libpappsomspp
Library for mass spectrometry
pappso::XtandemPresetSaxHandler Class Reference

#include <xtandempresetsaxhandler.h>

Inheritance diagram for pappso::XtandemPresetSaxHandler:

Public Member Functions

 XtandemPresetSaxHandler ()
 
 ~XtandemPresetSaxHandler ()
 
bool startElement (const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override
 
bool endElement (const QString &namespaceURI, const QString &localName, const QString &qName) override
 
bool startDocument () override
 
bool endDocument () override
 
bool characters (const QString &str) override
 
bool fatalError (const QXmlParseException &exception) override
 
bool error (const QXmlParseException &exception) override
 
QString errorString () const
 
int getNumberOfThreads () const
 
const QString & getCentroidOptions () const
 

Private Member Functions

bool startElement_note (QXmlAttributes attributes)
 
bool endElement_note ()
 

Private Attributes

QString m_errorString
 
std::vector< QString > m_tagStack
 
QString m_currentText
 
bool m_isTandemParameter = false
 
QString m_currentLabel
 
QString m_centroidOptions
 
int m_threads = -1
 

Detailed Description

Definition at line 39 of file xtandempresetsaxhandler.h.

Constructor & Destructor Documentation

◆ XtandemPresetSaxHandler()

pappso::XtandemPresetSaxHandler::XtandemPresetSaxHandler ( )

Default constructor

Definition at line 34 of file xtandempresetsaxhandler.cpp.

35 {
36 }

◆ ~XtandemPresetSaxHandler()

pappso::XtandemPresetSaxHandler::~XtandemPresetSaxHandler ( )

Destructor

Definition at line 38 of file xtandempresetsaxhandler.cpp.

39 {
40 }

Member Function Documentation

◆ characters()

bool pappso::XtandemPresetSaxHandler::characters ( const QString &  str)
override

Definition at line 161 of file xtandempresetsaxhandler.cpp.

162 {
163  m_currentText += str;
164  return true;
165 }

References m_currentText.

◆ endDocument()

bool pappso::XtandemPresetSaxHandler::endDocument ( )
override

Definition at line 155 of file xtandempresetsaxhandler.cpp.

156 {
157  return true;
158 }

◆ endElement()

bool pappso::XtandemPresetSaxHandler::endElement ( const QString &  namespaceURI,
const QString &  localName,
const QString &  qName 
)
override

Definition at line 104 of file xtandempresetsaxhandler.cpp.

108 {
109 
110  bool is_ok = true;
111  // endElement_peptide_list
112  try
113  {
114 
115  if(qName == "note")
116  {
117  is_ok = endElement_note();
118  }
119  else
120  {
121  }
122  }
123  catch(const pappso::PappsoException &exception_pappso)
124  {
125  m_errorString = QObject::tr(
126  "ERROR in XtandemPresetSaxHandler::endElement tag "
127  "%1, PAPPSO exception:\n%2")
128  .arg(qName)
129  .arg(exception_pappso.qwhat());
130  return false;
131  }
132  catch(const std::exception &exception_std)
133  {
134  m_errorString = QObject::tr(
135  "ERROR in XtandemPresetSaxHandler::endElement tag "
136  "%1, std exception:\n%2")
137  .arg(qName)
138  .arg(exception_std.what());
139  return false;
140  }
141 
142  m_currentText.clear();
143  m_tagStack.pop_back();
144 
145  return is_ok;
146 }

References endElement_note(), m_currentText, m_errorString, m_tagStack, and pappso::PappsoException::qwhat().

◆ endElement_note()

bool pappso::XtandemPresetSaxHandler::endElement_note ( )
private

Definition at line 222 of file xtandempresetsaxhandler.cpp.

