler.cpp:219
pappso::XtandemInputSaxHandler::m_originTandemPresetFileName
QString m_originTandemPresetFileName
Definition: xtandeminputsaxhandler.h:89
pappso::XtandemInputSaxHandler::m_destinationTandemInputFileName
QString m_destinationTandemInputFileName
Definition: xtandeminputsaxhandler.h:88
pappso::XtandemInputSaxHandler::m_errorString
QString m_errorString
Definition: xtandeminputsaxhandler.h:96
pappso::XtandemInputSaxHandler::getOriginalMsDataFileName
const QString & getOriginalMsDataFileName() const
Definition: xtandeminputsaxhandler.cpp:325
pappso::XtandemInputSaxHandler::m_isTandemParameter
bool m_isTandemParameter
Definition: xtandeminputsaxhandler.h:95
pappso::XtandemInputSaxHandler::m_tagStack
std::vector< QString > m_tagStack
Definition: xtandeminputsaxhandler.h:94
pappso::XtandemInputSaxHandler::m_destinationTandemOutputFileName
QString m_destinationTandemOutputFileName
Definition: xtandeminputsaxhandler.h:91