#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	getMs2FiltersOptions () 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

int	m_threads = -1

PrecisionUnit	m_ms2precisionUnit = PrecisionUnit::dalton

double	m_ms2precisionValue = 0

Detailed Description

Definition at line 40 of file xtandempresetsaxhandler.h.

Constructor & Destructor Documentation

◆ XtandemPresetSaxHandler()

pappso::XtandemPresetSaxHandler::XtandemPresetSaxHandler ( )

Default constructor

Definition at line 35 of file xtandempresetsaxhandler.cpp.

36 {

37 }

◆ ~XtandemPresetSaxHandler()

pappso::XtandemPresetSaxHandler::~XtandemPresetSaxHandler ( )

Destructor

Definition at line 39 of file xtandempresetsaxhandler.cpp.

40 {

41 }

Member Function Documentation

◆ characters()

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

override

Definition at line 162 of file xtandempresetsaxhandler.cpp.

 {
   m_currentText += str;
   return true;
 }

References m_currentText.

◆ endDocument()

bool pappso::XtandemPresetSaxHandler::endDocument ( )

override

Definition at line 156 of file xtandempresetsaxhandler.cpp.

 {
   return true;
 }

◆ endElement()

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

override

Definition at line 105 of file xtandempresetsaxhandler.cpp.

 {
  
   bool is_ok = true;
   // endElement_peptide_list
   try
     {
  
       if(qName == "note")
         {
           is_ok = endElement_note();
         }
       else
         {
         }
     }
   catch(const pappso::PappsoException &exception_pappso)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemPresetSaxHandler::endElement tag "
                         "%1, PAPPSO exception:\n%2")
                         .arg(qName)
                         .arg(exception_pappso.qwhat());
       return false;
     }
   catch(const 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;
 }

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

◆ endElement_note()

bool pappso::XtandemPresetSaxHandler::endElement_note ( )

private

Definition at line 223 of file xtandempresetsaxhandler.cpp.

 {
   //    qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
   //    _current_label << " " << _current_text.simplified();
   if(m_currentLabel == "spectrum, timstof MS2 filters")
     {
       // m_ms2filtersOptions = m_currentText;
     }
   else if(m_currentLabel == "spectrum, threads")
     {
       m_threads = m_currentText.toInt();
     }
   else if(m_currentLabel == "spectrum, fragment monoisotopic mass error units")
     {
       m_ms2precisionUnit = PrecisionUnit::dalton;
       if(m_currentText.trimmed().toLower() == "ppm")
         {
           m_ms2precisionUnit = PrecisionUnit::ppm;
         }
     }
   else if(m_currentLabel == "spectrum, fragment monoisotopic mass error")
     {
       m_ms2precisionValue = m_currentText.toDouble();
     }
   else
     {
     }
   return true;
 }

References m_currentLabel, m_currentText, m_ms2precisionUnit, m_ms2precisionValue, and m_threads.

Referenced by endElement().

◆ error()

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

override

Definition at line 170 of file xtandempresetsaxhandler.cpp.

 {
   m_errorString = QObject::tr(
                     "Parse error at line %1, column %2 :\n"
                     "%3")
                     .arg(exception.lineNumber())
                     .arg(exception.columnNumber())
                     .arg(exception.message());
   qDebug() << m_errorString;
   return false;
 }

References m_errorString.

◆ errorString()

QString pappso::XtandemPresetSaxHandler::errorString ( ) const

Definition at line 197 of file xtandempresetsaxhandler.cpp.

 {
   return m_errorString;
 }

References m_errorString.

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

◆ fatalError()

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

override

Definition at line 184 of file xtandempresetsaxhandler.cpp.

 {
   m_errorString = QObject::tr(
                     "Parse error at line %1, column %2 :\n"
                     "%3")
                     .arg(exception.lineNumber())
                     .arg(exception.columnNumber())
                     .arg(exception.message());
   qDebug() << m_errorString;
   return false;
 }

References m_errorString.