223 {
224  // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
225  // _current_label << " " << _current_text.simplified();
226  if(m_currentLabel == "spectrum, timstof MS2 centroid parameters")
227  {
229  }
230  else if(m_currentLabel == "spectrum, threads")
231  {
232  m_threads = m_currentText.toInt();
233  }
234  else
235  {
236  }
237  return true;
238 }

References m_centroidOptions, m_currentLabel, m_currentText, and m_threads.

Referenced by endElement().

◆ error()

bool pappso::XtandemPresetSaxHandler::error ( const QXmlParseException &  exception)
override

Definition at line 169 of file xtandempresetsaxhandler.cpp.

170 {
171  m_errorString = QObject::tr(
172  "Parse error at line %1, column %2 :\n"
173  "%3")
174  .arg(exception.lineNumber())
175  .arg(exception.columnNumber())
176  .arg(exception.message());
177  qDebug() << m_errorString;
178  return false;
179 }

References m_errorString.

◆ errorString()

QString pappso::XtandemPresetSaxHandler::errorString ( ) const

Definition at line 196 of file xtandempresetsaxhandler.cpp.

197 {
198  return m_errorString;
199 }

References m_errorString.

Referenced by pappso::TandemWrapperRun::readTandemPresetFile().

◆ fatalError()

bool pappso::XtandemPresetSaxHandler::fatalError ( const QXmlParseException &  exception)
override

Definition at line 183 of file xtandempresetsaxhandler.cpp.

184 {
185  m_errorString = QObject::tr(
186  "Parse error at line %1, column %2 :\n"
187  "%3")
188  .arg(exception.lineNumber())
189  .arg(exception.columnNumber())
190  .arg(exception.message());
191  qDebug() << m_errorString;
192  return false;
193 }

References m_errorString.

◆ getCentroidOptions()

const QString & pappso::XtandemPresetSaxHandler::getCentroidOptions ( ) const

Definition at line 249 of file xtandempresetsaxhandler.cpp.

250 {
251  return m_centroidOptions;
252 }

References m_centroidOptions.

◆ getNumberOfThreads()

int pappso::XtandemPresetSaxHandler::getNumberOfThreads ( ) const

Definition at line 242 of file xtandempresetsaxhandler.cpp.

243 {
244  return m_threads;
245 }

References m_threads.

Referenced by pappso::TandemWrapperRun::readTandemPresetFile().

◆ startDocument()

bool pappso::XtandemPresetSaxHandler::startDocument ( )
override

Definition at line 149 of file xtandempresetsaxhandler.cpp.

150 {
151  return true;
152 }

◆ startElement()

bool pappso::XtandemPresetSaxHandler::startElement ( const QString &  namespaceURI,
const QString &  localName,
const QString &  qName,
const QXmlAttributes &  attributes 
)
override

Definition at line 44 of file xtandempresetsaxhandler.cpp.

49 {
50  m_tagStack.push_back(qName);
51  bool is_ok = true;
52 
53  try
54  {
55  m_currentText.clear();
56  //<bioml label="example api document">
57  if(m_tagStack.size() == 1)
58  {
59  if(qName != "bioml")
60  {
62  QObject::tr(
63  "ERROR in XtandemPresetSaxHandler::startElement "
64  "root tag %1 is not <bioml>")
65  .arg(qName);
66  m_isTandemParameter = false;
67  return false;
68  }
69  else
70  {
71 
72  m_isTandemParameter = true;
73  }
74  }
75  // startElement_group
76 
77  if(qName == "note")
78  {
79  is_ok = startElement_note(attributes);
80  }
81  }
82  catch(const pappso::PappsoException &exception_pappso)
83  {
84  m_errorString = QObject::tr(
85  "ERROR in XtandemPresetSaxHandler::startElement "
86  "tag %1, PAPPSO exception:\n%2")
87  .arg(qName)
88  .arg(exception_pappso.qwhat());
89  return false;
90  }
91  catch(const std::exception &exception_std)
92  {
93  m_errorString = QObject::tr(
94  "ERROR in XtandemPresetSaxHandler::startElement "
95  "tag %1, std exception:\n%2")
96  .arg(qName)
97  .arg(exception_std.what());
98  return false;
99  }
100  return is_ok;
101 }

References m_currentText, m_errorString, m_isTandemParameter, m_tagStack, pappso::PappsoException::qwhat(), and startElement_note().

