#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 55 of file xtandempresetsaxhandler.h.

Constructor & Destructor Documentation

◆ XtandemPresetSaxHandler()

pappso::XtandemPresetSaxHandler::XtandemPresetSaxHandler ( )

Default constructor

Definition at line 50 of file xtandempresetsaxhandler.cpp.

53 {

◆ ~XtandemPresetSaxHandler()

pappso::XtandemPresetSaxHandler::~XtandemPresetSaxHandler ( )

Destructor

Definition at line 54 of file xtandempresetsaxhandler.cpp.

57 {

Member Function Documentation

◆ characters()

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

override

Definition at line 175 of file xtandempresetsaxhandler.cpp.

◆ endDocument()

bool pappso::XtandemPresetSaxHandler::endDocument ( )

override

Definition at line 169 of file xtandempresetsaxhandler.cpp.

                                                        :\n"
                     "%3")
                     .arg(exception.lineNumber())

◆ endElement()

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

override

Definition at line 119 of file xtandempresetsaxhandler.cpp.

     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemPresetSaxHandler::endElement tag "
                         "%1, PAPPSO exception:\n%2")
                         .arg(qName)
                         .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemPresetSaxHandler::endElement tag "
                         "%1, std exception:\n%2")
                         .arg(qName)
                         .arg(exception_std.what());
       return false;
     }
  
   m_currentText.clear();
   m_tagStack.pop_back();
  
   return is_ok;
 }
  
 bool
 XtandemPresetSaxHandler::startDocument()
 {
   return true;
 }
  
 bool
 XtandemPresetSaxHandler::endDocument()
 {
   return true;
 }
  
 bool
 XtandemPresetSaxHandler::characters(const QString &str)
 {

◆ endElement_note()

bool pappso::XtandemPresetSaxHandler::endElement_note ( )

private

Definition at line 236 of file xtandempresetsaxhandler.cpp.

 {
   return m_threads;
 }
  
  
 const QString &
 XtandemPresetSaxHandler::getCentroidOptions() const
 {
   return m_centroidOptions;
 }
 } // namespace pappso

◆ error()

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

override

Definition at line 183 of file xtandempresetsaxhandler.cpp.

                                                        :\n"
                     "%3")
                     .arg(exception.lineNumber())
                     .arg(exception.columnNumber())
                     .arg(exception.message());
   qDebug() << m_errorString;
   return false;
 }
  
 QString

◆ errorString()

QString pappso::XtandemPresetSaxHandler::errorString ( ) const

Definition at line 210 of file xtandempresetsaxhandler.cpp.

     {
       m_currentLabel = attributes.value("label");
     }
  

References m_currentLabel.

◆ fatalError()

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

override

Definition at line 197 of file xtandempresetsaxhandler.cpp.

 {
   // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
   // <note type="input"
   // 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>
  
   m_currentLabel = "";

◆ getCentroidOptions()

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

Definition at line 263 of file xtandempresetsaxhandler.cpp.

◆ getNumberOfThreads()

int pappso::XtandemPresetSaxHandler::getNumberOfThreads ( ) const

Definition at line 256 of file xtandempresetsaxhandler.cpp.

◆ startDocument()

bool pappso::XtandemPresetSaxHandler::startDocument ( )

override

Definition at line 163 of file xtandempresetsaxhandler.cpp.

◆ startElement()

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

override

Definition at line 60 of file xtandempresetsaxhandler.cpp.

             {
  
               m_isTandemParameter = true;
             }
         }
       // startElement_group
  
       if(qName == "note")
         {
           is_ok = startElement_note(attributes);
         }
     }
   catch(pappso::PappsoException exception_pappso)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemPresetSaxHandler::startElement "
                         "tag %1, PAPPSO exception:\n%2")
                         .arg(qName)
                         .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemPresetSaxHandler::startElement "
                         "tag %1, std exception:\n%2")
                         .arg(qName)
                         .arg(exception_std.what());
       return false;
     }
   return is_ok;
 }
  
 bool
 XtandemPresetSaxHandler::endElement(const QString &namespaceURI,
                                     const QString &localName,
                                     const QString &qName)
 {
  
   bool is_ok = true;
   // endElement_peptide_list
   try
     {
  
       if(qName == "note")
         {
           is_ok = endElement_note();
         }

◆ startElement_note()

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

private

Definition at line 217 of file xtandempresetsaxhandler.cpp.

 {
   //    qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
   //    _current_label << " " << _current_text.simplified();
   if(m_currentLabel == "spectrum, timstof MS2 centroid parameters")
     {
       m_centroidOptions = m_currentText;
     }
   else if(m_currentLabel == "spectrum, threads")
     {
       m_threads = m_currentText.toInt();
     }
   else
     {

Member Data Documentation

◆ m_centroidOptions

QString pappso::XtandemPresetSaxHandler::m_centroidOptions

private

Definition at line 118 of file xtandempresetsaxhandler.h.

◆ m_currentLabel

QString pappso::XtandemPresetSaxHandler::m_currentLabel

private

Definition at line 117 of file xtandempresetsaxhandler.h.

Referenced by errorString().

◆ m_currentText

QString pappso::XtandemPresetSaxHandler::m_currentText

private

Definition at line 115 of file xtandempresetsaxhandler.h.

◆ m_errorString

QString pappso::XtandemPresetSaxHandler::m_errorString

private

Definition at line 113 of file xtandempresetsaxhandler.h.

◆ m_isTandemParameter

bool pappso::XtandemPresetSaxHandler::m_isTandemParameter = false

private

Definition at line 116 of file xtandempresetsaxhandler.h.

◆ m_tagStack

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

private

Definition at line 114 of file xtandempresetsaxhandler.h.

◆ m_threads

int pappso::XtandemPresetSaxHandler::m_threads = -1

private

Definition at line 119 of file xtandempresetsaxhandler.h.

The documentation for this class was generated from the following files:

pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h
pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ XtandemPresetSaxHandler()

◆ ~XtandemPresetSaxHandler()

Member Function Documentation

◆ characters()

◆ endDocument()

◆ endElement()

◆ endElement_note()

◆ error()

◆ errorString()

◆ fatalError()

◆ getCentroidOptions()

◆ getNumberOfThreads()

◆ startDocument()

◆ startElement()

◆ startElement_note()

Member Data Documentation

◆ m_centroidOptions

◆ m_currentLabel

◆ m_currentText

◆ m_errorString

◆ m_isTandemParameter

◆ m_tagStack

◆ m_threads