◆ getMs2FiltersOptions()

const QString pappso::XtandemPresetSaxHandler::getMs2FiltersOptions ( ) const

Definition at line 262 of file xtandempresetsaxhandler.cpp.

 {
   PrecisionPtr precision = PrecisionFactory::getPrecisionPtrInstance(
     m_ms2precisionUnit, m_ms2precisionValue);
   return QString("chargeDeconvolution|%1")
     .arg(precision->toString().replace(" ", ""));
 }

References pappso::PrecisionFactory::getPrecisionPtrInstance(), m_ms2precisionUnit, m_ms2precisionValue, and pappso::PrecisionBase::toString().

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

◆ getNumberOfThreads()

int pappso::XtandemPresetSaxHandler::getNumberOfThreads ( ) const

Definition at line 255 of file xtandempresetsaxhandler.cpp.

 {
   return m_threads;
 }

References m_threads.

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

◆ startDocument()

bool pappso::XtandemPresetSaxHandler::startDocument ( )

override

Definition at line 150 of file xtandempresetsaxhandler.cpp.

 {
   return true;
 }

◆ startElement()

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

override

Definition at line 45 of file xtandempresetsaxhandler.cpp.

 {
   m_tagStack.push_back(qName);
   bool is_ok = true;
  
   try
     {
       m_currentText.clear();
       //<bioml label="example api document">
       if(m_tagStack.size() == 1)
         {
           if(qName != "bioml")
             {
               m_errorString =
                 QObject::tr(
                   "ERROR in XtandemPresetSaxHandler::startElement "
                   "root tag %1 is not <bioml>")
                   .arg(qName);
               m_isTandemParameter = false;
               return false;
             }
           else
             {
  
               m_isTandemParameter = true;
             }
         }
       // startElement_group
  
       if(qName == "note")
         {
           is_ok = startElement_note(attributes);
         }
     }
   catch(const 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(const 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;
 }

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 204 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 = "";
  
   if(attributes.value("type") == "input")
     {
       m_currentLabel = attributes.value("label");
     }
  
   //  qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
   //  _current_label;
   return true;
 }

References m_currentLabel.

Referenced by startElement().

Member Data Documentation

◆ m_currentLabel

QString pappso::XtandemPresetSaxHandler::m_currentLabel

private

Definition at line 85 of file xtandempresetsaxhandler.h.

Referenced by endElement_note(), and startElement_note().

◆ m_currentText

QString pappso::XtandemPresetSaxHandler::m_currentText

private

Definition at line 83 of file xtandempresetsaxhandler.h.

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

◆ m_errorString

QString pappso::XtandemPresetSaxHandler::m_errorString

private

Definition at line 81 of file xtandempresetsaxhandler.h.

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

◆ m_isTandemParameter

bool pappso::XtandemPresetSaxHandler::m_isTandemParameter = false

private

Definition at line 84 of file xtandempresetsaxhandler.h.

Referenced by startElement().

◆ m_ms2precisionUnit

PrecisionUnit pappso::XtandemPresetSaxHandler::m_ms2precisionUnit = PrecisionUnit::dalton

private

Definition at line 88 of file xtandempresetsaxhandler.h.

Referenced by endElement_note(), and getMs2FiltersOptions().

◆ m_ms2precisionValue

double pappso::XtandemPresetSaxHandler::m_ms2precisionValue = 0

private

Definition at line 89 of file xtandempresetsaxhandler.h.

Referenced by endElement_note(), and getMs2FiltersOptions().

◆ m_tagStack

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

private

Definition at line 82 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:

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()

◆ getMs2FiltersOptions()

◆ getNumberOfThreads()

◆ startDocument()

◆ startElement()

◆ startElement_note()

Member Data Documentation

◆ m_currentLabel

◆ m_currentText

◆ m_errorString

◆ m_isTandemParameter

◆ m_ms2precisionUnit

◆ m_ms2precisionValue

◆ m_tagStack

◆ m_threads