◆ startElement_note()

bool pappso::XtandemPresetSaxHandler::startElement_note ( QXmlAttributes  attributes)
private

Definition at line 203 of file xtandempresetsaxhandler.cpp.

204 {
205  // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
206  // <note type="input"
207  // label="output,path">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml</note>
208 
209  m_currentLabel = "";
210 
211  if(attributes.value("type") == "input")
212  {
213  m_currentLabel = attributes.value("label");
214  }
215 
216  // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
217  // _current_label;
218  return true;
219 }

References m_currentLabel.

Referenced by startElement().

Member Data Documentation

◆ m_centroidOptions

QString pappso::XtandemPresetSaxHandler::m_centroidOptions
private

Definition at line 85 of file xtandempresetsaxhandler.h.

Referenced by endElement_note(), and getCentroidOptions().

◆ m_currentLabel

QString pappso::XtandemPresetSaxHandler::m_currentLabel
private

Definition at line 84 of file xtandempresetsaxhandler.h.

Referenced by endElement_note(), and startElement_note().

◆ m_currentText

QString pappso::XtandemPresetSaxHandler::m_currentText
private

Definition at line 82 of file xtandempresetsaxhandler.h.

Referenced by characters(), endElement(), endElement_note(), and startElement().

◆ m_errorString

QString pappso::XtandemPresetSaxHandler::m_errorString
private

Definition at line 80 of file xtandempresetsaxhandler.h.

Referenced by endElement(), error(), errorString(), fatalError(), and startElement().

◆ m_isTandemParameter

bool pappso::XtandemPresetSaxHandler::m_isTandemParameter = false
private

Definition at line 83 of file xtandempresetsaxhandler.h.

Referenced by startElement().

◆ m_tagStack

std::vector<QString> pappso::XtandemPresetSaxHandler::m_tagStack
private

Definition at line 81 of file xtandempresetsaxhandler.h.

Referenced by endElement(), and startElement().

◆ m_threads

int pappso::XtandemPresetSaxHandler::m_threads = -1
private

Definition at line 86 of file xtandempresetsaxhandler.h.

Referenced by endElement_note(), and getNumberOfThreads().


The documentation for this class was generated from the following files:
pappso::XtandemPresetSaxHandler::m_isTandemParameter
bool m_isTandemParameter
Definition: xtandempresetsaxhandler.h:83
pappso::XtandemPresetSaxHandler::m_centroidOptions
QString m_centroidOptions
Definition: xtandempresetsaxhandler.h:85
pappso::XtandemPresetSaxHandler::m_currentLabel
QString m_currentLabel
Definition: xtandempresetsaxhandler.h:84
pappso::XtandemPresetSaxHandler::endElement_note
bool endElement_note()
Definition: xtandempresetsaxhandler.cpp:222
pappso::XtandemPresetSaxHandler::m_threads
int m_threads
Definition: xtandempresetsaxhandler.h:86
pappso::XtandemPresetSaxHandler::m_currentText
QString m_currentText
Definition: xtandempresetsaxhandler.h:82
pappso::PappsoException::qwhat
virtual const QString & qwhat() const
Definition: pappsoexception.h:66
pappso::XtandemPresetSaxHandler::startElement_note
bool startElement_note(QXmlAttributes attributes)
Definition: xtandempresetsaxhandler.cpp:203
pappso::XtandemPresetSaxHandler::m_errorString
QString m_errorString
Definition: xtandempresetsaxhandler.h:80
pappso::XtandemPresetSaxHandler::m_tagStack
std::vector< QString > m_tagStack
Definition: xtandempresetsaxhandler.h:81
pappso::PappsoException
Definition: pappsoexception.h:42